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Molecular & Cellular Proteomics 7:2270-2278, 2008.
© 2008 by The American Society for Biochemistry and Molecular Biology, Inc.

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Research

MRMer, an Interactive Open Source and Cross-platform System for Data Extraction and Visualization of Multiple Reaction Monitoring Experiments^*,S

Daniel B. Martin, Ted Holzman, Damon May, Amelia Peterson, Ashley Eastham, Jimmy Eng^,¶ and Martin McIntosh^,||

From the Institute for Systems Biology, Seattle, Washington 98103, Fred Hutchinson Cancer Research Center, Seattle, Washington 98112, and ^¶ University of Washington Medicine at South Lake Union, Seattle, Washington 98109

Multiple reaction monitoring (MRM) mass spectrometry identifies and quantifies specific peptides in a complex mixture with very high sensitivity and speed and thus has promise for the high throughput screening of clinical samples for candidate biomarkers. We have developed an interactive software platform, called MRMer, for managing highly complex MRM-MS experiments, including quantitative analyses using heavy/light isotopic peptide pairs. MRMer parses and extracts information from MS files encoded in the platform-independent mzXML data format. It extracts and infers precursor-product ion transition pairings, computes integrated ion intensities, and permits rapid visual curation for analyses exceeding 1000 precursor-product pairs. Results can be easily output for quantitative comparison of consecutive runs. Additionally MRMer incorporates features that permit the quantitative analysis experiments including heavy and light isotopic peptide pairs. MRMer is open source and provided under the Apache 2.0 license.

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