tag:blogger.com,1999:blog-69535490917845014222024-03-18T00:31:58.629-07:00NMR Analysis, Processing and PredictionCarlos Cobashttp://www.blogger.com/profile/13500275318435740775noreply@blogger.comBlogger102125tag:blogger.com,1999:blog-6953549091784501422.post-59955953222253473872019-05-11T04:54:00.001-07:002019-05-11T04:55:55.182-07:001H NMR Prediction: unity creates strength<div class="separator" style="clear: both; text-align: center;">
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<span style="font-family: inherit;">NMR Prediction in <a href="https://mestrelab.com/software/mnova/" target="_blank">Mnova </a>follows the concept of “unity creates strength”. The basic idea is to combine several predictors together to get a better predictive power. We have borrowed from the field of Machine Learning the term "<b>ensemble</b>" to define this new prediction procedure and I have written about it in this article, “<a href="https://resources.mestrelab.com/ensemble-nmr-prediction/" target="_blank">Ensemble NMR Prediction</a>” , where some results using 13C NMR data are given. </span></div>
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<span style="font-family: inherit;">To complement that article, in this post I will show some results for 1H NMR data. I have taken from the literature a few assigned molecules. Those molecules were not contained in the internal databases of Mnova predictors. The overall results are shown in table 1. </span></div>
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<b><span lang="EN-US" style="font-family: "calibri" , sans-serif; font-size: 10.0pt; line-height: 107%;">Table 1</span></b><span lang="EN-US" style="font-family: "calibri" , sans-serif; font-size: 10.0pt; line-height: 107%;">: <i>Mean
absolute errors for the individual and ensemble predictor. ML stands for Machine Learning</i></span></div>
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As in the <a href="https://resources.mestrelab.com/ensemble-nmr-prediction/" target="_blank">13C analysis</a>, the new <b>Ensemble Prediction</b> provides a smaller MAE than the individual predictors. </div>
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The error distribution also shows that the ensemble method helps reduce the number of prediction outliers</div>
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<b style="mso-bidi-font-weight: normal;"><span lang="EN-US" style="font-size: 10.0pt; line-height: 107%; mso-ansi-language: EN-US;">Table 2</span></b><span lang="EN-US" style="font-size: 10.0pt; line-height: 107%; mso-ansi-language: EN-US;">: <i style="mso-bidi-font-style: normal;">Distribution of prediction errors for the
different individual predictors as well as for the final, ensemble result. Freq.
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<br />Carlos Cobashttp://www.blogger.com/profile/13500275318435740775noreply@blogger.com0tag:blogger.com,1999:blog-6953549091784501422.post-58623651225279516572017-10-14T08:43:00.000-07:002017-10-14T08:44:25.588-07:00A Novel qNMR Technique: Quantitative Global Spectrum Deconvolution (qGSD)Ever since chemists meddled (successfully) into NMR, with the pioneer work made by <a href="http://www.ebyte.it/library/hist/ProctorWG_Reminiscences.html" target="_blank">Proctor </a>and <a href="http://www.ebyte.it/library/hist/YuFuchunBio.html" target="_blank">Yu </a>[1] more than 67 years ago, it was implicitly used as a <b>quantitative </b>technique. Indeed, from the very early days of NMR, it was found that the intensity (or area) of the NMR signals (under proper operating conditions) was proportional to the number of nuclides contributing to it. Already in 1953, Jarrett, Sadler, and Shoolery [2] showed the excellent precision of NMR (CW at that time) for the quantitative analysis of a tautomeric mixture, despite the limited measurement resources (see Figure below).<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjQ9In5c4ic4zyo2smlQWNJAOdBqCpOQRmoLR4R8a2-RFDqej3bWIXxlLB7Y-CqDPw2lOHIwMesu0bIlJrJOq629HEbz4BF41xsGGnxe_mQhK0Al7wMGVxl33TNl1Kfzk0LGHrA01lMwYc/s1600/1953.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="754" data-original-width="1530" height="314" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjQ9In5c4ic4zyo2smlQWNJAOdBqCpOQRmoLR4R8a2-RFDqej3bWIXxlLB7Y-CqDPw2lOHIwMesu0bIlJrJOq629HEbz4BF41xsGGnxe_mQhK0Al7wMGVxl33TNl1Kfzk0LGHrA01lMwYc/s640/1953.png" width="640" /></a></div>
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<b>Figure 1</b>. 1H-NMR spectrum from Reference [2]</div>
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Interestingly, quantitative analysis by NMR (<b>qNMR </b>from now on) is nowadays experiencing a kind of <i><b>Renaissance </b></i>with many applications in various fields, such as pharmaceutical and food sciences, manufacturing of reference materials, or metabolite determination in human body fluids. Furthermore, it is now being considered as an official analytical method for purity determination or assay of concentration of organic compounds.</div>
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From sum integration to qGSD</h2>
One of the key factors for the successful application of qNMR is the method used to estimate the peak integrals in the spectrum. This has been, and still is, largely dominated by the so-called <b>sum integration</b> in which the computer simply calculates the sum of all data points within a spectral region. It is well known that this method is very sensitive to phase or baseline distortions, but we can also assume that those spectral artefacts can be properly corrected (even fully automatically) by the NMR software.<br />
The main problem of this method is its <a href="http://nmr-analysis.blogspot.com.es/2010/01/basis-on-qnmr-integration-rudiments.html" target="_blank">inability to deal with overlapping peaks</a>. This is a particularly serious problem when an "external" signal overlaps within the area of interest. This signal can be solvent, it can come from another compound or even from the same compound itself.<br />
This problem is illustrated in the 1H-NMR spectrum of Santonine (Figure 2).<br />
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<b>Figure 2</b>. 1H NMR spectrum of Santonine. Integrals calculated using standard sum method</div>
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Notice the multiplet at ~1.7 ppm that is contaminated with residual water peaks and therefore, the integreal corresponding to the proton 6’ is <b>overestimated </b>by a significant amount.<br />
The contribution of that solvent peak could be removed by different methods, ranging from acquisition (e.g. pulse sequences for solvent suppression), post-processing or deconvolution techniques or a combination of the three.<br />
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<b>Global Spectral Deconvolution (GSD) </b>is a powerful alternative to the standard integration method providing a number of advantages. First, it is pretty <b>insensitive to baseline distortions</b>, although it requires the spectrum to be phase corrected. Most importantly, it can deal very efficiently with the <b>problem of peaks overlap</b> as it can be seen using the same example of Santonine used before.<br />
(Figure 3)<br />
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<b>Figure 3</b>. 1H NMR spectrum of Santonine. Integrals calculated using GSD</div>
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Compared to the classical point-to-point integration, <b>GSD yields better relative integrals</b>, but the quality of the fit is not optimal (notice the residues under the spectrum). Nevertheless, they are generally of sufficient quality to be used all but the most demanding quantitation, It has been at the core of <b>Mnova </b>data analysis for many years, and has proved to be highly reliable and computationally efficient. However, whilst GSD has been designed to be used for problems involving automatic spectral analysis such us those required to perform molecular structure characterization, it was not intended for very accurate quantitative analysis (e.g. qNMR). </div>
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GSD uses a <b>Generalized Lorentzian f</b>unction to model the experimental lineshapes. This is a very flexible model that covers a broad range of shape variations for NMR resonances (Figure 4). </div>
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<b>Figure 4</b>. The shape parameter in this graph ranges from –1.00 (blue) to +2.00 (red). For 0.00 (green), the line is a perfect Lorentzian. Red line is pure Gaussian and the gray lines are generalized Lorentzians.</div>
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The quality of the quantitation depends, amongst other factors, on how well theoretical models describe experimental NMR resonances. Careful analysis shows that even a flexible model like the Generalized Lorentzian cannot precisely fit all possible experimental lineshapes, as evidenced by non-zero fitting residual in Figure 3. </div>
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In order to overcome some of the limitations of GSD, we have now introduced <b>qGSD </b>(<b>q</b>uantitative <b>GSD</b>), available in <b>Mnova 12</b>. It is based on careful analysis of the residuals after GSD processing, and correcting GSD lineshapes in a way which minimizes the residuals. In Figure 5 we can see that now the residues are significantly smaller compared to the results obtained with plain GSD. </div>
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<b>Figure 5</b>. 1H NMR spectrum of Santonine. Integrals calculated using qGSD</div>
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Using qGSD with Mnova 12</h2>
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In order to enable qGSD, it is necessary to access to the <b>Peak Picking options</b> in Mnova making sure that <b>GSD </b>method is selected (see Figure 6). </div>
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<b>Figure 6</b>. Enabling qGSD in Mnova</div>
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Next, under the <b>Advanced </b>options, <b>qGSD </b>check box must be ticked and an appropriate number of <i><b>Improvement cycles</b></i> selected. A number between 5 and 10 usually gives good results. However, it is important to bear in mind that <b>qGSD is computationally intensive</b>: can take a couple of minutes, especially with a large number of cycles.</div>
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For this reason, it is recommended to use qGSD only when highly accurate integrals are needed. For other applications, such as multiplet analysis, or structure confirmation, plain GSD would be a more efficient method. </div>
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qGSD with poorly shimmed spectra</h2>
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To illustrate the lineshape flexibility offered by qGSD, a <b>poorly shimmed spectrum</b> has been used with GSD and qGSD (Figure 7). It is clear that qGSD does a much better job. That said, this should not not be a replacement for a properly acquired spectrum. </div>
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<b>Figure 7</b>. qGSD vs GSD on a poorly shimmed spectrum</div>
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Conclusions</h2>
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<b>qGSD </b>(quantitative Global Spectral Deconvolution) represents Mnova’s latest innovation that combines the power of <b>deconvolution </b>techniques to handle overlapped signals with the robustness of <b>sum integration</b> of isolated resonances but with the ability to deal efficiently with overlapped peaks.</div>
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Our preliminary tests demonstrate that qGSD is able to provide accuracy which is supperior to the sum integration even when there is signal overlap</div>
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References</h2>
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[1] W. G. Proctor, E C.Yu, Phys. Rev 77,717 (1950)</div>
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[2] H. S. Jarrett, M. S. Sadler, and J. N. Shoolery, J. Chem. Phys., 1953, 21, 2092.</div>
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Carlos Cobashttp://www.blogger.com/profile/13500275318435740775noreply@blogger.com0tag:blogger.com,1999:blog-6953549091784501422.post-2967800974760151512017-10-08T08:22:00.000-07:002017-10-09T07:33:33.223-07:00Free naming of organic structures<div class="MsoNormal">
<span lang="EN-US"><a href="http://mestrelab.com/software/mnova/" target="_blank">Mnova 12</a>
contains some nice little gems that may be specially appreciated by organic
chemists. For example, this new version features an improved molecular editor
which includes a new tool for the generation of IUPAC names from a molecular
structure.<o:p></o:p></span></div>
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At the moment, it only generates <b>systematic names </b>but next release of Mnova will also support <b>trivial names</b><br />
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<span lang="EN-US">Is it
really free?</span></h2>
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<span lang="EN-US">When you
download and install Mnova 12, you can get a license for the IUPAC Naming
component, with no restrictions. We are still deciding the final licensing
model for this feature, but for the moment, this license will be valid for 6
months. <o:p></o:p></span></div>
Carlos Cobashttp://www.blogger.com/profile/13500275318435740775noreply@blogger.com0tag:blogger.com,1999:blog-6953549091784501422.post-14778121524232831192017-09-30T09:11:00.002-07:002017-09-30T09:11:48.990-07:00Improved User Experience with Mnova 12In my last post I outlined the major <a href="http://nmr-analysis.blogspot.com.es/2017/09/mnova-12-introduces-new-look-and-feel.html" target="_blank">User Interface change in Mnova 12</a>. There are also another bunch of new little features aimed at making user experience even more agile and intuitive. In this post, I’m going to show a couple of them.<br />
<h2>
New spectral navigation tool</h2>
<div>
<div>
Whilst there were many tools in Mnova for the automatic analysis of NMR spectra, very often it is necessary to zoon in and out to get a closer look at different spectral regions in an interactive way. Mnova already had different commands for those operations but it lacked the ability to go back and forth between the different zooming operations. It was possible to use the undo/redo commands for that purpose, but this would not work if other commands were applied in-between two zooming comands.</div>
<div>
Mnova 12 introduces two new commands that can be used to go to the previous or next zoom applied to the spectrum (1D or 2D). Those new command are available either in the View Ribbond tab or in the spectrum toolbar as shown in the picture below</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjPz1i561EyueSotiaMdQ6eyNPUHk20XaRdp294is_C5fvqT5a7ai2GG4YI3LFAWiseEF5s94g3Zd3CKmeTC9-wJcmmRLBqXET7E6B6DPXog100kx2tq-PKxznnS_MiHEBdGVEbfbfYTnk/s1600/zoom.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="367" data-original-width="733" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjPz1i561EyueSotiaMdQ6eyNPUHk20XaRdp294is_C5fvqT5a7ai2GG4YI3LFAWiseEF5s94g3Zd3CKmeTC9-wJcmmRLBqXET7E6B6DPXog100kx2tq-PKxznnS_MiHEBdGVEbfbfYTnk/s640/zoom.png" width="640" /></a></div>
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<span lang="EN-US" style="font-family: "Calibri",sans-serif; font-size: 11.0pt; line-height: 107%; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">It
is also possible to use keyboard shortcuts: <b><i>Shift + left/right</i></b> arrow keys</span></div>
<div>
<span lang="EN-US" style="font-family: "Calibri",sans-serif; font-size: 11.0pt; line-height: 107%; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"><br /></span></div>
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<h2>
<span lang="EN-US" style="line-height: 107%;">Magnifying fonts</span></h2>
<span lang="EN-US" style="line-height: 107%;"><div>
<span style="font-family: Calibri, sans-serif;"><span style="font-size: 14.6667px;"> Sometimes I get Mnova documents generated by someone else in which the font size of different elements is just too tiny. Changing the font size for the multiplet labels, scales, integrals, assignments, etc is a tedious and cumbersome task. </span></span></div>
<div>
<span style="font-family: Calibri, sans-serif;"><span style="font-size: 14.6667px;">Now by simply pressing<b><i> Ctrl + or Ctrl -</i></b>, all fonts in an Mnova document will be magnified up and down. It can also be done from the View tab as shown below:</span></span></div>
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<span style="font-family: Calibri, sans-serif;"><span style="font-size: 14.6667px;"><br /></span></span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgRdv44fQTnqh6EefmlgkE-qBurR802Jio2S7wBwI9md-vDeYZcGOVKRcy4YiPAYav-o7i6ivUkZfcVAxWHDn0_s2wQNSrnKkq8uR-Mt79QT9PaNHqx7px0DVBbOumAOMoBimMVv4fBhe8/s1600/fonts.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" data-original-height="257" data-original-width="1284" height="128" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgRdv44fQTnqh6EefmlgkE-qBurR802Jio2S7wBwI9md-vDeYZcGOVKRcy4YiPAYav-o7i6ivUkZfcVAxWHDn0_s2wQNSrnKkq8uR-Mt79QT9PaNHqx7px0DVBbOumAOMoBimMVv4fBhe8/s640/fonts.png" width="640" /></a></div>
<div style="font-family: Calibri, sans-serif; font-size: 11pt;">
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Carlos Cobashttp://www.blogger.com/profile/13500275318435740775noreply@blogger.com0tag:blogger.com,1999:blog-6953549091784501422.post-87678888946139856202017-09-27T12:02:00.000-07:002017-09-27T12:02:00.343-07:00Mnova 12 Introduces a New Look and Feel<span lang="EN-US" style="font-family: "Calibri",sans-serif; font-size: 11.0pt; line-height: 107%; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">Yes,
it is official, Mnova 12 has finally been <a href="http://mestrelab.com/download/mnova/" target="_blank">released</a>! There's quite a lot to tell about it: better interface (optional), new processing and analysis features, improved tools, 64 bits and so on.</span><br />
<span lang="EN-US" style="font-size: 14.6667px; line-height: 107%;"><span style="font-family: Calibri, sans-serif;">Rather than making a comprehensive review on the new features of this version, I’m going to try to show the essentials changes in digestible chunks, starting with changes in the User Interface.</span></span><br />
<h2>
<span lang="EN-US" style="font-size: 14.6667px; line-height: 107%;"><span style="font-family: Calibri, sans-serif;">Embracing the Ribbon interface</span></span></h2>
<div>
<span lang="EN-US" style="line-height: 107%;"><span style="font-family: Calibri, sans-serif;"><div>
