Chenomx Blog

Chenomx NMR Suite 5.0 Tour (Part 1): Annotation Tools in Profiler

Colin Vitols — Mon, 11 Feb 2008 14:30:50 +0000

Profiling spectra can be complicated. There are a lot of compounds to consider, the spectra are usually quite busy, and it can be hard to even remember which compounds you’ve already profiled. Fortunately, the compound table in Profiler has a few tools that can help you keep track of your progress, and work more efficiently with the contents of your compound library.

Stars
Stars allow you to mark compounds in the compound table to indicate that they are different somehow. They are a generic method for marking compounds as being in either “this group” or “the other group”. Stars can also help you mark compounds for certain operations, like setting potential concentrations, scaling concentrations, and updating compound versions in your library.

You can star a compound by simply clicking on the star icon for the compound in the Compound Table. The Starred column is the second column from the left by default.

Highlights
Highlighting a compound “pins” it to the spectrum, so that its signature remains visible no matter which other compound you may select in the Compound Table. Highlighted compounds are particularly useful for fitting heavily overlapped regions, allowing you to better evaluate the individual contributions of each compound to the overlapped area. You can also use highlighted compounds along with custom colors (see below) to set up your Spectrum View for better results from the Export Spectrum Graphic feature (File > Export > Spectrum Graphic…).

You can highlight a compound by clicking the highlight check box for the compound in the Compound Table. You can enable the Highlighted column in the Compound Table by right-clicking on the header row and selecting Highlighted.

Compound Colors
Previous versions of Profiler selected colors for displayed compounds based on the order in which you selected them. Now, you can specify the color that you want to use to display a compound. All the colors of the rainbow are at your fingertips, so go wild!

You can assign a custom color for a compound by right-clicking on the compound in the Compound Table and selecting Assign Custom Color, then selecting a color in the Assign Custom Color dialog and clicking OK. The Color column is the left-most column in the Compound Table by default.

For more information on the features described here, please see your Chenomx NMR Suite User Manual by pressing F1 from any module, or opening the “Documentation\ChenomxNMRSuite.pdf” file in the folder where you installed Chenomx NMR Suite.

Announcing Chenomx NMR Suite 5.0

jnewton — Thu, 13 Dec 2007 03:14:08 +0000

Today we are shipping what is the most significant product release in Chenomx’s history: Chenomx NMR Suite 5.0. The software development, compound library development, and quality assurance teams at Chenomx have put a huge amount of effort into what is simply the best, easiest to use, and most powerful release we’ve done to date.

The number of new features, usability enhancements, and performance improvements in this release are too many to list in this posting - the best way to get a sense of what’s new in this release would be to install the free, fully-functional evaluation version. You can also check out the Product Overview, the Product Tour, and the What’s New documentation.

Chenomx in Chamonix

jnewton — Wed, 26 Sep 2007 15:04:37 +0000

Yes, that was the tongue twister we were wrestling with all of last week in Chamonix, France at SMASH 2007. Chenomx is a proud sponsor of SMASH, which is always one of the best NMR meetings of the year. This year was no exception, and the location couldn’t have been better - congratulations to the organizing committee on pulling off an excellent conference and a perfect venue.

The last big metabolomics conference of 2007 will be the Advances in Metabolic Profiling meeting, November 14-15 in Boston, MA. Chenomx will be there, so be sure to attend!

Publication Highlights

jnewton — Tue, 21 Aug 2007 01:35:38 +0000

Last week was a very exciting week for Chenomx, as our unique “targeted profiling” approach was used in two high-profile ACS journal publications (see Targeted Profiling: Quantitative Analysis of 1H-NMR Metabolomics Data if the term targeted profiling doesn’t ring a bell).

An Inflammatory Arthritis-Associated Metabolite Biomarker Pattern Revealed by 1H NMR Spectroscopy, published by Aalim Weljie et. al. at the University of Calgary, uses quantitative “targeted profiling” of known metabolites coupled with O-PLS-DA pattern recognition analysis to uncover biomarker candidates for rheumatoid arthritis.

Carolyn Slupsky et. al. at the University of Alberta’s Department of Medicine and Magnetic Resonance Diagnostic Centre published the second paper: Investigations of the Effects of Gender, Diurnal Variation, and Age in Human Urinary Metabolomic Profiles. In this paper Slupsky and her colleagues investigate differences in gender, diurnal variation, and age in a human population using quantitative “targeted profiling” of metabolites. The “targeted profiling” approach is compared to a more traditional spectral binning approach, and Slupsky et. al. show that targeted profiling produces robust models, generates accurate metabolite concentration data, and provides data that can be used to help understand metabolic differences in a healthy population.

