title: Software platform for rapidly creating computational tools for mass spectrometry-based proteomics.
abstract: We describe and demonstrate the proteomics computational toolkit provided in the open-source msInspect software distribution. The toolkit includes modules written in Java and in the R statistical programming language to aid the rapid development of proteomics software applications. It contains tools for processing and manipulating standard MS data files, including signal processing of LC-MS data and parsing of MS/MS search results, as well as for modeling proteomics data structures, creating charts, and other common tasks. We present this toolkit's capability to rapidly develop new computational tools by presenting an example application, Qurate, a graphical tool for manually curating isotopically labeled peptide quantitative events.
authors.affiliation: Molecular Diagnostics Program, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
authors.forename: Damon
authors.initials: D
authors.lastname: May
authors.forename: Wendy
authors.initials: W
authors.lastname: Law
authors.forename: Matt
authors.initials: M
authors.lastname: Fitzgibbon
authors.forename: Qiaojun
authors.initials: Q
authors.lastname: Fang
authors.forename: Martin
authors.initials: M
authors.lastname: McIntosh
mesh_terms: D002555:Cerebrospinal Fluid / Q000737:chemistry; D002556:Cerebrospinal Fluid Proteins / Q000737:chemistry; D002853:Chromatography, Liquid; D030562:Databases, Protein; D006801:Humans; D007553:Isotope Labeling; D013058:Mass Spectrometry; D010455:Peptides / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D012984:Software; D014584:User-Computer Interface
chemical_list: D002556:Cerebrospinal Fluid Proteins; D010455:Peptides