<span style="font-size: 14.6667px;">Mnova started as an NMR only application with limited functionality. Over the years, the application has been growing steadily, both in terms of NMR functionality and the addition of new <i>plug-ins</i> such as LC/GC/MS, molecular editing, DB, just to cite a few. </span></div>
<div>
<span style="font-size: 14.6667px;">As a result, what initially fit seamlessly within a traditional user interface (with menu bars and toolbars), has become an increasingly complex application to navigate, particularly when more than one <i>plug-in</i> is installed. </span></div>
<div>
<span style="font-size: 14.6667px;">For a few years we have been analyzing carefully alternatives to de-clutter the user interface. After much discussion, we finally came to the conclusion that the <b>Ribbon</b> interface was really the one that best suited our needs (or, more importantly, yours).</span></div>
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<span style="font-size: 14.6667px;"><br /></span></div>
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<span style="font-size: 14.6667px;"><br /></span></div>
<div>
<span style="font-size: 14.6667px;">One of the most interesting features of this interface is that it allows you to focus on a particular plugin (e.g. NMR) without the functionality of another plugin getting in the way.</span></div>
<h2>
<span style="font-size: 14.6667px;">Hate the Change? No problem</span></h2>
<div>
<div>
<span style="font-size: 14.6667px;">We understand that this change is drastic and not everyone will be happy with it. So, what if you absolutely hate this new interface? No problem, you won’t be forced to use it! You will just be able to switch it off in the <b>Preferences</b> (Modern == Ribbon).</span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgZfFPTbS7xNWgI-EyxqS7I7B3u3l6yAbWHpgy2jhzSx5It8Qg9JlIJOULL3cWM8FLLLEVU6WYe5fed9N9495fSKEvS9U-oGJNSGt5Z4M7K6nsYmCcdqDdlqHw0VzCgggnAf98MPj6pyf8/s1600/preferences.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="552" data-original-width="1063" height="332" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgZfFPTbS7xNWgI-EyxqS7I7B3u3l6yAbWHpgy2jhzSx5It8Qg9JlIJOULL3cWM8FLLLEVU6WYe5fed9N9495fSKEvS9U-oGJNSGt5Z4M7K6nsYmCcdqDdlqHw0VzCgggnAf98MPj6pyf8/s640/preferences.png" width="640" /></a></div>
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<span style="font-size: 14.6667px;">Nevertheless, from my point of view, the Ribbon interface improves usability and User Experience and therefore I strongly recommend it ahead of the traditional User Interface. This is our first ribbon implementation and, therefore, I am sure it still has a lot of room for improvement. If you use it, any suggestions will be very welcome!</span></div>
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Carlos Cobashttp://www.blogger.com/profile/13500275318435740775noreply@blogger.com0tag:blogger.com,1999:blog-6953549091784501422.post-20005668490473368702017-09-22T05:42:00.000-07:002018-01-22T10:16:26.191-08:00ELNs and the importance of live analytical data<h2 style="clear: both; text-align: left;">
Setting the scene</h2>
Over the last 25 years, during my bachelor's degree, PhD, Post Doc, and now as director of R&D at <a href="http://www.mestrelab.com/" target="_blank">Mestrelab</a>, I have had the opportunity to interact with many organic chemists. Most of them, although with their own singularities, share relatively similar procedures and workflows, with their strengths and weaknesses. I have witnessed many advances in the way they conduct their research, but I also must say that there are some areas of it that remain firmly rooted in the past.<br />
<br />
An example of the latter which I’m still seeing in many labs is the issue of <b>data loss</b>: In the particular case of academia, research teams are typically made up of (pre)doctoral or postdoctoral students whose residence time is usually between 3 and 8 years, roughly speaking.<br />
<br />
During that period, they produce an enormous amount of spectroscopic data (NMR, GC/LC/MS, UV/IR, etc.) to characterize their molecules. Whilst some groups have some sophisticated IT infrastructures equipped with either in-house or third party DBs (including <a href="http://mestrelab.com/software/mnova/db/">Mnova DB</a> for analytical data), I think it is not unreasonable to say that most of them save their spectroscopy data on their personal computers (e. g. laptops) or in shared folders of their research group (e. g. Dropbox). <b>Data leakage is the result as students leave</b>.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEieC1HHVzOwParRyRT4Txt7pcwUFIv0I8nAa5Eu5t77ALYpODPHx32GtjXVwebA7Bcx77IVNzPuyrEfHfxPOIfFTaTsEVnUDHyJe42JzLaOQoqgAYHwZ4FXytYNVPnfBT3-ebkmrrcDzmc/s1600/losing-data.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" data-original-height="747" data-original-width="897" height="531" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEieC1HHVzOwParRyRT4Txt7pcwUFIv0I8nAa5Eu5t77ALYpODPHx32GtjXVwebA7Bcx77IVNzPuyrEfHfxPOIfFTaTsEVnUDHyJe42JzLaOQoqgAYHwZ4FXytYNVPnfBT3-ebkmrrcDzmc/s640/losing-data.jpg" width="640" /></a></div>
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<br />
If you're a principal investigator, I'm sure you've found yourself in the following situation: one of your students synthesized a compound some time ago. However, for some reason, you are now considering the possibility that the proposed structure may not be the right one. Obviously, to review this structure, you need to have access to the <b>original spectroscopic data</b>, but unfortunately, the student is no longer part of your research group and you have no way of locating the NMR spectra. <br />
<br />
In the same plot line, some students only keep the spectroscopic data of the products that they have successfully synthesized but <b>discard the data of those reactions that did not work</b> in the way they had planned. <br />
<br />
These are just two examples of what I consider to be a more general problem associated with the difficulty of efficiently <b>managing analytical information in an organic chemistry laboratory</b>. <br />
<br />
Nowadays, <b>many labs are moving from paper-based to electronic laboratory notebooks</b> (ELNs) that offer significant benefits for long-term storage. However, <b>most of them lack the capability to understand and handle spectroscopy data in an integrated manner</b>. Some of them are just repository of <b>PDFs</b> of analytical data generated by some specialized software. This is, in my opinion, a very limited, unproductive and inefficient solution to the extent that data generated in this form has been dubbed as <b>“dead data”</b> where <b>all the valuable spectroscopy information has been removed</b>, reducing it to a series of unstructured set of images and text strings. As it is stored today, analytical data is virtually unusable and tasks like the ones listed below are simply impossible to perform:<br />
<br />
<br />
<ol>
<li><b>NMR data could have been processed incorrectly</b> making a comprehensive analysis of the data unfeasible.</li>
<li>Only some parts of the spectrum could have been reported or the resolution is too low to characterize a compound unambiguously. For instance, accurate determination of <b>coupling constants</b>, inspection of possible <b>impurities </b>or side products in a reaction would not be possible.</li>
<li><b>Spectroscopic data search</b>: Do I have any spectrum that contains a triplet at 3.5 ppm? This is a question that could not be answered with dead data.</li>
<li>Do I have any spectrum <b>similar </b>to this one?</li>
</ol>
<br />
Some ELNs, in addition to PDF or plain images, also store raw data but do not offer a solution with <b>real spectroscopy intelligence capabilities within a searchable and homogeneous environment</b>.<br />
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<h2>
<span lang="EN-US"><span lang="EN-US" style="line-height: 15.6934px;"><span style="font-family: "arial" , "helvetica" , sans-serif; font-size: large;">Mbook 2.0: A spectroscopy-aware ELN</span></span></span></h2>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjAGHffq7qF-qJ069nk0bsvVRu7lcuXy9w85a9gjPH8Phyphenhyphenf7cVXxC-ugYD6LZDtf_m1rNLxqytxbgcnHnQsUCjrvKae2Sz2LZwpyuGBDn9rja_9E_weRVWtHnzgBrS1y_5CQ5Qb9AbTtw0/s1600/mbook-screens-800px.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="342" data-original-width="800" height="272" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjAGHffq7qF-qJ069nk0bsvVRu7lcuXy9w85a9gjPH8Phyphenhyphenf7cVXxC-ugYD6LZDtf_m1rNLxqytxbgcnHnQsUCjrvKae2Sz2LZwpyuGBDn9rja_9E_weRVWtHnzgBrS1y_5CQ5Qb9AbTtw0/s640/mbook-screens-800px.jpg" width="640" /></a></div>
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Our ELN, <a href="http://www.mestrelab.com/mbook">MBook 2.0</a> is our answer to those issues. <b>It has been designed to take advantage of all the power of <a href="http://mestrelab.com/software/mnova/" target="_blank">Mnova </a>which is tightly integrated with Mbook</b> and is responsible for processing the analytical data acquired by the chemist. The scientist only needs to send the data in a zip file and Mnova will automatically recognize the file format (NMR data such as those from Bruker, JEOL, Varian / Agilent, Magritek, Thermo picoSpin, Nanalysis as well as many LC/GC/MS and UVIR files) and <b>process in a fully unattended way</b>. As a result, a new Mnova document is generated on the fly and saved into the ELN.<br />
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<span lang="EN-US" style="font-size: 11pt; line-height: 107%;"><span style="font-family: "arial" , "helvetica" , sans-serif;">This
file can be accessed and viewed directly from within Mbook with a new<b> spectral
viewer</b> which provides basic navigation tools such as zoom-in and out.</span></span><span lang="EN-US" style="font-family: "calibri" , sans-serif; font-size: 11.0pt; line-height: 107%;"> </span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgb9lwijnXX0lhw945nJSFH1OhoCE2XRGsDz0Q7-WPWthmXjVoQOnDMATIIhPgF7tw5PiJ0bmu4N8CilnAOTH8urmXAtMH1x0OmlmAHz0ekdKanj4uWEwNM_Fi-DBQ5jUQXgd_4L3-DbWc/s1600/spectralviewer.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="844" data-original-width="948" height="568" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgb9lwijnXX0lhw945nJSFH1OhoCE2XRGsDz0Q7-WPWthmXjVoQOnDMATIIhPgF7tw5PiJ0bmu4N8CilnAOTH8urmXAtMH1x0OmlmAHz0ekdKanj4uWEwNM_Fi-DBQ5jUQXgd_4L3-DbWc/s640/spectralviewer.jpg" width="640" /></a></div>
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<span style="font-size: 14.6667px;"><span style="font-family: "arial" , "helvetica" , sans-serif;">At this present time <a href="http://mestrelab.com/software/mbook/" target="_blank">Mbook 2.0</a> does not include spectral search capabilities, but we expect to offer this feature shortly once the integration of Mbook with <a href="http://mestrelab.com/software/mnova/db/" target="_blank">Mnova DB</a> is completed</span></span></div>
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Carlos Cobashttp://www.blogger.com/profile/13500275318435740775noreply@blogger.com2tag:blogger.com,1999:blog-6953549091784501422.post-13381063836215335942015-12-05T00:32:00.000-08:002015-12-05T00:33:52.014-08:00Stanning: A new NMR apodization function<div class="MsoNormal" style="text-align: justify;">
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Apodization refers to the mathematical processing technique
by which the FID is multiplied pointwise by some appropriate function in order
to improve the instrumental line shape. The term <i>apodize</i> actually derives from its Greek meaning <i>“removing the feet”</i>. The feet being
referred to are actually the side-lobes found in the FT spectrum resulting from
zero-filling a truncated FID (this phenomenon is also known as <i>leakage</i>). <o:p></o:p></span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Probably the most widely used apodization function in NMR,
especially in 13C spectroscopy, is the Exponential function although other
functions such as <a href="http://mathworld.wolfram.com/HanningFunction.html" target="_blank">Hanning </a>are also very popular. <o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: "arial" , "helvetica" , sans-serif;">In this short post, I want to introduce a new apodization
function, the so-called <i>Stanning</i>
function which gives superior results compared to Exponential and Hanning
apodization functions. <o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: "arial" , "helvetica" , sans-serif;">The name <b><i>Stanning </i></b>is a play on words which combines Hanning (which
forms the basis of this function) with <a href="http://www.ebyte.it/" target="_blank">Stan</a>, the inventor of
this apodization function to whom all credit should be given. <o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: "arial" , "helvetica" , sans-serif;">The performance of this apodization function is illustrated
with a 19F NMR spectrum whose FID is shown in Figure 1. <o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: "arial" , "helvetica" , sans-serif;"><br /></span></div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi4pjzXb3_n1LOFZPKwpzQg1Z2m2JGyGvHEMI5NbmVEimmD8KgBzI-sksGIjLiUoDa6l0KaT8zwSKuhpYz3zY4RqijSzh191CuSVgsnhkv1adh89vhkPfH0kG9SjL5s5mBvFehYPcm_7kQ/s1600/stan1.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="278" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi4pjzXb3_n1LOFZPKwpzQg1Z2m2JGyGvHEMI5NbmVEimmD8KgBzI-sksGIjLiUoDa6l0KaT8zwSKuhpYz3zY4RqijSzh191CuSVgsnhkv1adh89vhkPfH0kG9SjL5s5mBvFehYPcm_7kQ/s400/stan1.png" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Figure 1</td></tr>
</tbody></table>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: "arial" , "helvetica" , sans-serif;"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: "arial" , "helvetica" , sans-serif;">This FID consisted of ca 59K acquired data points which are
then extended by zero filling to a final size of 128K. As the FID has not fully
decayed to zero during acquisition, resulting FT spectrum will show the
expected truncation artefacts, as shown in Figure 2.<o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: "arial" , "helvetica" , sans-serif;"><br /></span></div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiEEOCbStt0Ne5oLWsLwMS-ZOB0pMUAib3x10rIzDiOvUImxtqBYKWFn_UBPeCV0ntyTaT7QvPbmSSX9TOnBzau1M9EPd13GSvjjdtoKZRScVu6N5uuoXA3bnCNLvt_KQC3Z4NjJxPzOP4/s1600/stan2.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="278" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiEEOCbStt0Ne5oLWsLwMS-ZOB0pMUAib3x10rIzDiOvUImxtqBYKWFn_UBPeCV0ntyTaT7QvPbmSSX9TOnBzau1M9EPd13GSvjjdtoKZRScVu6N5uuoXA3bnCNLvt_KQC3Z4NjJxPzOP4/s400/stan2.png" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Figure 2</td></tr>
</tbody></table>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: "arial" , "helvetica" , sans-serif;">Multiplication of the FID by an exponential function, in
this case with a line broadening value of 1.0 Hz results in the following
spectrum where the wiggles have been significantly reduced but not in a totally
satisfactory way (see Figure 3).</span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: "arial" , "helvetica" , sans-serif;"><br /></span></div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgwwtlXWlKzZX8rHHW0mSoqKbuhlZh3zZW5QyMZeMtDExS15ad6MU8s9c1J8-y7Qn3AVDKpd6y-F49RBl2CXok7Zgx_l-CYpzFJCTu_pPDwSiC7ZaqvDtzye_yf16ROCyOgREleNM_eIcA/s1600/stan3.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="278" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgwwtlXWlKzZX8rHHW0mSoqKbuhlZh3zZW5QyMZeMtDExS15ad6MU8s9c1J8-y7Qn3AVDKpd6y-F49RBl2CXok7Zgx_l-CYpzFJCTu_pPDwSiC7ZaqvDtzye_yf16ROCyOgREleNM_eIcA/s400/stan3.png" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Figure 3</td></tr>
</tbody></table>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: "arial" , "helvetica" , sans-serif;"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: "arial" , "helvetica" , sans-serif;">Application of the new Stanning function yields the result
depicted in Figure 4. As it can be seen, the truncation artifacts have been
further reduced whilst the resolution of the spectrum is slightly better compared
to the exponential function.</span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: "arial" , "helvetica" , sans-serif;"><br /></span></div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjfV8R5FiP9X0RqDiF5zoM9ahz-N0_L2ANyvnzlcHKRvbqzmv0tSvxAE8kOSnezK-gT9Q-A9eTV6__TSDL28aqcvXZsdmYdCn-_u3JyaW_YRF7yMLd01naUBVcZ8k2CoB5xkHZZY3C11Hk/s1600/stan4.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="278" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjfV8R5FiP9X0RqDiF5zoM9ahz-N0_L2ANyvnzlcHKRvbqzmv0tSvxAE8kOSnezK-gT9Q-A9eTV6__TSDL28aqcvXZsdmYdCn-_u3JyaW_YRF7yMLd01naUBVcZ8k2CoB5xkHZZY3C11Hk/s400/stan4.png" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Figure 4</td></tr>
</tbody></table>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: "arial" , "helvetica" , sans-serif;"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: "arial" , "helvetica" , sans-serif; font-size: 11pt; line-height: 107%;">The mathematical formulation of Stanning as well
as some additional illustrative examples will be covered in a future blog post. </span></div>
Carlos Cobashttp://www.blogger.com/profile/13500275318435740775noreply@blogger.com4tag:blogger.com,1999:blog-6953549091784501422.post-47855194672496724012015-05-02T10:08:00.005-07:002015-05-02T10:27:32.443-07:00NMR for iPad and Android: Beta testing<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhHstPcKHTGBXldsoB_tgqbYoaN-WHcJ9SIbrBJNvfEfqfJZj_BHH5N1ImJiNUadFfcjsl1n1jg-0uKIJezXnSMDPJrZJIiYbTSNKZ3mdu4NWu8matag98Wpa_0fcGfFuMcZK9zkgMx7Og/s1600/FIGURE2.PNG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhHstPcKHTGBXldsoB_tgqbYoaN-WHcJ9SIbrBJNvfEfqfJZj_BHH5N1ImJiNUadFfcjsl1n1jg-0uKIJezXnSMDPJrZJIiYbTSNKZ3mdu4NWu8matag98Wpa_0fcGfFuMcZK9zkgMx7Og/s1600/FIGURE2.PNG" height="300" width="400" /></a></div>
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<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<span style="font-family: Arial, Helvetica, sans-serif; line-height: 107%; text-align: justify;">We
at Mestrelab are delighted to announce our first iPad / Android app ever, </span><b style="font-family: Arial, Helvetica, sans-serif; line-height: 107%; text-align: justify;">Mnova Tablet.</b><span style="font-family: Arial, Helvetica, sans-serif; line-height: 107%; text-align: justify;"> You won’t find it in the
google or iPad stores though as it is still in the final </span><b style="font-family: Arial, Helvetica, sans-serif; line-height: 107%; text-align: justify;">Beta testing stage</b><span style="font-family: Arial, Helvetica, sans-serif; line-height: 107%; text-align: justify;">, but from these lines I’d like to welcome anyone
willing to test it out. </span><br />
<div style="text-align: justify;">
<span lang="EN-US" style="line-height: 107%;"><span style="font-family: Arial, Helvetica, sans-serif;">Just send me an email at carlos-at-mestrelab.com and I’ll
