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04 Dec 2019

Metandem, a free and online software for MS-based isobaric labeling metabolomics

By nickwiecien

Hao et al. (2019) recently published a paper in Analytica Chimica Acta detailing the utility of Metandem, a data analysis software which is aids in isobaric labeling-based metabolomics.

While mass spectrometry-based stable isotope labeling is advantageous compared to other methods of isotope labeling due to its multiplexing and accurate quantification capabilities, its data analysis requires specifically customized bioinformatic tools. However, Metandem, a free, unique and online software, can aid in the analysis of stable isotope labeling-based metabolomics data.

Metandem has a number of different features that assist in MS-based isobaric labeling, such as integrating feature extraction, metabolite quantification and identification, batch processing of multiple data files, online parameter optimization for custom datasets, data normalization and statistical analysis.

Metatandem is available free and online at http://metandem.com/web/. 

Graphical abstract for Metandem paper published by Hao et al in Analtica Chimica Acta demonstrating the software's utility in isobaric labeling, integrating feature extraction, and metabolite quantification.
27 Nov 2019

Software Highlight: Compass

By nickwiecien

The Coon OMSSA Proteomic Analysis Software Suite, or COMPASS, is one of many custom software and web-based data tools that NCQBCS offers in an effort to extend its expertise to the broader scientific community.

Compass is a free and open-source software pipeline designed around the Open Mass Spectrometry Search Algorithm. Compass aids in high-throughput analysis of proteomics data such as FASTA database creation, peptide-spectral matching, calculation of false discovery rates, and protein grouping, as well as spectral reduction, peptide quantitation via isobaric labeling (or without), and protein parsimony.

Furthermore Compass utilizes graphical user interfaces which work well with data files in original instrument vendor format, making it easy to use.

The manuscript for Compass is available here, and the software can be downloaded here. Additionally, information on other software that the National Center for Quantitative Biology of Complex Systems offers can be found here.

Graphical abstract from the COMPASS manual, demonstrating its uses as a database maker, dta generator, fdr optimizer, and protein herder.
16 Feb 2018

1st Annual North American Mass Spectrometry Summer School

By Nick Wilkes

Please join us for our first annual mass spectrometry summer school. We are proud to have assembled over a dozen world leading experts in mass spectrometry for this four-day course. Our goal is to provide our students, both from academia and industry, an engaging and inspiring program covering the latest in the application of mass spectrometry to omic analyses. Tutorial lectures range from experimental design, sample preparation, and quantification to the basics of high performance mass analyzers and data analysis. Also planned are several hands-on workshops – aimed at both scientific and professional development. Finally, we will take a break on one afternoon for a whole group experience at nearby Devil’s Lake State Park where workshop goers can choose from a slate of exciting recreational activities. This workshop is made possible by generous funding from the National Science Foundation (Integrated Organismal Systems, Plant Genome Research Program, Grant No. 1546742) and the National Institutes of Health National Center for Quantitative Biology of Complex Systems (P41 GM108538). As such, there is no cost to participate and several travel awards are available.

Learn More

Register for Summer School