title: MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments.
abstract: 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.
authors.affiliation: Institute for Systems Biology, Seattle, Washington 98103, USA.
authors.forename: Daniel B
authors.initials: DB
authors.lastname: Martin
authors.forename: Ted
authors.initials: T
authors.lastname: Holzman
authors.forename: Damon
authors.initials: D
authors.lastname: May
authors.forename: Amelia
authors.initials: A
authors.lastname: Peterson
authors.forename: Ashley
authors.initials: A
authors.lastname: Eastham
authors.forename: Jimmy
authors.initials: J
authors.lastname: Eng
authors.forename: Martin
authors.initials: M
authors.lastname: McIntosh
mesh_terms: D013058:Mass Spectrometry / Q000379:methods* / Q000706:statistics & numerical data*; D010446:Peptide Fragments / Q000302:isolation & purification; D010751:Phosphopyruvate Hydratase / Q000302:isolation & purification / Q000378:metabolism; D040901:Proteomics / Q000379:methods* / Q000706:statistics & numerical data*; D012441:Saccharomyces cerevisiae / Q000201:enzymology / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000302:isolation & purification / Q000378:metabolism; D012984:Software; D014357:Trypsin
chemical_list: D010446:Peptide Fragments; D029701:Saccharomyces cerevisiae Proteins; D014357:Trypsin; D010751:Phosphopyruvate Hydratase