be more than happy to give you the details on how to Beta test it for the platform of your choice</span></span></div>
<div style="text-align: justify;">
<span lang="EN-US" style="line-height: 107%;"><span style="font-family: Arial, Helvetica, sans-serif;"><br /></span></span></div>
<div style="text-align: justify;">
<span lang="EN-US" style="line-height: 107%;"><span style="font-family: Arial, Helvetica, sans-serif;"><br /></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">There is
also an article in Magnetic Resonance in Chemistry which describes the main
features of the app and how it was developed from a more technical point of
view.<o:p></o:p></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: Arial, Helvetica, sans-serif;"><b><span lang="EN-US" style="background: white; line-height: 107%;">“<a href="http://onlinelibrary.wiley.com/doi/10.1002/mrc.4234/abstract" target="_blank">NMR data visualization, processing, and analysis on mobile devices</a></span>”</b></span></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
<span lang="EN-US"><br /></span></div>
<div class="separator" style="clear: both; text-align: center;">
<img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiAZy0sfKsAa_8KO65IReRoF6d2JZG4BXYq_vvyLfs3Zn6bd_xjwXmy8Sn_hqQV1kulvGVw6xXMjMQfTPntGAmFbuHvgXZ6DiFc-0B3XObOQgeexOlMVlxlOFN2OpeTrIYWv_WwdeTEhPw/s1600/mrc4234-toc-0001.png" height="400" width="304" /></div>
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<span lang="EN-US"><br /></span></div>
<h2>
<span lang="EN-US">Free<o:p></o:p></span></h2>
<div class="MsoNormal" style="text-align: justify;">
<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">The beauty
of this app is that it provides a very simple and enjoyable mobile experience
for NMR data processing and viewing, not to mention the fact that it’s <b>free</b>, at
least for the basic functionality. This is how it works:</span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;"><br /></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">The free version reads
all NMR data (including molecules) supported by Mnova (meaning that virtually
all NMR data files will be supported) and transform the raw NMR data automatically,
if need be. It also allows basic graphical manipulations, including zoom-in,
panning, and spectral intensities expansions.<o:p></o:p></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">On the other hand, in order to edit or change any
processing operations (apodization, phase, baseline, etc) or apply any analysis
(peak picking, integration, multiplet analysis), it will be necessary to pay a small
fee via in-app purchases in the Google or Apple stores. More details about this
as soon as the official release becomes available. </span><o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<h2>
<span lang="EN-US">Key features<o:p></o:p></span></h2>
<div class="MsoNormal" style="text-align: justify;">
</div>
<ul>
<li><span style="font-family: Arial, Helvetica, sans-serif;">Automatic
processing of 1D and 2D NMR data sets in multiplet formats (Bruker,
Varian/Agilent, Jeol, Magritek, Oxford Instruments, Nanalysis, Thermo picoSpin,
amongst others)</span></li>
<li><span style="font-family: Arial, Helvetica, sans-serif;">Support of
1D arrayed experiments</span></li>
<li><span style="font-family: Arial, Helvetica, sans-serif;">Processing
of 2D-NUS spectra</span></li>
<li><span style="font-family: Arial, Helvetica, sans-serif;">Dropbox
support</span></li>
<li><span style="font-family: Arial, Helvetica, sans-serif;">Ability to import
spectra directly from the email client and share the spectra or images to
social media</span></li>
</ul>
<br />
<div style="text-align: justify;">
<span lang="EN-US" style="line-height: 107%;"><span style="font-family: Arial, Helvetica, sans-serif;">
</span></span></div>
<div style="text-align: justify;">
<span lang="EN-US" style="line-height: 107%;"><span style="font-family: Arial, Helvetica, sans-serif;"><br /></span></span></div>
<h2 style="text-align: justify;">
<span style="font-family: Arial, Helvetica, sans-serif;"><span style="line-height: 17.1200008392334px;">Screen shots</span></span></h2>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg1zVOVsHT7KRhcSEKqxNTPJri1mdqhgeURHG5x9MLVLXtlhyphenhyphensOzviB6us9pyUcw2eL36NFtjVhBUbIPDDkjvULvCANYiyunOgVVZvuPfkNQdAvv0O1K5c16dUH3qpesKI5q3Zskslvvqg/s1600/FIGURE3.PNG" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg1zVOVsHT7KRhcSEKqxNTPJri1mdqhgeURHG5x9MLVLXtlhyphenhyphensOzviB6us9pyUcw2eL36NFtjVhBUbIPDDkjvULvCANYiyunOgVVZvuPfkNQdAvv0O1K5c16dUH3qpesKI5q3Zskslvvqg/s1600/FIGURE3.PNG" height="480" width="640" /></a></div>
<span lang="EN-US" style="font-family: "Calibri",sans-serif; font-size: 11.0pt; line-height: 107%; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"><br /></span>
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<br />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEia09SDra2IdXwd7He_rSeK-SVpFVRZ-mqATBgZGA5yC4b-qIjIyJUrPK_lCjz1-v5pc4sMoCtL_e6Ns5M9bISadnjhT91PBa1OCtKsGWy72tMuFqKwh6-PxtBjFWozKnmU7-xZouUY_YM/s1600/FIGURE4.PNG" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEia09SDra2IdXwd7He_rSeK-SVpFVRZ-mqATBgZGA5yC4b-qIjIyJUrPK_lCjz1-v5pc4sMoCtL_e6Ns5M9bISadnjhT91PBa1OCtKsGWy72tMuFqKwh6-PxtBjFWozKnmU7-xZouUY_YM/s1600/FIGURE4.PNG" height="480" width="640" /></a>Carlos Cobashttp://www.blogger.com/profile/13500275318435740775noreply@blogger.com3tag:blogger.com,1999:blog-6953549091784501422.post-32059374033940808712015-04-10T10:18:00.001-07:002015-04-10T10:33:13.675-07:00Mbook: A new Electronic Laboratory Notebook that speaks NMR<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgYZaLZLguMoz8u1VImjJckCHYVr2IAoRtkmajsF1_qpuXWX47WsxI4VcMuokH_4yw8RhiBj3ZX8NVoXdqqIMhVcAQ5ar2E8kt69cKFe6ibOfJjWWLa0Yk-4uXU2B9KApeMbqJk-7hlBJs/s1600/mbook1.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgYZaLZLguMoz8u1VImjJckCHYVr2IAoRtkmajsF1_qpuXWX47WsxI4VcMuokH_4yw8RhiBj3ZX8NVoXdqqIMhVcAQ5ar2E8kt69cKFe6ibOfJjWWLa0Yk-4uXU2B9KApeMbqJk-7hlBJs/s1600/mbook1.png" height="272" width="400" /></a></div>
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<br /></div>
<div class="MsoNormal" style="text-align: justify;">
<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;"><br /></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">When we founded
Mestrelab back in 2005, our only commercial product was 100% about NMR data
processing / analysis. Over these years, our NMR products have matured with an increasing
number of features and robustness. At the same time, we have released other
products such as LC/GC/MS and analytical DB software.<o:p></o:p></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">This week,
we have released a new brand product, <a href="http://mestrelab.com/software/mbook/" target="_blank">Mbook</a>: This is an electronic Lab Notebook which we have been developing in collaboration with the Universities of Santiago de Compostela
and Vigo, both in Spain. <o:p></o:p></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">There are
many ELNs out there already so why have we ventured into developing a new one?
The short answer is that we believed that most of the existing solutions lacked
a real integration between chemistry (i.e. reactions) and analytical data (e.g. NMR): One of the unique features of <a href="http://mestrelab.com/software/mbook/" target="_blank">Mbook </a>is that it is tightly integrated with
Mnova so that any analytical data supported by the latter (1D & 2D NMR, LC/GC/MS) will be automatically
handled by Mbook. Technically speaking, Mbook comes with a special version of
Mnova which runs in the background. This means that when you upload, for
example, and NMR experiment (i.e. raw FID), <a href="http://mestrelab.com/software/mbook/" target="_blank">Mbook</a> will process it automatically
for you (via Mnova) so that you will see the processed spectrum automatically
in your reaction. Of course, the raw data will always be available should you
want to process it differently, either with your Mnova client or with any other
NMR processing software. <o:p></o:p></span></span></div>
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<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;"><br /></span></span></div>
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<span lang="EN-US"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgB-1nGQEWi3UvI1P8Jj-IIcGyoXMcEMwzWakHDRbZuERN91xSyzvsRbPto9p9OZXv9n000kKigPj66LaQmlVohtR_UO3J8tsUyYHLe8jL_j_NJNfI6eIqYy18ynz7u8mAMRFcBCbWAzN4/s1600/mbook2.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgB-1nGQEWi3UvI1P8Jj-IIcGyoXMcEMwzWakHDRbZuERN91xSyzvsRbPto9p9OZXv9n000kKigPj66LaQmlVohtR_UO3J8tsUyYHLe8jL_j_NJNfI6eIqYy18ynz7u8mAMRFcBCbWAzN4/s1600/mbook2.png" height="253" width="400" /></a></span></div>
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<br /></div>
<div style="text-align: justify;">
<span lang="EN-US" style="line-height: 107%;"><span style="font-family: Arial, Helvetica, sans-serif;">Another feature worth mentioning is that Mbook
has been designed solely and exclusively for synthetic organic chemists. If you
do any other type of chemistry, <a href="http://mestrelab.com/software/mbook/" target="_blank">Mbook </a>will not be for you. If you are an
organic chemist and you are looking for a new ELN, please give Mbook a try, we
will be very happy to hear your feedback!</span></span><br />
<span style="background-color: white; color: #222222; font-family: Arial, Helvetica, sans-serif;">Oh! And it
will soon be available as a native Android and iOS application, and, on that,
we think it might be the first of its kind!</span></div>
Carlos Cobashttp://www.blogger.com/profile/13500275318435740775noreply@blogger.com0tag:blogger.com,1999:blog-6953549091784501422.post-83328105439955375812014-12-14T08:04:00.001-08:002014-12-15T07:39:03.456-08:00Quadruplet, triplet … so simple?<span style="font-family: Arial, Helvetica, sans-serif;">In the
picture below I’m showing the ‘synthetic’ NMR spectrum of Ethanol. It has been
synthesized using <b>Mnova Spin Simulation</b> capabilities and the experimental
values (chemical shifts and couplings) taken from the NMR spectrum of ethanol
recorded at 600 MHz in water, so the OH signal will not show up.</span><br />
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<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi47sqPiPyrf5Wsvjbayp3xtyc4R_kPXgtxadXwq-e6MCfQlIH2av9_cVdFIJb6vphj5XNjn3jgAvKY8Ngq8VcfPzMTd5UmnKhkIrY4QYM1NnZw7C8DqD0JGgM-hnmZeGodCGREAZfTR0w/s1600/Ethanol1.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi47sqPiPyrf5Wsvjbayp3xtyc4R_kPXgtxadXwq-e6MCfQlIH2av9_cVdFIJb6vphj5XNjn3jgAvKY8Ngq8VcfPzMTd5UmnKhkIrY4QYM1NnZw7C8DqD0JGgM-hnmZeGodCGREAZfTR0w/s1600/Ethanol1.png" height="278" width="400" /></a></div>
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<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">Nothing new
under the sun. This is a very simple spectrum where the two observed multiplets
seem to follow very nicely the well-known first order multiplet rules that most
chemists use on daily basis. In this case, a very simple <b>A3X2 </b>spin system. <o:p></o:p></span></span></div>
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<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">But does
this mean that this spectrum is actually composed by only 7 peaks? The answer
is, of course not, there are many more peaks! But because of the very <b>limited
resolution</b>, most of them are not observed and merge in such a way that only 7
peaks are ultimately observed. <o:p></o:p></span></span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;"><span lang="EN-US">In other
words, the number of NMR <i>transitions</i>
is usually much larger than the number of peaks we actually observe in the spectrum.
Just to give an example: A molecule containing 30 coupled protons will result
in a spectrum having 16106127360 (=</span><span lang="EN-US">1.61E+10) transitions. As its corresponding NMR
spectrum will show only about 100-200 peaks, that makes it well over eighty
million quantum transitions per resolved peak!<o:p></o:p></span></span><br />
<span style="font-family: Arial, Helvetica, sans-serif;"><span lang="EN-US"><br /></span></span></div>
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<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;"><o:p></o:p></span></span></div>
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<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">For
example, let’s magnify the quadruplet and use Mnova unique capabilities to
display the individual transitions by simply hovering with the mouse cursor
over the atoms in the molecule (CH2 in this case). We can see that there are
some ‘hidden peaks’, these are the <b>NMR transitions</b> calculated by diagonalizing
the <b>NMR Hamiltonian</b>. <o:p></o:p></span></span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiIQ04cD_nCRzpqUJCo0JeXWfGBUqeu0ILJqJWEePwcTx_XE9LLyDjQj-OqUq6O6LRYBsDaL54SRLHnhRSRn9vIM0LC5w9lY7iIIgdp5QDXiPYEtrnJzAw4IEGtoWnqK3e97YpzEOfZgXY/s1600/Ethanol2.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiIQ04cD_nCRzpqUJCo0JeXWfGBUqeu0ILJqJWEePwcTx_XE9LLyDjQj-OqUq6O6LRYBsDaL54SRLHnhRSRn9vIM0LC5w9lY7iIIgdp5QDXiPYEtrnJzAw4IEGtoWnqK3e97YpzEOfZgXY/s1600/Ethanol2.png" height="288" width="400" /></a></div>
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<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;"><br /></span></span>
<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">These
transitions are so close that they cannot be resolved under the usual NMR
resolution conditions. In fact, to separate all these signals, it would be
necessary to have a spectral resolution of <!--0--><!--0--></span></span>< 0.01 Hz<br />
<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;"><br /></span></span></div>
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<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">Whilst this
is far from being feasible experimentally nowadays, it is easy to do
numerically. In the figure below I’m displaying the same synthetic spectrum of
Ethanol but this time synthesized using a line width of just 0.01 Hz and 1 MB
of digital data points. Now the individual transitions can be seen as resolved
peaks so in this example a transition will be virtually equivalent to an NMR
peak. <o:p></o:p></span></span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi1-ggjk0EWO91rblj2CLNFQbZkNU-0maKysYJZr3upKGX41FG580Rh5uWRshPa58-PYcZqcYApVcrxztkWJLQ8emC193Qha0fvMqLKNTUEm02xps32UUF4ew4AgQJhxV-076CedlZT0z0/s1600/Ethanol3.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi1-ggjk0EWO91rblj2CLNFQbZkNU-0maKysYJZr3upKGX41FG580Rh5uWRshPa58-PYcZqcYApVcrxztkWJLQ8emC193Qha0fvMqLKNTUEm02xps32UUF4ew4AgQJhxV-076CedlZT0z0/s1600/Ethanol3.png" height="202" width="400" /></a></div>
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<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">Simply put,
an NMR spectrum is just a <b>superposition of all spectral transitions</b> (which can
be in the order of millions), <b>transitions compose peaks</b>, <b>peaks group into
multiplets</b>, and <b>multiplets compose the spectrum</b>. <o:p></o:p></span></span><br />
<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;"><br /></span></span></div>
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<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">The ability
of Mnova to show the individual NMR transitions in a synthetic spectrum can be
a good teaching tool <o:p></o:p></span></span></div>
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<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;"><br /></span></span></div>
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<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">For a more theoretical and rigorous discussion on NMR transitions, see </span></span><span style="font-family: Arial, Helvetica, sans-serif;"><span style="background-color: white;">A.D. Bain, D.A. Fletcher and P. Hazendonk. "What is a transition?" </span><i style="background-color: white;">Concepts in Magnetic Resonance </i><b style="background-color: white;">10</b><span style="background-color: white;"> 85- 98 (1998)</span></span><span style="background-color: white; font-size: medium;"> (<a href="http://onlinelibrary.wiley.com/doi/10.1002/%28SICI%291099-0534%281998%2910:2%3C85::AID-CMR2%3E3.0.CO;2-R/abstract" target="_blank">link</a>)</span></div>
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Carlos Cobashttp://www.blogger.com/profile/13500275318435740775noreply@blogger.com0tag:blogger.com,1999:blog-6953549091784501422.post-88526074140707234202014-09-20T07:56:00.000-07:002014-09-20T07:59:23.394-07:00From NMR multiplets reports to synthetic spectra <div class="MsoNormal">
<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">I admit
that I was never a fan of the traditional way in which NMR spectra are usually
reported in organic chemistry journals, something like:<o:p></o:p></span></span></div>
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<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;"><br /></span></span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;"><sup><span lang="EN-US">1</span></sup><span lang="EN-US">H NMR (300 MHz, CDCl<sub>3</sub>)
7.91 (d, J=8.2 Hz, 2H), 7.31 (d, J=8.2 Hz, 2H), 3.65 (t, J=6.3 Hz, 2H), 3.13
(t, J=6.9 Hz, 2H), 2.95 (p, J=6.9 Hz, 1H), 2.20 (p, J=6.6 Hz, 2H), 1.26 (d,
J=6.9 Hz, 6H)<o:p></o:p></span></span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;"><span lang="EN-US"><br /></span></span></div>
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<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">It is not
only that there is not a standard format that is strictly followed by all
journals. It is also that it does not convey all the NMR information contained
in the actual spectrum (reducing a spectrum into a multiplet report results in
an irreversible loss of important information) and facilitates the job to those
willing to cheat ( see <a href="http://nmr-analysis.blogspot.com.es/2011/03/hexacyclinol-nmr-spectra-vs-plain.html" target="_blank">this </a>and <a href="http://cenblog.org/2009/02/hexacyclinol-the-data-debate" target="_blank">this</a>).<o:p></o:p></span></span></div>
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<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;"><br /></span></span></div>
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<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">Today, in
the 21st century, I don’t see any reason why the experimental raw data (i.e.
FID+metadata) should not be an integral part of any article where NMR spectra
have been used to characterize a chemical structure. In any event, there are
millions of articles with NMR spectra in the form of those old fashioned multiplet
reports and we thought that it would be a good idea to implement some tools to facilitate
the analysis of those <i>reduced spectra</i>.
