Metabolomics—Young Field, Bright Future

Emerging Market Predicted to Double in the Next Five Years to Well Over One Billion Dollars

New version of XCMS Online released

A new version of XCMS Online was released today. The upgraded website now includes an interactive cloud plot to visualize results from untargeted metabolomic experiments,  a job sharing center, a parameter manager to organize existing parameter sets, support for Bruker raw data files and more. The detailed list of changes can be found here.

Cloud Plot

Review about bioinformatic tools for metabolomics

follow-up to my last posting: Today I was reading the review below and I found it amusing to read this:
"... However, the relatively low sensitivity of NMR, and the spectral overlap that often occurs, limits the number and variety of metabolites than can be simultaneously observed. Hyphenated mass spectrometry (MS) methods, such as GC-MS, LC-MS, and CE-MS, currently provide higher sensitivity, and are the leading analytical platform for metabolite profiling."

Bioinformatics Tools for Mass Spectroscopy-Based Metabolomic Data Processing and Analysis
Sugimoto, Masahiro; Kawakami, Masato; Robert, Martin; Soga, Tomoyoshi; Tomita, Masaru
Current Bioinformatics, Volume 7, Number 1, March 2012 , pp. 96-108(13)

"Slightly" biased review

Metabolomics of sepsis-induced acute lung injury: a new approach for biomarkers
Paige Lacy
Am J Physiol Lung Cell Mol Physiol. 2011 Jan;300(1):L1-3. Epub 2010 Nov 5.

"... In particular, NMR is widely used for “classic” metabolic studies, because this approach has an exceptional capacity to rapidly identify and quantify multiple metabolites in biological fluids. Other approaches involving mass spectrometry are limited in their ability to identify more than a few small molecules in complex mixtures and are unable to quantify metabolites accurately."

For a review, I think this is a more than questionable statement.

Retention time prediction software

 Easy and accurate high-performance liquid chromatography retention prediction with different gradients, flow rates, and instruments by back-calculation of gradient and flow rate profiles  Paul G. Boswell, Jonathan R. Schellenberg, Peter W. Carr, Jerry D. Cohen, Adrian D. Hegeman

An implementation and source code is available here. 

".. This approach provides a simple way to correct for all instrument-related factors affecting retention, allowing dramatically streamlined and improved retention projection across gradients, flow rates, and HPLC instruments."

And here are the limitations:
1) Solvent A must be 0.1% formic acid in water and solvent B must be pure acetonitrile
2) The column temperature must be set to 35 °C
3) The stationary phase must be Waters Acquity BEH C18 (1.7 μm, 130 Å)
4) The  retention database only contains 35 compounds.

Dancing with the yeast cells

Some guys from New Zeland at the Centre for Microbial Innovation designed what I think is the funniest metabolomics experiment so far. They compared the metabolome of yeast cells growing in defined liquid medium exposed to music and silence. The biomass production was decreased by 14% when the cells were exposed to sonic stimuli, and the metabolite profile was also significantly different compared with silence.

http://www.springerlink.com/content/e6143q34160g633r/

Unfortunately, they didn't specify in their methods what kind of music they used. Was it Britney Spears or Enrique Iglesias? that might clearly explain the lower biomass production... I bet they also activated signaling for apoptosis.

Clearly, a great candidate paper for the Ig Nobel Prize ;-)

Global Metabolomics Market to Reach $863.8 Million by 2017, According to a New Report by Global Industry Analysts, Inc

http://www.prweb.com/releases/metabolomics_metabonomics/biomarker_discovery/prweb8519517.htm