Congratulations to both groups, and we hope these papers give some inspiration as to how targeted profiling can be used in metabolomics research.

Chenomx’s Baseline Correction Algorithm Published in JMR

jnewton — Wed, 01 Aug 2007 16:39:44 +0000

Congratulations to David Chang and Cory Banack, two Chenomx employees that recently published details of the baseline correction algorithm implemented in Chenomx NMR Suite.Â The innovation in the algorithm described in the paper centers around its suitability for use in “signal-dense” NMR spectra, such as typical metabolomics samples.Â Many existing baseline correction algorithms are optimized for “sparse” NMR spectra, where there is only a small number of signals.

The paper has been published in the August 2007 issue of JMR.

Metabolics Society 2007 Wrap-Up

jnewton — Wed, 20 Jun 2007 14:43:59 +0000

We just returned from an exciting (but rainy) week in Manchester, England, where the Chenomx-sponsored Metabolomics Society 2007 meeting just wrapped up. The meeting was a huge success with over 500 participants.

Here are some of the highlights from what was a busy and exciting conference:

Chenomx announced a relationship with GeneGo - metabolomics information generated by Chenomx NMR Suite can now be integrated directly into GeneGo’s software for metabolic pathway visualization and analysis.
The following researchers presented work which used Chenomx software for metabolite identification and quantification:

The Human Metabolome Project: An Update for 2007
David Wishart (University of Alberta, Canada)
Characterization of Multi-age Rodent Pediatric Models of Toxicity
Laura Schnackenberg (FDA, USA) .
Can the Etiology of Pneumonia be Determined using Metabolomics?
Carolyn Slupsky (University of Alberta, Canada)
Metabolomics and `Non-modelÂ´ Organisms â€“ Earthworms as a Case Study
Jake Bundy (Imperial College London, UK)
Metabolomics in Small Fish Toxicology and Ecological Risk Assessments
Tim Collette (Environmental Protection Agency, USA)
Can Metabolomics be used for Environmental Monitoring in Free Living Aquatic Wildlife? - Building the Weight of Evidence
Mark Viant (University of Birmingham, UK)
Wine, Soils and Complex Community Interactions
Simone Rochfort (The Department of Primary Industries, Australia)
Metabolite Biomarkers of Scleroderma Elucidated using 1H NMR Metabolomics
Aalim Weljie (University of Calgary, Canada)
The OPLS and O2PLS Approach in Metabolomics and Metabonomics
Johan Trygg (University of UmeÃ¥, Sweden)

More posters than we could count used Chenomx’s software as part of the research presented!
Chenomx and Umetrics held the first joint “Chenomx-Umetrics Metabolomics Workshop” on June 15, following the meeting. The workshop was sold out and, based on feedback from attendees, a great success.

Human Metabolome Project Completed

jnewton — Fri, 26 Jan 2007 17:48:26 +0000

The Human Metabolome Project (http://www.metabolomics.ca/), which Chenomx is proud to be partnered with, has announced it has completed the human metabolome. David Wishart, the project’s lead researcher and one of Chenomx’s scientific advisors, has been interviewed recently in the Edmonton Journal and on Canada AM.

Announcing the Chenomx Forums

jnewton — Mon, 13 Nov 2006 22:42:37 +0000

Today we’re happy to announce the public launch of the Chenomx Forums, a place for you to ask questions, suggest new features, and interact with our team and other members of the Chenomx NMR Suite community. The Chenomx team actively monitors the forums, so you can expect to get a response back to your questions within one business day.

Visit http://forum.chenomx.com to get started. To make new postings you’ll have to register, which is a quick and painless process.

Chenomx NMR Suite 4.6 Feature Tours

jnewton — Thu, 09 Nov 2006 23:27:35 +0000

We’ve just finished updating the Feature Tours to highlight some of the new features in 4.6 - check out the tours for each of the four modules:

What are my favorite new features? Baseline correction in Processor and Residual-based binning in Profiler.

Announcing Chenomx NMR Suite 4.6

jnewton — Mon, 06 Nov 2006 21:58:40 +0000

Chenomx is pleased to announce the immediate availability of Chenomx NMR Suite 4.6. For information on what’s new with Chenomx NMR Suite, please see the press release, our Chenomx NMR Suite 4.6 overview page, or get right down to it and download the evaluation edition of Chenomx NMR Suite and see what all the buzz is about.