<o:p></o:p></span></span></div>
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<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;"><br /></span></span></div>
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<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">That is why
we developed the Mnova script <b>“Multiplet
Report to Spectrum”</b>, a tool which is available in Mnova from the scripts
menu:<o:p></o:p></span></span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjGUnN805w86LLLyZKbjQLrw0YgEUCxEJD-Ip5LvXpXg0QpAOwZ38r3gkB55flHLPeUpx5dBS6hRXRF0SAy5jE6FoCFL4fnajOFoNA7xkJrANKAk3OJiYRrL2vGo9XXaVMjyqcy_d6W9h8/s1600/MultipletReport1.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjGUnN805w86LLLyZKbjQLrw0YgEUCxEJD-Ip5LvXpXg0QpAOwZ38r3gkB55flHLPeUpx5dBS6hRXRF0SAy5jE6FoCFL4fnajOFoNA7xkJrANKAk3OJiYRrL2vGo9XXaVMjyqcy_d6W9h8/s1600/MultipletReport1.png" height="161" width="400" /></a></div>
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<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">It is very
easy to use: Once this command is issued, you only need to copy to the
clipboard your multiplet report from the article (PDF, Word document, etc) and
paste it into the Multiplet report edit box at the top of the dialog:</span><o:p></o:p></span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjz9A_hh-6EbxLODS8ekh5S746_X9p9YSuWD1grbV6Jh4K-0hsAwPBVIV_qpNfxhB0nfnU8WDe2srbcrUN7dcYZ8SaqL0hN7h9yRxcBXzN3QnSuUL5Q6FOHFBaC1FkzBsF6jgfLSIcRf4c/s1600/MultipletReport2.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjz9A_hh-6EbxLODS8ekh5S746_X9p9YSuWD1grbV6Jh4K-0hsAwPBVIV_qpNfxhB0nfnU8WDe2srbcrUN7dcYZ8SaqL0hN7h9yRxcBXzN3QnSuUL5Q6FOHFBaC1FkzBsF6jgfLSIcRf4c/s1600/MultipletReport2.png" height="357" width="400" /></a></div>
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<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">As soon as
it is pasted, this application will parse the multiplets and the different
fields (chemical shifts, number of protons, multiplicity, solvent, nucleus,
etc) will be automatically populated. If for any reason some of those values
are not correctly parse, you can manually amend them.<o:p></o:p></span></span></div>
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<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">Once you
are happy with those values, you can press OK so that Mnova will <i>synthesize </i>a spectrum with those values.
</span><o:p></o:p></span></div>
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<span lang="EN-US"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh9iVmswVlU1kdOiwZ8jYOeexsQlkEjYeSra_1z2t1dgtjIVOucgD9489ceQzSsbSev0297DJonVb6sXIjeUWIOPhtc4s5DfkHUUbicm3hliVfp6e0VcHa6XEXHXQrwFjxdn2dcTIuqS-E/s1600/MultipletReport3.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh9iVmswVlU1kdOiwZ8jYOeexsQlkEjYeSra_1z2t1dgtjIVOucgD9489ceQzSsbSev0297DJonVb6sXIjeUWIOPhtc4s5DfkHUUbicm3hliVfp6e0VcHa6XEXHXQrwFjxdn2dcTIuqS-E/s1600/MultipletReport3.png" height="278" width="400" /></a></span></div>
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<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">We believe
that this is a very useful tool, in particular for organic chemists. It can be
used to easily compare an experimental spectrum with a multiplet report from a
journal, for example</span>. <o:p></o:p></span></div>
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Carlos Cobashttp://www.blogger.com/profile/13500275318435740775noreply@blogger.com3tag:blogger.com,1999:blog-6953549091784501422.post-72796666412100523922014-07-31T04:43:00.000-07:002014-08-06T00:33:35.092-07:00PCA and NMR: Practical aspects<div style="text-align: justify;">
<span style="font-family: Arial, Helvetica, sans-serif;">As of version 9.0, it is possible to perform </span><b style="font-family: Arial, Helvetica, sans-serif;">PCA </b><span style="font-family: Arial, Helvetica, sans-serif;">of </span><b style="font-family: Arial, Helvetica, sans-serif;">NMR </b><span style="font-family: Arial, Helvetica, sans-serif;">data sets directly from within the </span><b style="font-family: Arial, Helvetica, sans-serif;">Mnova </b><span style="font-family: Arial, Helvetica, sans-serif;">User Interface without having to resort to third party applications. The basic PCA functionality has been previously covered in this blog (</span><a href="http://nmr-analysis.blogspot.com.es/2014/01/chemometrics-under-mnova-9-pca.html" style="font-family: Arial, Helvetica, sans-serif;">see Chemometrics under Mnova 9 – PCA</a><span style="font-family: Arial, Helvetica, sans-serif;">)</span><span style="font-family: Arial, Helvetica, sans-serif;"> </span><span style="font-family: Arial, Helvetica, sans-serif;">and in this entry we are going to discuss in more detail some more practical aspects, particularly on the different binning, filtering and scaling options. </span></div>
<div style="text-align: justify;">
<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span></div>
<div style="text-align: justify;">
<span style="font-family: Arial, Helvetica, sans-serif;">What follows has been kindly written by Silvia Mari (project leader of the PCA module) and Isaac Iglesias, who programmed this module in Mnova.</span></div>
<div style="font-family: Arial, Helvetica, sans-serif; text-align: justify;">
<br /></div>
<h2 style="font-family: Arial, Helvetica, sans-serif; text-align: justify;">
Introduction</h2>
<div style="font-family: Arial, Helvetica, sans-serif; text-align: justify;">
Matrix
generation from an array of NMR spectra is the core step in chemometric
analysis. This procedure involves several options that the user should chose. In
this entry we want to focus on the practical aspects concerning matrix
preparation from NMR data. Broadly speaking, we can consider three main issues:</div>
<div style="text-align: justify;">
<ol style="font-family: Arial, Helvetica, sans-serif;">
<li><span style="text-indent: -18pt;">Choice of binning method: Sum vs
Peak</span></li>
<li><span style="text-indent: -18pt;">Filtering or not filtering?</span></li>
<li>Choice of Scaling strategy</li>
</ol>
<div style="font-family: Arial, Helvetica, sans-serif;">
<h2>
<span lang="EN-US">Choice of
binning method: Sum vs Peak</span></h2>
</div>
<div>
<span lang="EN-US"></span><br />
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<span lang="EN-US"><span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">When
dealing with high resolution NMR spectra it is in general impracticable to work
with the entire data points of the spectra which are usually in the order of
32Kb and bigger. The most common strategy used to reduce the number of
variables consists in dividing each spectrum in a defined number of regions,
the so called </span><i style="font-family: Arial, Helvetica, sans-serif;">bins. </i><span style="font-family: Arial, Helvetica, sans-serif;"> Several binning strategies are available
today, from regular binning, where bins have fixed width, to more sophisticated
strategies such as gaussian or dynamic adaptive binning</span> [1]<span style="font-family: Arial, Helvetica, sans-serif;">.
But even for these cases, when dealing with particularly crowded spectra, it usually
happens that shifts in peaks close to bin boundaries can cause dramatic
quantitative changes in adjacent bins. A good help in solving this problem
could come from peak deconvolution strategies.
Generally speaking, a deconvolved peak is a mathematical entity characterized
by a chemical shift (frequency), intensity and half-height line width. The
integral of a peak can be automatically derived assuming a peak shape (i.e.
Lorentzian) and the intensity and line width. For this reason, binning a
spectrum of deconvolved peaks reads out virtually completely the problem of bin
boundaries as illustrated in figure 1.<o:p></o:p></span></span></span></div>
<span lang="EN-US">
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg_1_yI2BEh3iYBT3q2D375Pamb4yuIPleBL3ilrGkDB9azenm6zwIRWRMFmjxGUN1ZoPINxqlnHcDMn9jDn2BtHnVgGK7K6KOaj3PcQB9zX7d8L4hpRW3mVKIdGdSY2B-xDeE67viqons/s1600/Figure1.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg_1_yI2BEh3iYBT3q2D375Pamb4yuIPleBL3ilrGkDB9azenm6zwIRWRMFmjxGUN1ZoPINxqlnHcDMn9jDn2BtHnVgGK7K6KOaj3PcQB9zX7d8L4hpRW3mVKIdGdSY2B-xDeE67viqons/s1600/Figure1.png" height="354" width="400" /></a></div>
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<div style="font-family: Arial, Helvetica, sans-serif; text-align: center;">
<span style="font-size: x-small;"><b><span lang="EN-GB">Figure </span><span lang="EN-GB">1</span></b><span lang="EN-GB"> – Binning real peaks versus binning deconvolved peaks</span></span></div>
<div style="font-family: Arial, Helvetica, sans-serif; text-align: center;">
<span style="font-size: x-small;"><span lang="EN-GB"><br /></span></span></div>
<div style="font-family: Arial, Helvetica, sans-serif; text-align: justify;">
<span lang="EN-US" style="line-height: 115%;">When
dealing with an array of NMR spectra, whilst regular binning of a number </span><b><span lang="EN-US" style="line-height: 115%;">b</span></b><span lang="EN-US" style="line-height: 115%;"> of bins over stacked spectra containing </span><b><span lang="EN-US" style="line-height: 115%;">s</span></b><span lang="EN-US" style="line-height: 115%;"> spectra will generate a matrix </span><b><span lang="EN-US" style="line-height: 115%;">b</span></b><span lang="EN-US" style="line-height: 115%;">x<b>s </b></span><span lang="EN-US" style="line-height: 115%;">(see figure 2), it is not possible to generate a
similar matrix using directly deconvolved peaks (peak list) since the number
and position of peaks varies from spectrum to spectrum</span></div>
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<span lang="EN-US" style="line-height: 115%;"><br /></span></div>
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<span style="font-size: x-small;"><b><span lang="EN-GB">Figure </span><!--[if supportFields]><span
lang=EN-GB><span style='mso-element:field-begin'></span><span
style='mso-spacerun:yes'> </span>SEQ Figura \* ARABIC <span style='mso-element:
field-separator'></span></span><![endif]--><span lang="EN-GB">2</span></b><!--[if supportFields]><span
lang=EN-GB style='mso-no-proof:yes'><span style='mso-element:field-end'></span></span><![endif]--></span><span lang="EN-GB"><span style="font-size: x-small;"> – Matrix generation from regular binning or peak list.</span><o:p></o:p></span></div>
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<span lang="EN-US">To
encompass this problem there are two main strategies: (1) provide algorithms
for peak alignment over the spectra series, as well as strategies for dealing
with missing peaks in order to end up with the same number of peaks and the
same peak positions for all the spectra; (2) perform binning over the peak
table. <o:p></o:p></span></div>
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<span lang="EN-GB">
<span lang="EN-US" style="line-height: 115%;">In the PCA module available in Mnova, we adopt the
second solution. User can decide whether to use regular binning (Sum) or
binning over deconvolved peaks (Peak) from the binning options. An example of
better classification is qualitatively represented in figure 3, where score
plots are represented for binning using Sum method (panel A) and binning using
Peak method (panel B).</span></span></div>
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<span style="font-size: x-small;"><b><span lang="EN-GB">Figure </span><!--[if supportFields]><span
lang=EN-GB><span style='mso-element:field-begin'></span><span
style='mso-spacerun:yes'> </span>SEQ Figura \* ARABIC <span style='mso-element:
field-separator'></span></span><![endif]--><span lang="EN-GB">3</span></b><!--[if supportFields]><span
lang=EN-GB style='mso-no-proof:yes'><span style='mso-element:field-end'></span></span><![endif]--></span><span lang="EN-GB"><span style="font-size: x-small;"> – Score plots obtained using same bin width of 0.03ppm; in both
cases data were normalized by the sum and pareto scaled. In panel A bins were
obtained directly as integration of real spectra; in panel B bins were obtained
by binning of the corresponding peak list obtained after global spectral
deconvolution.</span><o:p></o:p></span></div>
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<span lang="EN-GB"><span style="font-size: x-small;"><br /></span></span></div>
<h2 style="font-family: Arial, Helvetica, sans-serif;">
<span lang="EN-US">Filtering
or not filtering?</span></h2>
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<span lang="EN-GB">
<span lang="EN-US" style="line-height: 115%;">When reducing bin width to approximate spectral
resolution, and hence increasing the number of variables, it is generally
required to introduce filtering strategies in order to filter out those
variables that do not show significantly changes. There are established
filtering strategies that are commonly applied to genomics type of data and
that could also be successfully used for NMR-based type of data<span class="MsoFootnoteReference"><span class="MsoFootnoteReference"><span lang="EN-US" style="line-height: 115%;">[1]</span></span><!--[endif]--></span>.
In the PCA module we have implemented
five filtering options, namely: </span></span></div>
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<ol>
<li><span style="line-height: 115%;">Standard Deviation</span></li>
<li><span style="line-height: 115%;">Median Absolute Deviation</span></li>
<li><span style="line-height: 115%;">Interquartile Range</span></li>
<li><span style="line-height: 115%;">Mean Value</span></li>
<li><span style="line-height: 115%;">Median
Value </span></li>
</ol>
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<span lang="EN-GB"><span lang="EN-US" style="line-height: 115%;"><br /></span></span></div>
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<span lang="EN-GB"><span lang="EN-US" style="line-height: 115%;">In the first three cases a fixed fraction (default 10%) of
the bins is discarded (e.g. if the matrix is composed by 100 bins it means that
10 bins are discarded) and the selection is based on the Filter method chosen. In
the case of Mean Value or Median Value, user is asked to input a value for the
Mean or the Median. By doing so, only bins that display a lower value of the
inputted one are discarded. In the following figure, the difference in
clustering capability when the filtering is applied or not is illustrated.
