MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments

Mol Cell Proteomics. 2008 Nov;7(11):2270-8. doi: 10.1074/mcp.M700504-MCP200. Epub 2008 Jul 18.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Mass Spectrometry / methods*
  • Mass Spectrometry / statistics & numerical data*
  • Peptide Fragments / isolation & purification
  • Phosphopyruvate Hydratase / isolation & purification
  • Phosphopyruvate Hydratase / metabolism
  • Proteomics / methods*
  • Proteomics / statistics & numerical data*
  • Saccharomyces cerevisiae / enzymology
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae Proteins / isolation & purification
  • Saccharomyces cerevisiae Proteins / metabolism
  • Software*
  • Trypsin


  • Peptide Fragments
  • Saccharomyces cerevisiae Proteins
  • Trypsin
  • Phosphopyruvate Hydratase