Monday, March 05, 2007


"Chenomx NMR Suite is designed to fit spectra in a computer-assisted fashion" says the manual and it says it all. Don't be mislead by the term "suite": this software (a more appropriate term, in my humble opinion) has a single task to perform. Translation: you will be measuring the single concentrations of known compounds into a mixture not by integration, but by visual fitting, and the computer will provide you with all the tools for the task. Eventually it will be you alone to judge the goodness of the fit. Obviously there is much more than this both in NMR and in metabolomics, so the name suite is misleading (it makes me think at MS Office, which is an unfitting example; the name "suite" is also used to indicate the most expensive room of an hotel, and the "NMR Suite" actually seems to be the most expensive of all NMR programs).
I have downloaded version 4.6 of the software, courtesy of Chenomx, and followed the enclosed tutorials. (Before running the software, you need to receive two e-mails back from Chenomx).
I can't comment on the correctness of visual fitting, compared to integration or to deconvolution. The mere fact that this software is commercialized is a measure of the effectiveness of the method. I have not worked with real life examples; I was however convinced by what I have seen. Generally speaking, integration is the best method we have to measure concentrations by NMR, followed by deconvolution in frequency domain. In biological mixtures, if they give a nice spectrum and if you process it properly, you can use the height of the peaks (instead of the areas) as a measure of concentration. The condition is that the shapes in your spectrum correspond to the shapes in the reference library you are using, and you fulfill this condition with reference deconvolution (pardon me for the pun).
Suddenly everything gets complicated, doesn't it? Let me explain the single terms. The libraries, also provided by Chenomx, are the natural complement of the suite (they also are what makes the product so expensive). Each library contains the multiplets of a good deal of metabolites, at a given magnetic field. The word "multiplet" is never used, "cluster" is used instead, both for not forcing the user to learn spectroscopy and also because sometimes they are really clusters (or singlets), not true multiplets. The library takes into account the pH, because many chemical shifts are pH sensitive. There are also unpredictable matrix effects, so the frequencies can also be finely tuned by hand.
Reference Deconvolution is one of the tricks of Digital Signal Processing. Although more often useful for resolution enhancement, here it is implemented with the opposite aim of line broadening. The purpose is the obtain nearly perfect lorentzian lineshapes, whose width match that of the library peaks. Without matching shapes and width, fitting the heights would be of no use, hence the central importance of reference deconvolution. This particular implementation seems optimized for line broadening. I'll explain why in the next post.
While most of the software interfaces use to puzzle the chemists with countless icons, aligned in rows, double rows and triple rows, most of which are never touched, Chenomx comes with a simple and clean layout, very well designed that should make for a pleasant working experience. The latter is unfortunately marred by the irritating slowness of the program. I have tested the Suite on a iMac G5 running at 2 GHz and it is as slow, if not slower, as my old Centris running at 25 MHz, while on paper it should be 80 times faster. The computational needs are basic (the most heavy one being the traditional monodimensional FT), so there would be no necessity of a 2 GHz computer. Even a 200 MHz machine, if properly programmed, should rarely display the "wait a moment" cursor when performing these kind of calculations. This 2 GHz model, instead, hangs often. The same machine, with other software, easily performs a whole 2D FT in less time! I mean: this whole work could be carried out with a ten years old computer. They are forcing us to buy a new computer, with all the negative consequences for the environment, not to run faster, but simply because today's programmers like Java instead of other languages. I really don't see why I should care for programmers. This particular application, for example, is so specialistic, that it was not so important to have it developed cross-platform, but even if it was so, faster alternatives were still available. Even if they weren't, other Java programs used by spectroscopists react in much less time. There is no excuse for such slowness and it's a pity, because the user interface is so nice. Other programs cause the user to spend a lot of time just to locate the icon (or the menu item) they need, while with the Suite you soon learn where to find them.
After completing my tutorial, I can swiftly find in the library the compound I am looking for, either by name or by frequency. In the latter case, I normally get a list of candidates. After selecting one of them, a control appears, called the "cluster navigator". With it I can zoom, in succession, into the regions where signal of the selected compound resonate and I can verify if the metabolite is present or not into the mixture. In the affirmative case I usually activate an automatic fit of the heights. The program remains on the safe side and usually underestimates the concentrations, so I shall refine the fit manually. As soon as I bring the cursor near the top of the peak, a new displacement control appears. Dragging it I can change both the frequency and the height of the peak. It would be better if the cursor disappeared during dragging, because it hides the top of the curve.
The suite is actually a single executable, that can launch four windows: the profiler (the one just described), the Library Manager, the Signature Builder (each signature corresponds to a single compound into the libraries) and the Processor. It's like a modal program, with the difference that you can have the four modules running concurrently. You cannot, however, open more than one window per module. The processor in itself also comes in modes, so you have a modality inside another modality. You know that I consider modality a bad programming style, and I am not alone. Once for a while, it is given some good reason to exist, because each mode is intuitively interactive. You can graphically define the DSS position (a hydrophilic equivalent of TMS), and you can graphically define the breakpoints for the Spline that corrects the baseline. There is a price to pay for modality: you need a double click to enter into selection mode and another double click to expand the selection...
The processor is the weak link in the chain. I wonder why Varian has invested money into Chenomx and has not lent their algorithms. Everything is slow, even opening a file. The phase correction mode does not allow to specify a pivot point, like all software do today. This feature will be added, they say, in version 5. There is a useless command called "Water Deletion" and all that it does is to hide the central region of the spectrum: the tails of water remains in the outer regions. I'd suggest them reading an article published 18 years ago on JMR (Vol. 84, page 425) by Marion et al. and titled "Improved Solvent Suppression in One- and Two-Dimensional NMR Spectra by Convolution of Time-Domain Data". Convolution in TD is not useful because it hides the water, but because it improves the baseline and doesn't cancel nearby signals.
I also know that many spectroscopists like the Spline for baseline correction, yet I prefer the more regular polynomial. This option is not available. The Spline lets you cancel humps and solvents, but I prefer a baseline correction that corrects the baseline and nothing else. The reference deconvolution works, but you should be careful not to play with it too much: the first attempt should be the definitive one.
The processor also implements binning, but the analysis of the output requires an external software. Other tools are prettier, I mean the "tape measure" (to measure distances) and the thumbnail of the spectrum. Under it, the status line constantly reports the frequency value corresponding to the cursor.
If you want to test this software, I recommend reading the manual and following the tutorials exactly as they are explained, otherwise you are wasting hours before discovering that the defaults are not compatible with the given example. The manual comes in two versions: embedded, with lovely icons but a small character set, and the customary pdf file.
The staff at Chenomx is kind and helpful and can give you all the information you need, including a live demo of the product. Their web site hosts more specific information, including copies of their published articles and papers. If you find them too difficult, the story of the company, including photographs, as published by the Alberta Venture magazine, does not require any scientific background.


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