Finally, it worth noting that very often, NMR data can contain regions which
should discarded and included into the so called blind regions; these regions
will not be taken into account in the principal component calculation.</span>
</span></div>
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<span style="font-size: x-small;"><b><span lang="EN-GB" style="text-align: justify;">Figure </span><span lang="EN-GB" style="text-align: justify;">4</span></b><span lang="EN-GB" style="text-align: justify;"> - Score plots obtained using same bin width of 0.01ppm; in both
cases data were normalized by the sum and pareto scaled. In panel A no filter
was applied; in panel B filtering strategy based on Mean Value was applied. A cut-off
value of 100 was used.</span></span></div>
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<h2>
<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">Choice of
Scaling strategy</span></span></h2>
<div class="MsoSubtitle">
<span style="font-family: Arial, Helvetica, sans-serif; line-height: 115%;">Scaling is an operation that is performed on the
variables (columns) of the matrix. Scaling strategy depends from one hand from
the biological information we wish to extract, but on the other hand also on
the data analysis method chosen (in our case PCA). As a first approach the
so-called </span><i style="font-family: Arial, Helvetica, sans-serif; line-height: 115%;">Centering<u> </u></i><span style="font-family: Arial, Helvetica, sans-serif; line-height: 115%;">is generally applied to every analysis. With </span><i style="font-family: Arial, Helvetica, sans-serif; line-height: 115%;">Centering</i><span style="font-family: Arial, Helvetica, sans-serif; line-height: 115%;"> all bin values fluctuate around
zero instead of around the mean of each bin; therefore </span><i style="font-family: Arial, Helvetica, sans-serif; line-height: 115%;">Centering</i><span style="font-family: Arial, Helvetica, sans-serif; line-height: 115%;"> is a method that adjusts for differences in the offset
between high and low abundant compounds. There are several methods available in
literature for scaling</span><u style="font-family: Arial, Helvetica, sans-serif; line-height: 115%;"> [3]</u><span style="font-family: Arial, Helvetica, sans-serif; line-height: 115%;">,
and generally centering is applied in combination with these methods. Scaling
strategies could be divided in two subclasses:</span><span style="font-family: Arial, Helvetica, sans-serif; line-height: 115%;">
</span><span style="font-family: Arial, Helvetica, sans-serif; line-height: 115%;">methods that use data dispersion (such as standard deviation) as scaling
factor; and methods that use size measure (such as the mean). For the first
group Mnova includes Auto, Pareto and</span><span style="font-family: Arial, Helvetica, sans-serif; line-height: 115%;">
</span><span style="font-family: Arial, Helvetica, sans-serif; line-height: 115%;">Vast scaling strategies. For the second group Range and Level scaling
are available. Generally speaking, when dealing with PCA analysis, the first
group is normally preferred. Figure 5 shows score plot differences between PCA
that used Pareto scaling (A panel) in comparison with PCA that used Level
scaling</span></div>
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<span lang="EN-GB"></span></div>
<span style="font-size: x-small;"><div style="text-align: center;">
<b>Figure 5</b> - Score plots obtained using same bin width of 0.05 ppm and normalization by the sum. In panel A Pareto scaling was applied; in panel B Level scaling was applied.</div>
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<h2>
<span lang="EN-US">Conclusions<o:p></o:p></span></h2>
<div class="MsoNormal">
<span style="font-family: Arial, Helvetica, sans-serif;"><span lang="EN-US">We have
focused on some very practical aspects when dealing with PCA analysis. But it
is always necessary to think about how good was our experimental design. Quoting Stanley Deming [4] in
his overview of Chemometrics of 1986: ”<i>Chemometrics is primarily concerned with the acquisition of data and
the extraction of useful information from that data</i>” and again:”</span><span lang="EN-US"> </span><i><span lang="EN-US">In a given situation, it is far better to err
on the side of too many pieces of experimental data. If too few data are available,
one might not be able to make any conclusion, and the whole set of experiments
will have been wasted</span></i></span><span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">”.</span><o:p></o:p></span></div>
<h2>
<span lang="EN-US">Acknowledgments<o:p></o:p></span></h2>
<div class="MsoNormal">
<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">We are
grateful to Dr. Giovanna Musco and Dr. Jose Garcia-Manteiga for providing
dataset for testing purposes.</span><o:p></o:p></span></div>
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References</h2>
<div style="font-family: Arial, Helvetica, sans-serif;">
[1] Amber J Hackstadt, Filtering for increased power for microarray data analysis. BMC Bioinformatics 2009, 10:11</div>
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<span lang="EN-GB">[2] <span style="font-family: Arial, Helvetica, sans-serif;">Paul E. Anderson, Metabolomics, Volume 7, Issue 2, pp 179-190
(2010)</span></span></div>
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<span lang="EN-GB"><span style="font-family: Arial, Helvetica, sans-serif;"><br /></span></span></div>
<div class="MsoFootnoteText">
<span lang="EN-GB"><span style="font-family: Arial, Helvetica, sans-serif;">[3] </span></span><span style="font-family: Arial, Helvetica, sans-serif;">Robert A van den Berg, Centering, scaling, and transformations: improving the biological information content of metabolomics data. BMC Genomics 2006, 7:142</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span>
<span style="font-family: Arial, Helvetica, sans-serif;">[4] Stanley N. Deming, Chemometrics:an Overview. CLIN. CHEM. 32/9, 1702-1706 (1986)</span><br />
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Carlos Cobashttp://www.blogger.com/profile/13500275318435740775noreply@blogger.com1tag:blogger.com,1999:blog-6953549091784501422.post-87370283928516791532014-02-28T01:38:00.001-08:002014-02-28T01:38:26.970-08:00Learn NMR FID<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiVbWp7DXMsK8mEM3fe3A2aZJfnr7-HeUMaNyB7o0Se_AjKeJqIvIzTCeqpb8-7fJtsJGGYopJ2cgeZGi_xgBX20KWmjNehmboXEdsM_YFQbehqjv50jdCBarQZjGCkQuEyBSXMvY8Vxh8/s1600/iPadNMR.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiVbWp7DXMsK8mEM3fe3A2aZJfnr7-HeUMaNyB7o0Se_AjKeJqIvIzTCeqpb8-7fJtsJGGYopJ2cgeZGi_xgBX20KWmjNehmboXEdsM_YFQbehqjv50jdCBarQZjGCkQuEyBSXMvY8Vxh8/s1600/iPadNMR.JPG" height="300" width="400" /></a></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">Last September, in SMASH 2013, I had the privilege of getting a personal demo from Tim E. Burrow of a cool iPad application he was developing that showed in a very nice way the basics of NMR data processing. This app simulates an FID and shows the effects on the corresponding FT spectrum when different apodization functions, zero filling or other time-domain operations are applied to the FID.</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">Since that day, I nearly forgot about <b><i>Learn NMR FID </i></b>until it was very recently brought to my attention after reading <a href="http://u-of-o-nmr-facility.blogspot.com.es/2014/02/educational-nmr-app-for-ipad.htm" target="_blank">this article</a> in <a href="http://u-of-o-nmr-facility.blogspot.com/" target="_blank">Glenn Facey’s blog</a>.</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">When I installed this app, I was happy to notice one very nice feature that I had discussed with Tim: The FID can be simulated with two spins (1/2) and add a coupling in such a way that it is possible to see, in an interactive way, the difference between weak (i.e. AX spin system) and strong (i.e. AB spin system) coupling.</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">I believe this is a great educational tool which I will certainly use in any lecture on NMR processing. Tim did a great job and I look forward to seeing more cool things from him!</span></div>
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<br />Carlos Cobashttp://www.blogger.com/profile/13500275318435740775noreply@blogger.com0tag:blogger.com,1999:blog-6953549091784501422.post-79426195090352950762014-01-09T01:28:00.002-08:002014-01-09T01:28:31.562-08:00Chemometrics under Mnova 9 - PCA<div class="separator" style="clear: both; text-align: center;">
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhh8lPxS-BdvgM0dthyrW4pBYQ5Wr9eGeb-UGx3BaEOJm8bmA8EhmIrMfb_CU8sJYlhe_5wuk8-T-0YEgax6Ge4Q0J-ZP2uHA3PRdWyOeSnnbNTdwqFDZF5rTsCA7LFhHi9GITiDqESoPg/s1600/PCA1.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhh8lPxS-BdvgM0dthyrW4pBYQ5Wr9eGeb-UGx3BaEOJm8bmA8EhmIrMfb_CU8sJYlhe_5wuk8-T-0YEgax6Ge4Q0J-ZP2uHA3PRdWyOeSnnbNTdwqFDZF5rTsCA7LFhHi9GITiDqESoPg/s1600/PCA1.png" height="220" width="400" /></a></h2>
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<i><span style="font-size: small;"><span style="background-color: white; color: #222222; font-family: Arial, Helvetica, sans-serif; font-weight: normal; line-height: 12.319999694824219px; text-align: justify;">(</span><span style="background-color: white; color: #222222; font-family: Arial, Helvetica, sans-serif; line-height: 12.319999694824219px; text-align: justify;">Note</span><span style="background-color: white; color: #222222; font-family: Arial, Helvetica, sans-serif; font-weight: normal; line-height: 12.319999694824219px; text-align: justify;">: </span><span style="background-color: white; color: #222222; font-family: Arial, Helvetica, sans-serif; font-weight: normal; line-height: 12.319999694824219px; text-align: justify;">This entry has been written by Dr. Silvia Mari, from <a href="http://www.research4rent.com/" target="_blank">R4R </a>who has helped us to design and implement this module</span><span style="background-color: white; color: #222222; font-family: Arial, Helvetica, sans-serif; font-weight: normal; line-height: 12.319999694824219px; text-align: justify;">)</span></span></i></h2>
<h2>
<span style="font-family: Arial, Helvetica, sans-serif; font-size: x-large;">Background: spectroscopy and chemometrics</span></h2>
<div style="text-align: justify;">
<span style="font-family: Arial, Helvetica, sans-serif;"><i>“For many years, there was the prevailing view that if one needed fancy data analyses, then the experiment was not planned correctly, but now it is recognized that most systems are multivariate in nature and univariate approaches are unlikely to result in optimum solutions.”</i></span></div>
<span style="font-family: Arial, Helvetica, sans-serif;"><i> <span style="font-size: x-small;"> </span></i><span style="font-size: x-small;">Hopke, P. K. (2003). The evolution of chemometrics. <i>Analytica Chimica Acta</i>, 500(1-2), 365–377]</span></span><br />
<span style="font-size: x-small;"><i style="font-family: Arial, Helvetica, sans-serif;"> </i></span><br />
<span style="font-family: Arial, Helvetica, sans-serif;"><i>Either we apply analytical chemistry for quality and control or we attempt to a more “system biology” approach for our R&D we do need advanced methods to design experiments, calibrate instruments, and analyze the resulting data. And the “emergence of chemometrics thinking came from the realization that traditional univariate statistics is not sufficient to describe and model chemical experiments”</i></span><br />
<span style="font-family: Arial, Helvetica, sans-serif;"> <span style="font-size: x-small;">Geladi, P. (2003). Chemometrics in spectroscopy . Part 1 . Classical chemometrics, 58, 767–782</span></span><br />
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<span style="font-family: Arial, Helvetica, sans-serif;">With this in mind <b>Mnova 9</b> now offers to its users a module called <b>PCA </b>which could be found under the main menu <b><i>“Advanced”</i></b>. It is the result of our first efforts to include <b>chemometric </b>tools into Mnova and it is meant to give spectroscopist the possibility to interactively work on both stacked spectra and its corresponding statistical plots.</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">Starting from mid ‘70s where the first paper with chemometrics in the title appeared in 1975 [1], chemometrics has grown up and is now considered a functioning research area in the chemical science. It has expanded widely from its beginnings into a variety of other areas including multivariate calibration, pattern recognition, and mixture resolution and today there are several applications of interest for the NMR spectroscopists [2-5].</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif; font-size: x-large;">PCA module</span></h2>
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<span style="font-family: Arial, Helvetica, sans-serif;"><b>Principal Component Analysis</b> (<b>PCA</b>) is a procedure which uses orthogonal transformation to convert a set of observations from correlated variables into a set of values of linearly uncorrelated variables (named principal components) [6].</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">PCA module under <b><i>Advanced </i></b>menu is working in two subsequent steps: <b>(1) matrix generation and (2) principal component analysis</b>. The overall workflow can be represented with the following illustration, where general steps available in Mnova are highlighted in blue whilst specific functionalities of this new PCA module are highlighted in yellow.</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">With the aim to help the spectroscopist to refine and optimize the data matrix to be used for advanced analysis, PCA in Mnova makes it very easy the detection and removal of spectrum outliers, reveal problems in spectral alignment as well as in its phase or baseline. Once the user has properly corrected those regions of interest, the PCA module allows to <b>re-run</b> the analysis, either replacing the previous analysis or creating a new one for comparison.</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;"><span style="font-size: x-large;">Interaction with the stacked spectra</span>.</span></h2>
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<span style="font-family: Arial, Helvetica, sans-serif;">The main effort applied during the design and development could be summarized in one word: <b><i>SYNCHRONIZATION</i></b>. PCA plots, PCA tables and stacked plot are always synchronized. By doing so selections of a point in the score plot imply a selection in the stacked plot. </span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjW6F8CTqVeVw1RA0BFbWHRp92v2UOuG95D5F_iugkEsDWxmZDg4zyFOO8fI3vgRlBq_NR8D0q4kO61Xp7y6cXytPraXGngqzHSr8oNqQBo1SozGe0HOomf9fcu_353yfGHVrksDQDIAJA/s1600/PCA3.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjW6F8CTqVeVw1RA0BFbWHRp92v2UOuG95D5F_iugkEsDWxmZDg4zyFOO8fI3vgRlBq_NR8D0q4kO61Xp7y6cXytPraXGngqzHSr8oNqQBo1SozGe0HOomf9fcu_353yfGHVrksDQDIAJA/s1600/PCA3.png" height="265" width="640" /></a></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">In the same way, a selection of a point in the <b>loading plots</b> (hence a selection of a variable of the matrix) generate a shadow into the <b>stacked plot</b> according to the bin position and size.</span><br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj-i-EyRdJEdnyxv9INiY2VGjOiKW9tquV6ZsuRvBc_iDtreXVWqcVFOnSnIe-CYPDg40dNng6nL0JuY9f9YP4bRCJLonRGGWA7CQPgz9kwXZAsoF4X3RRH4x9-v4ns6otS3yWqSg_1hfo/s1600/PCA4.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj-i-EyRdJEdnyxv9INiY2VGjOiKW9tquV6ZsuRvBc_iDtreXVWqcVFOnSnIe-CYPDg40dNng6nL0JuY9f9YP4bRCJLonRGGWA7CQPgz9kwXZAsoF4X3RRH4x9-v4ns6otS3yWqSg_1hfo/s1600/PCA4.png" height="276" width="640" /></a></div>
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<span style="font-family: Arial, Helvetica, sans-serif; font-size: x-large;">Colors and graphics</span></h2>
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<span style="font-family: Arial, Helvetica, sans-serif;">When dealing with large dataset, <b>color coding</b> plays a very important role and eventually essential. Even if PCA does not use class definition in its algorithm since it is an <i>unsupervised </i>method, the kind of patterns expected is generally known.</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">The driving concept here is that colors are assigned on the basis of class belonging. Again, as in the previous section, colors are always <i>synchronized </i>from PCA tables to PCA plots and to stacked spectra as well</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">Moreover, in the loading plot, the user is allowed to select more than one bin (see flag option in the loading plot table, or multiple selection of table entry using <i>shift </i>or <i>ctrl </i>key). Visualization of a bin region is obtained with a colored box that is displayed superimposed over the stacked plot. The User can associate different colors to different bins regions</span></div>
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<h2>
<span style="font-family: Arial, Helvetica, sans-serif; font-size: x-large;">Data filtering and scaling</span></h2>
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<span style="font-family: Arial, Helvetica, sans-serif;">The results of the analysis depend on the types of <b>filtering </b>and <b>scaling </b>of the matrix that user selects, which therefore must be specified. It can be demonstrated how both factors greatly affect the outcome of the data analysis and thus the rank of the most important variables. PCA module includes several possibilities in terms of data cleaning and scaling.</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">There is not a general rule in the selection of the <b>type of scaling.</b> For that purposes we recommend the manuscript from van den Berg et. al. [7] which describes extensively how these transformations could improve the information content of the data matrix. Finally, bear in mind that visual inspection and assessment is ultimately one of the most important steps in chemometrics.</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif; font-size: x-large;">Conclusion</span></h2>
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<div class="MsoNormal">
<span style="font-family: Arial, Helvetica, sans-serif;"><span lang="EN-US">We have introduced in <b>Mnova 9</b> a
<b>chemometric</b> module called <b>PCA </b>(Principal Component Analysis). PCA have been
shown to be very effective in compressing large volume of noisy correlated data
into a subspace of much lower dimension than the original data set. Data
pretreatment method is crucial to the outcome of the data analysis. The
resulting low dimensional representation of the data set has been shown to be
of great utility for analysis or monitoring the system under study, as well as
in selecting variables for control or markers of the expected pattern. <u1:p></u1:p></span><span lang="EN-GB"><o:p></o:p></span></span></div>
<div class="MsoNormal">
<span style="font-family: Arial, Helvetica, sans-serif;"><span lang="EN-US">The possibility to <b>interactively
</b>play with <b>PCA plots and spectra at the same time</b>, and the user friendly
interface provided by Mnova will be of great advantages also for
spectroscopists that are not familiar with multivariate analysis but would like
to learn more and test it. <br />
As has always been for Mnova community, the future of this new first step in
chemometrics will be driven by user requirements. For that reason we look
forward to get feedback, criticisms, suggestions, comments and lots of requests
for future development. So, play with it and have fun at looking at your own datasets from a different perspective!<u1:p></u1:p></span><span lang="EN-GB"><o:p></o:p></span></span></div>
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<span style="font-family: Arial, Helvetica, sans-serif; font-size: x-large;">References</span></h2>
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<span style="font-family: Arial, Helvetica, sans-serif;">[1] </span><span style="font-family: Arial, Helvetica, sans-serif;">B.R. Kowalski, Chemometrics: views and propositions, <i>J. Chem. Inf. Comp. Sci</i>. 15 (1975) 201–203</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">[2] Chemometrics in bioreactor monitoring. Lourenço, N. D., Lopes, J. a, Almeida, C. F., Sarraguça, M. C., & Pinheiro, H. M. (2012). Bioreactor monitoring with spectroscopy and chemometrics: a review. <i>Analytical and bioanalytical chemistry</i>, 404(4), 1211–37. doi:10.1007/s00216-012-6073-9</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">[3] Metabonomics and chemometrics in food science and nutrition. Kuang, H., Li, Z., Peng, C., Liu, L., Xu, L., Zhu, Y., Wang, L., et al. (2012). Metabonomics approaches and the potential application in food safety evaluation. <i>Critical reviews in food science and nutrition,</i> 52(9), 761–74. doi:10.1080/10408398.2010.508345</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">[4] Pharmaco-metabonomic phenotyping and chemometrics. Robertson, D. G., Reily, M. D., & Baker, J. D. (2007).<i> Metabonomics in Pharmaceutical Discovery and Development</i>, 526–539.</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">[5] Metabonomics and chemometrics in drug safety and toxicology. Griffin, J. (2004). The potential of metabonomics in drug safety and toxicology. <i>Drug Discovery Today Technologies</i>, 1(3), 285–293. doi:10.1016/j.ddtec.2004.10.011</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">[6] </span><span style="font-family: Arial, Helvetica, sans-serif; text-align: justify;">Principal component analysis, Svante Wold, Kim Esbensen, Paul Geladi. Volume 2, Issues 1–3, August 1987, Pages 37–52</span></div>
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<div style="text-align: justify;">
<span style="font-family: Arial, Helvetica, sans-serif;">[7] Van den Berg, R. A., Hoefsloot, H. C. J., Westerhuis, J. A., Smilde, A. K., & van der Werf, M. J. (2006). Centering, scaling, and transformations: improving the biological information content of metabolomics data. BMC genomics, 7(1), 142. doi:10.1186/1471-2164-7-142</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span>Carlos Cobashttp://www.blogger.com/profile/13500275318435740775noreply@blogger.com0tag:blogger.com,1999:blog-6953549091784501422.post-23057749817081989232014-01-07T12:15:00.000-08:002014-01-07T12:19:51.021-08:00Chemical Shift, Absolutely!<div class="separator" style="clear: both; text-align: justify;">
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<span style="font-family: Arial, Helvetica, sans-serif;">(</span><b style="font-family: Arial, Helvetica, sans-serif;"><i>Note</i></b><span style="font-family: Arial, Helvetica, sans-serif;">: </span><i style="font-family: Arial, Helvetica, sans-serif;">This entry has been written by Dr. Mike Bernstein - Thank you, Mike!</i><span style="font-family: Arial, Helvetica, sans-serif;">)</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">It’s a “given” that for NMR the chemical shift must be reported relative to standard. The most widely used is the 1H signal of tetramethylsilane (TMS) in chloroform, which has an assigned value of exactly zero. This is convention, and we all adhere to it. Correctly referencing 1H NMR spectra is seldom a difficulty, whether we use co-dissolved TMS (or a water-soluble equivalent), or the residual proton signal from the deuterated solvent. Things can get more complex, but this works for the vast majority of us. The chemical shift, </span><span style="font-family: Symbol; font-size: 11pt; line-height: 107%;">d</span><span style="font-family: Arial, Helvetica, sans-serif;">, is defined thus:</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">Venturing to the “dark side” of NMR – nuclei other than 1H – seldom stretches beyond 13C for most, and a residual solvent signal is very often present that can be used as a secondary chemical shift reference. But beautiful possibilities tempt many of us. Whether you are interested in biomolecular NMR and live and breathe 15N and possibly 31P, or 2H, or an orgametallic chemist with an interest in far more exotic nuclei, each heteronucleus has its charms and challenges. One thing unites NMR of all nuclei: adherence to a convention for chemical shifts. This can be easier said than done, given that some reference materials are difficult to handle, expensive, etc. The chemical shift reference compound for 19F NMR is the banned substance, Freon-11.</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif; font-size: x-large;">Absolute chemical shifts</span></h2>
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<span style="font-family: Arial, Helvetica, sans-serif;">We get help from a group working under the IUPAC [1] guise for their work in helping us calculate the chemical shift scale for all NMR-active nuclei [2]. That is, they provide us with a standard way to get the chemical shift precisely correct for any and all heteronuclear NMR spectra. That’s amazing - and hugely useful!</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">So how does it work? Well, it’s quite simple, really. At the heart of the calculation is the <b><i>absolute frequency</i></b> of the 1H signal of TMS for your NMR spectrometer hardware (console, probe, etc.) and sample (solvent, temperature, etc.). You need to be able to determine the exact frequency of this reference signal to seven decimal figures, at least. The following equation applies (sometimes expressed as a percentage) and uses a ratio to describe a constant, </span><i><span lang="EN-GB" style="font-family: Symbol; font-size: 11.0pt; line-height: 107%; mso-ansi-language: EN-GB; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin;">X </span></i><span style="font-family: Arial, Helvetica, sans-serif;">(Greek capital Xi):</span></div>
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<span lang="EN-GB"><span style="font-family: Arial, Helvetica, sans-serif;"><span style="font-size: x-large;">Making it easy with Mnova</span><o:p></o:p></span></span></h2>
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<span lang="EN-GB"><span style="font-family: Arial, Helvetica, sans-serif;">We make heavy use of absolute referencing
(AR) in Mnova, with the following available:</span></span></div>
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<li><span style="font-family: Arial, Helvetica, sans-serif;">Correctly
reference an X-nucleus spectrum when the referenced 1H spectrum is available</span></li>
<li><span style="font-family: Arial, Helvetica, sans-serif;">Apply AR to heteronuclear
axes in 2D experiments</span></li>
<li><span style="font-family: Arial, Helvetica, sans-serif;"><span lang="EN-GB">Allow users to
customise the </span><span lang="EN-GB"><i><span lang="EN-GB" style="font-family: Symbol; font-size: 11.0pt; line-height: 107%; mso-ansi-language: EN-GB; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin;">X</span></i><span lang="EN-GB" style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 107%; mso-ansi-language: EN-GB; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"> </span> values</span></span></li>
<li><span style="font-family: Arial, Helvetica, sans-serif;"><span lang="EN-GB">Indirect 1H
spectrum referencing using </span><span lang="EN-GB"><span lang="EN-GB" style="font-family: Symbol; font-size: 11.0pt; line-height: 107%; mso-ansi-language: EN-GB; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin;">n</span><sub><span lang="EN-GB" style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 107%; mso-ansi-language: EN-GB; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">TMS</span></sub><span lang="EN-GB" style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 107%; mso-ansi-language: EN-GB; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"> </span> for a specific hardware and
solvent (locked)</span></span></li>
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<span lang="EN-GB"><span style="font-size: x-large;">Referencing heteronuclear spectra</span></span></h2>
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<span lang="EN-GB"><span style="font-family: Arial, Helvetica, sans-serif;">Ensure that you have a document having (a)
a correctly referenced 1H NMR spectrum, and (b) one or more –nucleus spectra. <o:p></o:p></span></span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;"><span lang="EN-GB">Select <i><b>Analysis </b></i></span></span><b><i><span lang="EN-GB" style="font-family: Wingdings; font-size: 11.0pt; line-height: 107%; mso-ansi-language: EN-GB; mso-ascii-font-family: Calibri; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-char-type: symbol; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-font-family: Calibri; mso-hansi-theme-font: minor-latin; mso-symbol-font-family: Wingdings;">è</span></i><span style="font-family: Arial, Helvetica, sans-serif;"><i><span lang="EN-GB"> Reference </span></i></span><i><span lang="EN-GB" style="font-family: Wingdings; font-size: 11.0pt; line-height: 107%; mso-ansi-language: EN-GB; mso-ascii-font-family: Calibri; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-char-type: symbol; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-font-family: Calibri; mso-hansi-theme-font: minor-latin; mso-symbol-font-family: Wingdings;">è</span></i><span style="font-family: Arial, Helvetica, sans-serif;"><i><span lang="EN-GB"> Absolute reference…</span></i></span></b><span lang="EN-GB"><span style="font-family: Arial, Helvetica, sans-serif;"> and choose the X-axis spectrum/spectra to reference.</span> </span><span style="font-family: Arial, Helvetica, sans-serif; text-align: justify;"> </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif; font-size: x-large;">The table of X values</span></h2>
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<span style="font-family: Arial, Helvetica, sans-serif;">Note that by tapping on the <b>“X values…”</b> button you will be presented with the table of X-nuclei. In the case of 15N, for example, you can choose which reference standard you want to use. By clicking on the blue <b>“+”</b> button you can enter your own, customised value. </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif; font-size: x-large;">Referencing 2D spectra</span></h2>
<span style="font-family: Arial, Helvetica, sans-serif;">When there are 2D spectra in the document then the Absolute reference… selection will reflect this, and allow you to choose which spectrum is used for referencing purposes, and the traces to which this should be applied. Note that you can adjust the referencing of 1H and X-nuclei.</span><br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhWkQ48RLiBXCTm7Ag76tMs0ybPsktKGLku8u8fIg_cs4RWyKT8nTPkyHRclit_9_2aRsxxBcSVin-p-UhDWHjuVRA9wxcpPkF2OooI3LbI1xAWob33gIFeSU7eVbDWXW6ZnFQ3jC9DX2A/s1600/AR_6.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: justify;"><span style="font-family: Arial, Helvetica, sans-serif;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhWkQ48RLiBXCTm7Ag76tMs0ybPsktKGLku8u8fIg_cs4RWyKT8nTPkyHRclit_9_2aRsxxBcSVin-p-UhDWHjuVRA9wxcpPkF2OooI3LbI1xAWob33gIFeSU7eVbDWXW6ZnFQ3jC9DX2A/s1600/AR_6.png" height="305" width="400" /></span></a><br />
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<span style="font-family: Arial, Helvetica, sans-serif; font-size: x-large;">Referencing a 1H spectrum</span></h2>
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<span style="font-family: Arial, Helvetica, sans-serif;">You can use saved </span><span lang="EN-GB" style="font-family: Symbol; font-size: 11.0pt; line-height: 107%; mso-ansi-language: EN-GB; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin;">n</span><sub><span lang="EN-GB" style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 107%; mso-ansi-language: EN-GB; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">TMS</span></sub><span lang="EN-GB" style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 107%; mso-ansi-language: EN-GB; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"> </span><span style="font-family: Arial, Helvetica, sans-serif;">values to reference another 1H spectrum from the same NMR spectrometer. Start with a correctly-referenced 1H NMR spectrum, and select <b><i>Analysis </i></b></span><b><i><span lang="EN-GB" style="font-family: Wingdings; font-size: 11.0pt; line-height: 107%; mso-ansi-language: EN-GB; mso-ascii-font-family: Calibri; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-char-type: symbol; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-font-family: Calibri; mso-hansi-theme-font: minor-latin; mso-symbol-font-family: Wingdings;">è</span><span style="font-family: Arial, Helvetica, sans-serif;"> Reference </span><span lang="EN-GB" style="font-family: Wingdings; font-size: 11.0pt; line-height: 107%; mso-ansi-language: EN-GB; mso-ascii-font-family: Calibri; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-char-type: symbol; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-font-family: Calibri; mso-hansi-theme-font: minor-latin; mso-symbol-font-family: Wingdings;">è</span></i></b><span style="font-family: Arial, Helvetica, sans-serif;"><b><i> Edit saved references…</i></b> From this dialogue you can add the value for the particular hardware and measurement conditions – solvent, temperature, etc. </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">Now, when you select <b><i>Analysis </i></b></span><b><i><span lang="EN-GB" style="font-family: Wingdings; font-size: 11pt; line-height: 15.199999809265137px;">è</span><span style="font-family: Arial, Helvetica, sans-serif;"> Reference </span><span lang="EN-GB" style="font-family: Wingdings; font-size: 11pt; line-height: 15.199999809265137px;">è</span></i></b><span style="font-family: Arial, Helvetica, sans-serif;"><b><i> Apply saved reference</i></b> then the saved value will be used if the criteria are met. </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif; font-size: x-large;">Conclusions</span></h2>
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<span style="font-family: Arial, Helvetica, sans-serif;"><b>Absolute referencing</b> is a powerful way to ensure that data are correctly referenced. This is equally important in open-access environments as it is under automation, where it helps processes such as <b>Verify </b>be more robust. </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif; font-size: x-large;">References</span></h2>
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<span style="font-family: Arial, Helvetica, sans-serif;">[1] (a) Harris RK, Becker ED, Cabral de Menzes SM, Goodfellow R, Granger P. Pure Appl. Chem. 2001; 73: 1795</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">(b) Harris RK, Becker ED. J. Magn. Reson. 2003; 156: 323.</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">[2] </span><span style="font-family: Arial, Helvetica, sans-serif;">This is nicely described here: <a href="http://www.chem.wisc.edu/~cic/nmr/Guides/Other/Xi_chem_shift_scale.pdf">http://www.chem.wisc.edu/~cic/nmr/Guides/Other/Xi_chem_shift_scale.pdf</a></span></div>
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Carlos Cobashttp://www.blogger.com/profile/13500275318435740775noreply@blogger.com0tag:blogger.com,1999:blog-6953549091784501422.post-7627553530950518972014-01-06T08:21:00.002-08:002014-01-06T08:22:10.149-08:00Copy and Paste NMR spectra<div style="text-align: justify;">
<span style="font-family: Arial, Helvetica, sans-serif;">This is just a short entry to illustrate one nice little tool in Mnova NMR that I believe can be very handy in many situations.</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">Let’s suppose you have an NMR spectrum in which you have spent some time trying to customize its visual aspect. For example, you have changed the default line color and width, hidden the vertical scale, modified the background color, customized the chemical shift scale, etc. As a result, you may have something like this:</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;"> </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">Now you open a new spectrum and you find that it is using the old default graphical properties and you want that this spectrum has exactly the same visual aspect as the previous one. </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">There are several ways in Mnova to achieve that goal. For example, you can go to the first spectrum, go to spectral properties and save these properties to a file which can then be loaded in the target spectrum. </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">However, in this post I want to show a simple shortcut that yields the same result. The procedure is as simple as this:</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">1)<span class="Apple-tab-span" style="white-space: pre;"> </span>Go to the first spectrum and press <b><i>Ctrl+C</i></b> (<i><b>Edit / Copy</b></i>)</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">2)<span class="Apple-tab-span" style="white-space: pre;"> </span>Move to the second spectrum and issue this command: <b><i>Edit / Paste Properties / NMR Graphic Properties</i></b> </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">This is it, the second spectrum will have now the same visual aspect as the first one. </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">The same trick can be used to copy and paste integral regions, zoom & cuts regions, etc.</span></div>
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Carlos Cobashttp://www.blogger.com/profile/13500275318435740775noreply@blogger.com0tag:blogger.com,1999:blog-6953549091784501422.post-90789629750536865152014-01-05T03:04:00.007-08:002014-01-05T03:06:11.418-08:00Reference Deconvolution<h2>
<span style="font-family: Arial, Helvetica, sans-serif;">Introduction</span></h2>
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<span style="font-family: Arial, Helvetica, sans-serif;">In an idealized situation, according to quantum mechanics theory, NMR transitions in liquid state and excluding dynamic effects such as chemical exchange are of <b>Lorentzian </b>shape [1]. In practice NMR lineshapes are never pure Lorentzians due to a number of reasons [2], ranging from magnetic field inhomogeneity and magnetic field noise to sample temperature gradients, sample spinning or FID weighting, to cite a few. </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">Another important property that might affect significantly the final observed lineshape is the following: Even in molecules of modest size the number of distinct peaks might be thousands times smaller than that of quantum transitions. As a simple example, the number of transitions of a molecule containing 15 would be 245760 whereas only a few hundreds of peaks would be observed in the spectrum. As a result, an NMR peak is actually an envelope of a <b>distribution of myriads of Lorentzians</b> and its shape is dominated by the coupling pattern of the spin system. </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">Whilst this kind of line broadening affects signals differently across the spectrum and is very difficult (or even impossible) to resolve by post-processing operations, there are many other distortions that affect all resonances in the spectrum in the same way. These include lineshape distortions caused by poorly shimmed samples and they can be removed by using a post-processing technique known as <b>Reference Deconvolution</b> [3] </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;"><b>Reference Deconvolution</b></span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">This technique is used to <b>remove the instrumental lineshape distortion </b>by deconvolving the experimental NMR spectrum using a <b>reference signal</b>, usually one within the same spectrum (which should be an isolated singlet) known to be subject to the identical lineshape distortions. Finally, once the lineshape distortion is removed, the spectrum can be reconvoluted with a known lineshape, typically a Lorentzian, so that the result will be a corrected spectrum in which the instrumental distortion has been replaced by the ideal lineshape. </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">Actually, the concept of deconvolution is very simple: If <b>S(f)</b> is the experimental frequency domain spectrum, it can be decomposed into two main components, the ideal spectrum <b>I(f)</b> and the instrumental distortion <b>D(f)</b>. In other words, the observed experimental spectrum is the result of a <i>contaminated</i> ideal spectrum. Mathematically, this <i>contamination </i>is expressed with the concept of <b>convolution </b>which is represented by the symbol *</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;"><b>S(f) = I(f) * D(f)</b></span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">The goal here is to find the function <b>D(f)</b> so that the ideal spectrum <b>I(f)</b> can be recovered:</span></div>
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<b><span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">I(f) = S(f) [*]<sup>-1</sup> D(f)</span><o:p></o:p></span></b></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">Where </span><b><span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">[*]<sup>-1</sup> </span></span></b><span style="font-family: Arial, Helvetica, sans-serif;">denotes <b>deconvolution</b>. That is to say that the ideal spectrum can be recovered by means of a deconvolution which consists basically in reversing the effects of the convolution. </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">In practice, this process is more efficiently done in the time domain:</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;"><b>I(t) = S(t) / D(t)</b></span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">This is possibly by considering the <b>Convolution Theorem</b> which states that point-wise multiplication in one domain (i.e. time domain) is equivalent to convolution in the other FT domain (e.g. frequency domain). </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">The complete process of <b>Reference Deconvolution</b> will be illustrated with an example using <b>Mnova NMR</b> and one 300MHz 1H-NMR spectrum in deuterated acetone (kindly provided by Gareth Morris) in which the homogeneity of the static field was deliberately perturbed. The spectrum corresponds to ODBC (ortho-dichlorobenzene) and has been folded several times in order to optimize digitization:</span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhHFn1VbNeOJnUq5Agsv899NUZGUY6-cCsHJmiDth81Tgpr6TTO6mYUnXAT7iR7Jw_4x8IMoPZrtMC0nqxURiFFxl1BXx_9FtNoVX-8Ditf4XxcnQIlOEBbr4TOyiDVx9egBfH1ldo5qW4/s1600/ODBC1.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhHFn1VbNeOJnUq5Agsv899NUZGUY6-cCsHJmiDth81Tgpr6TTO6mYUnXAT7iR7Jw_4x8IMoPZrtMC0nqxURiFFxl1BXx_9FtNoVX-8Ditf4XxcnQIlOEBbr4TOyiDVx9egBfH1ldo5qW4/s1600/ODBC1.png" height="279" width="400" /></a></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">First, after issuing command <b><i>Process/Reference deconvolution</i></b> in Mnova, the User needs to select a <i>well resolved reference signal i</i>n the frequency domain spectrum. In order to avoid numerical instabilities this signal should be a <b>singlet</b>. The reason is that if the reference signal has some multiplicity (i.e. a doublet), inverse FT of this reference signal (remember that Reference Deconvolution takes place in the time domain) might result in an FID with zeroes at regular intervals. As this time domain signal will be used in the denominator of the reference deconvolution function, this would result in severe discontinuities. </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">In this particular example, as in many others, a convenient reference could be the <b>TMS</b> signal (0 ppm), which in principle should be a singlet (disregarding the 13C and 29Si satellites, more about this in a moment), but as it can be noticed, it shows lineshape errors and spinning sidebands due to a combination of poor shimming and sample spinning. </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">In the figure below, the result of selecting the reference signal with Mnova is depicted. </span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjLUC5rnTgCaLHdelLTOuId2DhHuYh9xa34LE56x5ievKas8zoUup1Nf_kBxEDTbpN-7pHYBdQ1x5G09NDOjMdcdJexazoScAS2xHoyuUKIifShk96eOqV3PPvLQQm0c0eNq3698JBDskI/s1600/TMS.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjLUC5rnTgCaLHdelLTOuId2DhHuYh9xa34LE56x5ievKas8zoUup1Nf_kBxEDTbpN-7pHYBdQ1x5G09NDOjMdcdJexazoScAS2xHoyuUKIifShk96eOqV3PPvLQQm0c0eNq3698JBDskI/s1600/TMS.png" height="275" width="400" /></a></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">In the Reference Deconvolution dialog box, there are two check boxes, <b>29Si </b>and <b>13C</b> <b>satellites </b>and the explanation is this: The TMS reference signal comes with the presence of small 29Si and 13C satellites flanking the central peak at 3.3 and 59 Hz, respectively. Since the reference line is supposed to be representative of all signals in the spectrum, any fine structure which is unique to the reference should generally be removed before deconvolution is performed. The 13C satellites are not usually a concern as they are quite distant from the main TMS peak, but the 29Si satellites are more problematic owing to their close proximity to the central signal. </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">So when, for example, the 29Si satellites option is ticket, the software will automatically synthesize the peaks corresponding to the 29Si satellites which in turn will be part of the reference FID model. </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;"> </span><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhgFPjUE6ycSHoYXykFomeSZ1J61pahcTm1eGkwDgqOlBHt30YI74CdAr-waM6nMCRL17Qix56t2qOuXVkakB-u1yQdkJ-lzwYD6EsYl-exx46BdYHNOxq2hNwp3V6u3A13koZMcxsdCiI/s1600/29Si.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhgFPjUE6ycSHoYXykFomeSZ1J61pahcTm1eGkwDgqOlBHt30YI74CdAr-waM6nMCRL17Qix56t2qOuXVkakB-u1yQdkJ-lzwYD6EsYl-exx46BdYHNOxq2hNwp3V6u3A13koZMcxsdCiI/s1600/29Si.png" height="360" width="400" /></a></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">Once the reference region is selected, the software calculates a <b>reference FID</b>, <b>Sr(t)</b>, by zeroing all the spectrum except the selected region followed by an inverse FT (there are some additional processing steps required to avoid the negative effects of the long tails of the imaginary components – The interested reader is referred to the [2-3] for further details). </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">Having calculated the reference FID, <b>Sr(t)</b>, an <b>ideal reference FID Si(t)</b> can be computed by simply simulating an FID using the set of frequencies and amplitudes for the parent signal (e.g. TMS) and any attendant satellites, and decay rate which depends on the target lineshape, a value that can be specified in the reference deconvolution dialog box (in this example a value of 0.35 Hz has been used). With these two reference FIDs, it is possible to calculate the correction function <b>c(t) </b>by simply taking the (complex) ratio of both:</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;"><b>c(t) = Si(t) / Sr(t)</b></span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">This correction function <b>c(t)</b> simply represents the (inverse of the) instrumental function responsible of the lineshape distortion. Multiplying the original experimental FID, <b>Se(t)</b>, by this function yields a <b>corrected FID</b>, <b>Sc(t)</b> which may then Fourier Transformed to yield a corrected spectrum <b>Fc</b> having the lineshape of the specified ideal lineshape:</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;"><b>Sc(t) = c(t) x Se(t)</b></span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;"><b>Fc = FT[Sc(t)]</b></span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">Overall, the result of applying reference deconvolution to the ODBC spectrum used in this example is shown in the figure below. </span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj0OcO7Y1MQqIqe04NrfvkVAgMqnqvBzRCfB862sy-G-LAZ8CnDQs77f4N-EQh0Qrr1LhT0lOqFQhL57vVnpYmyYemv6SBdDrKOS68J5jBRu3ybboFzb25U_cP8XtxKB3mWyIEOMToj50I/s1600/ODBC2.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj0OcO7Y1MQqIqe04NrfvkVAgMqnqvBzRCfB862sy-G-LAZ8CnDQs77f4N-EQh0Qrr1LhT0lOqFQhL57vVnpYmyYemv6SBdDrKOS68J5jBRu3ybboFzb25U_cP8XtxKB3mWyIEOMToj50I/s1600/ODBC2.png" height="280" width="400" /></a></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">Reference deconvolution is a powerful processing method to remove some distortions that affect all the peaks in a spectrum in the same way. In practice, this is done by extracting the distorted component from a reference signal and deconvolving the whole imperfect spectrum. </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">Present implementation of the algorithm in Mnova 9.0 supports 1D spectra only thus far, but extensions to 2D spectra are planned. </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">Biblography</span></h2>
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<span style="font-family: Arial, Helvetica, sans-serif;">[1] Why are spectral lines Lorentzian? </span><a href="http://www.ebyte.it/stan/blog10b.html#10May16" style="font-family: Arial, Helvetica, sans-serif;">http://www.ebyte.it/stan/blog10b.html#10May16</a><span style="font-family: Arial, Helvetica, sans-serif;"> </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">[2] Metz, K. R., Lam, M. M., & Webb, A. G. (2000). <i>Reference deconvolution: A simple and effective method for resolution enhancement in nuclear magnetic resonance spectroscopy</i>. Concepts in Magnetic Resonance, 12(1), 21–42. (<a href="http://dx.doi.org/10.1002/(SICI)1099-0534(2000)12:1%3C21::AID-CMR4%3E3.0.CO;2-R" target="_blank">link</a>) </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">[3] Morris, G. A., Barjat, H., & Home, T. J. (1997). <i>Reference deconvolution methods</i>. Progress in Nuclear Magnetic Resonance Spectroscopy, 31(2), 197–257. </span></div>
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Carlos Cobashttp://www.blogger.com/profile/13500275318435740775noreply@blogger.com0tag:blogger.com,1999:blog-6953549091784501422.post-33077746703600393632013-12-28T01:49:00.000-08:002013-12-28T01:49:21.630-08:00Smaller NMR files<h2>
Background</h2>
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One important issue we had noticed with Mnova NMR files is that they can be quite large, particularly when a document contains several 2D spectra. At first sight, file size should not be a big concern, especially considering the large storage capabilities available today, either locally (i.e. hard disks with sizes in the order of Terabytes) or in the cloud (Dropbox, Google Drive, Skydrive, etc).</div>
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On the other hand, the tremendous advancements on both technological and methodological fronts have made possible the acquisition of enormous volumes of data. For example, IBM has estimated that 2.5 quintibillion bytes of data are being generated each day, with more than 90 per cent of which created in the last two years. Whilst it is difficult to scale this level of information into analytical data (i.e. NMR spectra), it is quite likely that they also follow a similar growth. </div>
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At Mestrelab we have devoted major efforts to the development of new technologies which would allow Mnova to reduce the size of NMR spectra while preserving their informational content. This will be elaborated in the following section.</div>
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Lossless and lossy compression</h2>
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Roughly speaking, there are two two different classes of compression methods: <b>lossless </b>and <b>lossy</b>. </div>
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<b>Lossless </b>techniques allow the data to be compressed, then decompressed back to its original state without any loss of data. Well-known algorithms for this type of compression are Zip and Rar methods. Compression rates for lossless techniques vary but are typically around 2:1 to 3:1, e.g in medical images. In the particular case of high resolution NMR spectra, there re some relevant characteristics that diminish the performance of this type of algorithms.NMR spectra consist mostly of a noisy background and hence appear as essentially random numbers to the algorithm which makes lossless compression rather ineffective; in general, NMR spectra can be compressed by no more than 10-30% (on average) using lossless compression schemes. </div>
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<b>Lossy </b>techniques do not allow the exact recovery of the original data once it has been compressed, but this loss of information can be modulated in such a way that it can be virtually negligible. In the particular case of NMR, we have applied several advanced compression techniques [1, 2] which afford extraordinarily high compression rates while preserving all the spectral information. In some cases, compression rates in the order of 800:1 can be achieved, although for practical uses and in order to avoid any potential loss of information, more moderate rates are recommended.</div>
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An example</h2>
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In the figure below, the DQF-COSY of Taxol (Paclitaxel) is shown at its original uncompressed format (left) and after being compressed 100 times with the new built-in compression algorithm in Mnova and decompressed back (right). Both spectra have been displayed with the same contour levels. Can you spot the differences?</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhheIJNnZmwhq-M2p4Z5hSRfVk1ZmGRpb8hyphenhyphen1L01aVhtPw-VL6Tkj_GgETXXYJ_-epCx-yY6yPz3PajK8KJI4qwRw_qjQw9ek2hngSwM8EXguphPMQs_Mmasx7aub8sOL2mlb0xDMTHIMo/s1600/Taxol1.jpeg" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" height="368" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhheIJNnZmwhq-M2p4Z5hSRfVk1ZmGRpb8hyphenhyphen1L01aVhtPw-VL6Tkj_GgETXXYJ_-epCx-yY6yPz3PajK8KJI4qwRw_qjQw9ek2hngSwM8EXguphPMQs_Mmasx7aub8sOL2mlb0xDMTHIMo/s1600/Taxol1.jpeg" width="640" /></a></div>
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Whilst we have done lots of numerical tests to make sure that at this high level of compression all the spectral information is preserved (see [1] and [2] for more details), a simple yet intuitive way to visualize whether the compression has been effective is by subtracting the uncompressed spectrum with the compressed counterpart. In this example, this is the residual spectrum:</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgb-OQ02w2IHKmnE4LYsDKy6kaOJO720GpaKzHKWqkt4JV9QuSgSCzjE5JYpfZSUQLraKYRJomqD9k2lR1PgzSgGCFdMmERFi3SFXW04FJNhnJI-au2Rjg5GucyrUP8qiyTCNYYrShEUrU/s1600/Taxol-Residue.jpeg" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgb-OQ02w2IHKmnE4LYsDKy6kaOJO720GpaKzHKWqkt4JV9QuSgSCzjE5JYpfZSUQLraKYRJomqD9k2lR1PgzSgGCFdMmERFi3SFXW04FJNhnJI-au2Rjg5GucyrUP8qiyTCNYYrShEUrU/s1600/Taxol-Residue.jpeg" width="360" /></a></div>
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Basically, all that it remains is noise and no structures (cross peaks) are visible on the residual. </div>
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A practical guide with Mnova 9.0</h2>
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This is how compression works in Mnova NMR. First, all the compression options are available in the global Preferences of the software (command <i>Edit / Preferences</i>), in the <b>NMR/Save </b>page (see below):</div>
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At this point, there are two different compression mechanisms:</div>
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<b><u>FID compression</u></b>: The FID is the most important component of an NMR spectra where all the actual recorded information is stored. We don’t want to miss even a single bit of this data and hence, the FID is only compressed using a lossless algorithm. Of course, the compression ratio will be much more modest, but it is critical to preserve all this information. </div>
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<u><b>FT spectrum Compression</b></u>: This is where the lossy compression algorithm can be applied, in the frequency domain spectrum. Actually, it is also possible to use a lossless algorithm but in order to achieve high compression ratios, the lossy method should be selected. Whilst values of 100:1 or even higher should give good results, it would be more sensible to use more moderate values, in the range of 10:1 – 20:1.</div>
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Final notes</h2>
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The fact that Mnova NMR documents keep both the original recorded FID (which can optionally be compressed using the lossless technique) as well as the processed NMR spectrum (which can optionally be compressed using the lossy technique) explains why the resulting compressed document is not as small as one could expect after having compressed the data with high compression ratios. The FID might contribute significantly to the final file size. Of course, the differences will be more appreciated in 2D NMR spectra processed with Zero Filling or Linear Prediction so that the final data matrix becomes significantly larger than the time domain vectors. </div>
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On the other hand and considering again the point that Mnova always keeps a copy of the original FID, why we don’t just save this FID plus the processing commands required to reconstruct the processed spectrum as other NMR applications do? Actually, this is a nice approach (under some circumstances) and would yield the best compression ratio achievable. Unfortunately, this does not work well for many applications and introduce some additional difficulties. Just to give a simple example: You have processed a 2D spectrum which was acquired with a NUS scheme and you have applied some additional time-consuming analysis operations (i.e. 2D-GSD based peak picking). In this particular case, opening this single spectrum would take several seconds (if not minutes). Having the ability to access directly to the processed spectrum without the need to reprocess it may be very handy. </div>
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References:</h2>
[1] Carlos Cobas, Pablo G. Tahoces, Manuel Martin-Pastor, Mónica Penedo, F. Javier Sardina (2004), Wavelet-based ultra-high compression of multidimensional NMR data sets, J. Magn. Reson. 168: Pages 288–295.<br />
DOI: <a href="http://dx.doi.org/10.1016/j.jmr.2004.03.016">http://dx.doi.org/10.1016/j.jmr.2004.03.016</a><br />
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[2] C. Cobas, P. G. Tahoces, I. Iglesias Fernández (2008), Compression of high resolution 1D and 2D NMR data sets using JPEG2000, Chemometrics and Intelligent Laboratory Systems, 91, 141-150<br />
DOI:: <a href="http://dx.doi.org/10.1016/j.chemolab.2007.10.009">http://dx.doi.org/10.1016/j.chemolab.2007.10.009</a><br />
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Carlos Cobashttp://www.blogger.com/profile/13500275318435740775noreply@blogger.com0tag:blogger.com,1999:blog-6953549091784501422.post-40794429831535071802013-12-26T16:52:00.000-08:002013-12-26T16:52:12.286-08:00NMR Baseline Correction - New method in Mnova 9<div class="MsoNormal" style="text-align: justify;">
<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">One of the
most ubiquitous issues present in FT-NMR spectra is the existence of
<b>baseline artifacts</b> which might adversely affect the <b>identification </b>and
<b>quantification </b>of NMR resonances. Whilst modern NMR instruments are equipped
with powerful digital filtering employing also oversampling techniques that
produce high quality baselines, it is usually the case that some minor baseline
corrections might be needed in order to get optimal results. Also, it should
not be forgotten that there are thousands of old NMR instruments lacking those
latest instrumental advances where the necessity of a post-processing baseline
correction might be critical. <o:p></o:p></span></span></div>
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<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">Many
baseline correction algorithms have been published since the very early era of
FT-NMR, ranging from manual to fully automatic methods. Some of them have been
implemented first in MestReC and then in Mnova. Whilst the automatic methods
give quite satisfactory results in most of the cases, there are spectra in
which a manual procedure could be more convenient.<o:p></o:p></span></span></div>
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<span lang="EN-US" style="line-height: 115%;"><span style="font-family: Arial, Helvetica, sans-serif;">Former
versions of Mnova included the so-called ‘<b>Multipoint Baseline Correction</b>’ in
which the User had to identify the points corresponding to baseline regions
(also known as <b>control points</b>) which are then used by the software to build a
<b>baseline model</b> using different interpolation algorithms (linear segments,
polynomials, splines, etc).</span></span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhsyyMZd6HxnsZZbDqxesOWh-e0Y-p3EMiNpsqs433axb_fbbdnjAAxNSS_73XYQu7dKL6FHYAioQNDFyv8TXnNX21j-P63LcNyLzhbbf36AHj2Q6uhGB-qf2nj_55eAN7lhNHzmNM07cU/s1600/baseline1.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhsyyMZd6HxnsZZbDqxesOWh-e0Y-p3EMiNpsqs433axb_fbbdnjAAxNSS_73XYQu7dKL6FHYAioQNDFyv8TXnNX21j-P63LcNyLzhbbf36AHj2Q6uhGB-qf2nj_55eAN7lhNHzmNM07cU/s320/baseline1.png" width="320" /></a></div>
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<span style="font-family: Arial, Helvetica, sans-serif; text-align: justify;">Unfortunately,
this manual method was not as robust as we initially thought and the process of
selecting the control points was fully manual.</span><br />
<div class="MsoNormal" style="text-align: justify;">
<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">We thought
that it would be very useful to implement a quick button to automatically
detect these control points so that the User would only need to review them and
if need be, edit or add a few more in order to get the optimal baseline. <o:p></o:p></span></span></div>
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<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;"><br /></span></span></div>
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<span lang="EN-US" style="line-height: 115%;"><span style="font-family: Arial, Helvetica, sans-serif;">This is
exactly what is available now in <b>version 9 of Mnova NMR</b>: This new button runs a
novel algorithm that analyzes all the points in a spectrum which is further split
in different spectral windows. As a result of this process, a number of <b>control
points</b> are automatically added to the spectrum.</span></span></div>
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<span lang="EN-US" style="line-height: 115%;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjoHE9ZVdaa2ms8mRHr8odbWlLgp4hR87CaOHuIXVC0KM4Dui10Q_6clo7eMxMppHZ3fUY1kWFw-RRaQyTVwZgMZ4MNj26jQCMM7p178SYsXySrR20IUgZyQFwxb49vbQl_nc_AX3A9tsQ/s1600/automatic.png" imageanchor="1" style="line-height: normal; margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" height="285" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjoHE9ZVdaa2ms8mRHr8odbWlLgp4hR87CaOHuIXVC0KM4Dui10Q_6clo7eMxMppHZ3fUY1kWFw-RRaQyTVwZgMZ4MNj26jQCMM7p178SYsXySrR20IUgZyQFwxb49vbQl_nc_AX3A9tsQ/s400/automatic.png" width="400" /></a></span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">Once all
the control points are available, this module offers several possibilities to
create the final <b>baseline mode</b>l: Whittaker, linear segments, smoothed linear
segments, polynomials and splines. Of these, we recommend the <b>cubic splines</b>,
they usually give very good results provided there are a <b>sufficient number of
control points well spread across the spectral width</b>.</span></div>
<h2 style="text-align: justify;">
<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif; font-size: small;">Automating the new
algorithm<o:p></o:p></span></span></h2>
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<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">After
having implemented this algorithm, we found that it would make sense to fully
<b>automate </b>it and add it to our set of automatic baseline correction algorithms,
both for 1D and 2D. It works as simple as this: First the algorithm detects
automatically all the control points using the same method that has just been
mentioned. Next, the baseline distortion is modeled using splines that go
through all those control points. <o:p></o:p></span></span></div>
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<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">This new
algorithm is available from the <b>baseline correction command</b>:<o:p></o:p></span></span></div>
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<span lang="EN-US"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjPDJeGAWobHiVJSSnhbEQotUftuMe7liTNNYOesKLbEa9POw5Z2H1iryeFQ5FNyXs8amQ-XXd9-VnJ0yO9S6YXBkjMq0rhY05_zTEyX_v6fngI_qHYuSVDA4SH4MOZ1NtJ4JJuUQJHZzo/s1600/newsplines.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" height="202" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjPDJeGAWobHiVJSSnhbEQotUftuMe7liTNNYOesKLbEa9POw5Z2H1iryeFQ5FNyXs8amQ-XXd9-VnJ0yO9S6YXBkjMq0rhY05_zTEyX_v6fngI_qHYuSVDA4SH4MOZ1NtJ4JJuUQJHZzo/s400/newsplines.png" width="400" /></a></span></div>
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<span lang="EN-US"><span style="font-family: Arial, Helvetica, sans-serif;">These are
just some <b>examples</b>:</span><o:p></o:p></span></div>
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<span lang="EN-US"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgZNswmnEXlqKAncWcLdnXQ0BMGmWcGYaupuBXGyIWHR9GMhFScG_VbK1GAu353Ni9PA382OxogNaZ7SUyRyY0lJgSR3a__KDUEdsSlWRfbrjORnCef-kQVLmn6joUYRr5YENKk4vDuqsE/s1600/examples.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" height="441" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgZNswmnEXlqKAncWcLdnXQ0BMGmWcGYaupuBXGyIWHR9GMhFScG_VbK1GAu353Ni9PA382OxogNaZ7SUyRyY0lJgSR3a__KDUEdsSlWRfbrjORnCef-kQVLmn6joUYRr5YENKk4vDuqsE/s640/examples.png" width="640" /></a></span></div>
Carlos Cobashttp://www.blogger.com/profile/13500275318435740775noreply@blogger.com0tag:blogger.com,1999:blog-6953549091784501422.post-78081447000629492172013-12-23T08:25:00.000-08:002013-12-23T08:25:03.294-08:00Faster NMR Data Processing with Mnova 9 <div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi_97qFwIcf4eYPoBxuMrCXZs7yEqlPUkBWX41BWrEvOJZoRmd5KMBMPrKvPLae39l7Lr15zDqW2lDdw0AvimPZz8P6g6p_FJ_8Jc52L9qVH_czxQm3v3mCE0vbow4Ndzvt-I3Wbkkyu3g/s1600/FASTNMR.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="193" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi_97qFwIcf4eYPoBxuMrCXZs7yEqlPUkBWX41BWrEvOJZoRmd5KMBMPrKvPLae39l7Lr15zDqW2lDdw0AvimPZz8P6g6p_FJ_8Jc52L9qVH_czxQm3v3mCE0vbow4Ndzvt-I3Wbkkyu3g/s1600/FASTNMR.png" width="320" /></a></div>
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<div style="text-align: justify;">
<span style="font-family: Arial, Helvetica, sans-serif;">For nearly a decade, computer CPU chip makers have gradually adopted the use of <b>multiple cores</b> to increase performance. For instance, the computer from which I’m writing this entry has 4 cores. Roughly speaking, this makes it possible to run different tasks in each core so ideally, depending on the specific application or algorithm; it would be possible to make some operations faster proportionally to the number of available cores.</span></div>
<div style="text-align: justify;">
<span style="font-family: Arial, Helvetica, sans-serif;">However, <b>Mnova NMR</b> has not exploited this technological advantage until now so the number of cores in your computer would not make any difference. It is also true that most of the algorithms in Mnova have been highly optimized and, typically, its computational performance is usually more than adequate to provide a sufficiently smooth experience. Nevertheless, it is not sensible to let this technological opportunity pass and so, in the past few months we have been parallelizing a number of routines in <b>Mnova </b>in order to take full advantage of these multi-core CPUs. </span></div>
<div style="text-align: justify;">
<span style="font-family: Arial, Helvetica, sans-serif;">This is just a starting point and ultimately, we will parallelize ALL algorithms in Mnova but, for the moment, we have just selected a few of the most computationally expensive algorithms, namely:</span></div>
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<h2 style="text-align: justify;">
<span style="font-family: Arial, Helvetica, sans-serif;">
2D Linear Prediction</span></h2>
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<span style="font-family: Arial, Helvetica, sans-serif;">Mnova NMR includes two procedures for <b>Linear Prediction</b>, the so-called <b>Toeplitz </b>and the <b>Zhu-Bax</b> algorithms. Whilst the former is already extremely fast, it is mathematically less robust than the Zhu-Bax, which, in our experience gives much better results, especially in non-phase sensitive (i.e. magnitude-like) 2D spectra. However, because Zhu-Bax was quite slow, Mnova NMR had, as a default method, the Toeplitz one.</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">Now that we have parallelized the Zhu-Bax method, this has become the new default forward LP algorithm. In our tests, this algorithm performs nearly as fast as the (non-parallelized) Toeplitz counterpart, but with the additional advantage of its mathematical robustness. </span></div>
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<h2 style="text-align: justify;">
<a href="http://nmr-analysis.blogspot.com.es/2013/12/non-uniform-sampling-nus-nmr-processing.html" target="_blank"><span style="font-family: Arial, Helvetica, sans-serif;">Non Uniform Sampling (NUS)</span></a></h2>
<div style="text-align: justify;">
<span style="font-family: Arial, Helvetica, sans-serif;">This algorithm was initially developed in a single thread mode (in Beta versions of the software) but <b>Mnova 9</b> comes with a highly optimized parallelized version. </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span></div>
<h2 style="text-align: justify;">
<span style="font-family: Arial, Helvetica, sans-serif;">
Processing of multiple (stacked) spectra</span></h2>
<div style="text-align: justify;">
<span style="font-family: Arial, Helvetica, sans-serif;">Stacked or arrayed spectra are perfect candidates for parallelization as it is possible to process each spectrum in different cores. Whilst this advantage might be negligible for basic processing, parallelization really makes a difference when all these spectra need to be analyzed using, for example, Global Spectral Deconvolution (GSD). </span></div>
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<h2 style="text-align: justify;">
<span style="font-family: Arial, Helvetica, sans-serif;">
2D contour plots</span></h2>
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<span style="font-family: Arial, Helvetica, sans-serif;">Calculation of 2D contour lines have also been parallelized resulting in a faster display of 2D spectra. </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span></div>
<h2 style="text-align: justify;">
<span style="font-family: Arial, Helvetica, sans-serif;">
More to come</span></h2>
<div style="text-align: justify;">
<span style="font-family: Arial, Helvetica, sans-serif;">Again, our ultimate goal is to optimize / parallelize every single processing and analysis algorithms in Mnova. Nevertheless, I believe that these enhancements are already worth the upgrade to this new version of Mnova. </span></div>
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<div>
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Carlos Cobashttp://www.blogger.com/profile/13500275318435740775noreply@blogger.com0tag:blogger.com,1999:blog-6953549091784501422.post-33552486629879370502013-12-22T08:55:00.000-08:002013-12-22T08:55:44.296-08:00Mnova goes NUS<span style="font-family: Arial, Helvetica, sans-serif;">This is one example of a NUS spectrum (HMQC) acquired by Dr. Manuel Martín-Pastor at the University of Santiago de Compostela and processed with Mnova 9.0.</span><div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj5sxbb7T_Ma_m2syYeknkzFanN14d1pBOzL3B1kDAi1lOVBxb1tS_JVx8R3gbp7qPIij4VOYQeT-bhiUD7XC6wCxo2oqSUsEY5ABCq-p_Dpl9IfStXUSpPIVnyOm9AkAp1__K5S-BgxKI/s1600/HMQC.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj5sxbb7T_Ma_m2syYeknkzFanN14d1pBOzL3B1kDAi1lOVBxb1tS_JVx8R3gbp7qPIij4VOYQeT-bhiUD7XC6wCxo2oqSUsEY5ABCq-p_Dpl9IfStXUSpPIVnyOm9AkAp1__K5S-BgxKI/s1600/HMQC.png" height="280" width="400" /></a></div>
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Carlos Cobashttp://www.blogger.com/profile/13500275318435740775noreply@blogger.com0tag:blogger.com,1999:blog-6953549091784501422.post-7500979342733823872013-12-20T14:41:00.001-08:002013-12-20T14:47:18.963-08:00Non Uniform Sampling (NUS) NMR Processing<h2>
Background</h2>
<div>
<div style="text-align: justify;">
In the last few years, Non-Uniform Sampling (<b>NUS</b>) has emerged as a very powerful tool to significantly speed up the acquisition of multidimensional NMR experiments due to the fact that only a subset of the usual linearly sampled data in the Nyquist grid is measured. </div>
<div style="text-align: justify;">
Unfortunately, this fast acquisition modality introduces a new challenge as the normal Fourier Transform will fail and consequently, special processing techniques are required.</div>
<div style="text-align: justify;">
A number of sophisticated methods have been proposed for reconstructing sparsely sampled 2D and higher dimensionality NMR data, including Maximum Entropy, CLEAN, multidimensional decomposition method (MDD), Forward Maximum entropy (FM) and its fast version (FFM), SIFT and IST [1]. Most of these procedures are computationally very expensive and usually require the adjustment of some parameters.</div>
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<h2>
NUS processing and Mnova 9.0: M.I.S.T</h2>
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It has been the objective of Mestrelab to implement within Mnova 9.0 a new 2D NUS processing module that fulfills the following criteria:</div>
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<div>
<ul>
<li>It must be computationally <b>very fast</b> whilst reconstructing the data reliably. </li>
<li>It should work fully <b>automatically </b>without user intervention. A minimum set of adjustable parameters might be used for special cases</li>
<li>It should be compatible with any <b>2D acquisition protocol and with NMR instrument</b>. </li>
<li>All these requirements have been met with the development of <b>M.I.S.T</b>, a <b>M</b>odified Iterative <b>S</b>oft <b>T</b>hresholding algorithm </li>
</ul>
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<h2>
Proof of Concept: 1D NUS Processing:</h2>
<div>
<div>
Initial development of the MIST algorithm was done using synthetic, noise-free 1D-FIDs in which a number of points have been randomly set to zero using a <b>Poisson gap </b>sampling method. After having optimized the algorithm under these conditions, the same procedure was carried out using experimental 1D spectra. </div>
<div>
Figure 1 shows the results obtained with the 1H NMR spectrum of Ondansetron in which 75% of samples have been set to zero using a random Poisson gap sampling method. Regular FFT of this spectrum shows a spectrum heavily corrupted with noise. Finally, reconstruction of the FID using the MIST algorithm shows a spectrum that resembles the ideal FT spectrum very closely. </div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhWZFsrF2RlBM2w0qPAG_eKSwvOQyY_9MbDX1itxjNPEvVDCqQdnPYJ5fK_ulajXRl8L2P5iFzCCfZt7Nme1i2vfz3LDebwv9ZV2OYKofrnitOD_vaoDGXmMB1C6u-5zEPDlOZu2_6ENlY/s1600/Figure1-NUS.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhWZFsrF2RlBM2w0qPAG_eKSwvOQyY_9MbDX1itxjNPEvVDCqQdnPYJ5fK_ulajXRl8L2P5iFzCCfZt7Nme1i2vfz3LDebwv9ZV2OYKofrnitOD_vaoDGXmMB1C6u-5zEPDlOZu2_6ENlY/s1600/Figure1-NUS.png" height="180" width="400" /></a></div>
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<b>Figure 1</b>: <i>(a) Standard, regularly sampled 1H NMR spectrum of Ondansetron. (b) FFT spectrum of the same experimental FID where 75% of the original data points have been set to zero using a random Poisson gap sampling method. (c) Result of reconstructing previously ‘corrupted’ FID using the MIST algorithm</i></div>
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<div>
Next step in our work consisted in extending the 1D MIST algorithm to operate with 2D spectra. </div>
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<h2>
MIST in action: 2D NUS Processing:</h2>
</div>
<div>
<div>
The performance of the algorithm is demonstrated with the HSQC spectrum shown in Figure 2. On the left, the uniformly sampled spectrum acquired with 96 complex increments in the indirect t1 dimension is shown. On the right, the NUS spectrum acquired with 48 complex increments randomly sampled (50% NUS). </div>
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<div>
<b>Figure 2</b>: <i>(a) Linearly sampled HSQC spectrum (96 complex increments) (b) MIST reconstruction of a NUS spectrum acquired with 48 complex increments randomly sampled. The two figures are shown using the same contour levels</i></div>
<div>
<br /></div>
<div>
Processing of the NUS spectrum was done fully automatically (just drag & drop into Mnova) and total processing time was less than 4 seconds (in my 4 core computer).<br />
<h2>
Supported NMR experiments</h2>
Presently, NUS algorithm implemented in Mnova 9.0 supports HSQC and HMBC experiments, both magnitude and phase sensitive. We have also found good results with COSY spectra. We have also tried it successfully with some NOESY/ROESY experiments, although we have to warn that with a few of them the performance has not been so good. </div>
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<h2>
CONCLUSIONS</h2>
<div>
<div>
<b>Mnova 9.0 </b>supports now NUS 2D spectra acquired in Bruker or Agilent instruments (more vendors will be included shortly).</div>
<div>
Processing of these spectra is done via the new MIST algorithm. It has been shown that this algorithm is very fast, robust and can be executed in a fully unattended way. Furthermore, our method is not sensitive to phase distortions.<br />
<br />
<b>Note: </b>Mnova 9 will be available in Mestrelab Web site (<a href="http://www.mestrelab.com/">www.mestrelab.com</a>) very soon. Meantime, this version can be downloaded it directly from <a href="https://www.dropbox.com/s/r5xhlz4ex0efflc/MestReNova-9.0.0-12821.msi" target="_blank">HERE</a> (Windows only for now). This link will only work for a few days though. </div>
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<div>
<br /></div>
<div>
<h2>
Acknowledgments:</h2>
<div>
I thank Frank Delaglio, David Russell, Paul J Bowyer and Manolo Martin for kindly providing 2D NUS spectra</div>
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[1] S. G. Hyberts et al., “Application of iterative Soft thresholding for fast reconstruction of NMR data non-uniformly sampled with multidimensional Poisson Gap scheduling”, J. Biomol. NMR 52, 315–327 (2012) and references therein</div>
Carlos Cobashttp://www.blogger.com/profile/13500275318435740775noreply@blogger.com1tag:blogger.com,1999:blog-6953549091784501422.post-74517599249461997732013-12-20T14:30:00.000-08:002013-12-20T14:30:10.769-08:00Mnova 9.0<div class="separator" style="clear: both; text-align: center;">
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<span style="font-family: Arial, Helvetica, sans-serif;">I’m very happy to announce that after a long period of very intensive work, <b>version 9.0 of Mnova is finally ready!</b> From our point of view, this version is probably the most ambitious release we have attempted since Mnova was created. Aside from many improvements and bug fixes, this new version comes with great new features, including support for <b>Non Uniform Sampling</b> (NUS), a powerful <b>PCA </b>module, <b>Reference Deconvolution</b>, <b>Absolute Referencing</b> and many, many more. </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">We are currently updating our <a href="http://www.mestrelab.com/" target="_blank">Web site</a> from where this new version can be downloaded and more details about all these new exciting features of <b>Mnova </b>will be explained in more detail. Also, in the next few days, I will be putting together some blog entries to describe some of the new functionality.</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">If you don’t want to wait until the new version is available from our Web site, you can download it from <a href="https://www.dropbox.com/s/r5xhlz4ex0efflc/MestReNova-9.0.0-12821.msi" target="_blank"><b>HERE</b> </a>(Windows only for now).</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">I really hope that this new version will meet your expectations and we are looking forward to your feedback! </span> </div>
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Carlos Cobashttp://www.blogger.com/profile/13500275318435740775noreply@blogger.com0tag:blogger.com,1999:blog-6953549091784501422.post-39565348973541721492013-05-30T00:38:00.000-07:002013-05-30T04:11:19.217-07:00qNMR: What is under the hoodI have blogged quite a few times about qNMR where I tried to cover some very basic concepts (<a href="http://nmr-analysis.blogspot.com.es/2009/11/basis-on-qnmr-integration-rudiments.html" target="_blank">here </a>and <a href="http://nmr-analysis.blogspot.com.es/2010/01/basis-on-qnmr-integration-rudiments.html" target="_blank">here</a>) and tricks on how to integrate overlapped multiplets (<a href="http://nmr-analysis.blogspot.com.es/2010/01/on-integrating-overlapped-peaks.html" target="_blank">here</a>). In my last post I announced the release of a new qNMR module for Mnova aimed at automating the quantitative analysis of NMR spectra in an efficient and robust way. Now I’m glad to write that a paper describing this functionality has now just been published in Analytical Chemistry:<br />
<a href="http://pubs.acs.org/doi/abs/10.1021/ac400411q" target="_blank">Optimization and Automation of Quantitative NMR Data Extraction</a><br />
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BTW, Mnova qNMR is free for academia or non-profit organizations.<br />
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Carlos Cobashttp://www.blogger.com/profile/13500275318435740775noreply@blogger.com0tag:blogger.com,1999:blog-6953549091784501422.post-67227401188391147202012-12-14T03:01:00.001-08:002012-12-14T03:01:08.663-08:00High-Throughput qNMR<div class="separator" style="clear: both; text-align: center;">
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<span style="font-family: Arial, Helvetica, sans-serif;">It is well known that NMR is a very convenient technique for quantification, provided the amount of the material is within the limits of detection in NMR. </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">When it comes to the actual calculations, this is a very straightforward process that does not require any fancy mathematics. Typically you will select the most convenient signal(s) or multiplet(s) in your spectrum and calculate the integral which can then be mapped to the corresponding concentration units by using a scaling factor that was previously calculated using some internal or external references. </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">It is however a laborious process. You have to make sure that the signal or multiplet you have selected is isolated enough to avoid contaminations from other signals (solvents, impurities, other compound resonances, etc). Furthermore, you need to know the number of nuclides (i.e. protons) of the integrated signal / multiplet. Again, this is not rocket science but it is particularly labor-intensive. It could take perfectly a few minutes for one single data set. </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">Now suppose that you have to do this with a library of several hundred or thousands of compounds with their corresponding NMR spectra. Clearly a manual analysis is completely impractical. </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">There are several approaches out there that can be used to automate this process in some way or another, but to the best of my knowledge they are not optimized to take into account a number of factors that could adversely affect the accuracy and precision of the quantification calculations. Features such as spectral quality variability from sample to sample, different degrees of peak overlap, amongst others, are very important in order to have a robust system.</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">That is precisely one of the main objectives that we’ve pursued with the development of a new qNMR module for Mnova that we have <a href="http://mestrelab.com/software/mnova-qnmr/" target="_blank">just released</a>, the ability to process any number of data sets in the most robust way possible. </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">It has been designed in such a way that it can detect those multiplets in the spectrum that gives the best results whilst discarding those problematic ones (for example, multiplets showing overlapping problems, or having impurities or artifacts). It also calculates the number of nuclides for each of those multiplets, etc. </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">Bottom line is that this new module is aimed at streamlining qNMR analyses and reporting whilst eliminating tedious and repetitious manual steps. </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">We believe that it is a useful tool not only in the traditional exploitation of qNMR where the final result is required to the highest level of precision, and the utmost care must be taken in collecting the NMR data, but also in the world of high-throughput NMR where this very careful data acquisition is often not possible. Whilst the first thought may be that qNMR therefore is not possible, we know from collaborative studies that quite reasonable and useful quantitative data can be obtained in this scenario. The error expectation obviously has to be lowered and actual numbers will depend on factors such as the rate of data acquisition, SNR, and impurity levels, but concentration determination to within 5-10% of the actual value is not an unrealistic expectation. </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">This new module can be tried for free, just go <a href="http://mestrelab.com/software/mnova-qnmr/" target="_blank">here</a>. </span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">You can also find more information <a href="http://mestrelab.com/blog/article/what-is-qnmr/" target="_blank">here</a></span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">Of course, should you have any question or need any further information, please feel free to get in touch with us.</span></div>
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Carlos Cobashttp://www.blogger.com/profile/13500275318435740775noreply@blogger.com0