title: A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS.
abstract: BACKGROUND
  Comparing two or more complex protein mixtures using liquid chromatography mass spectrometry (LC-MS) requires multiple analysis steps to locate and quantitate natural peptides within a single experiment and to align and normalize findings across multiple experiments.
  
  
  RESULTS
  We describe msInspect, an open-source application comprising algorithms and visualization tools for the analysis of multiple LC-MS experimental measurements. The platform integrates novel algorithms for detecting signatures of natural peptides within a single LC-MS measurement and combines multiple experimental measurements into a peptide array, which may then be mined using analysis tools traditionally applied to genomic array analysis. The platform supports quantitation by both label-free and isotopic labeling approaches. The software implementation has been designed so that many key components may be easily replaced, making it useful as a workbench for integrating other novel algorithms developed by a growing research community.
  
  
  BACKGROUND
  The msInspect software is distributed freely under an Apache 2.0 license. The software as well as a Zip file with all peptide feature files and scripts needed to generate the tables and figures in this article are available at http://proteomics.fhcrc.org/.
authors.affiliation: LabKey Software, Seattle, WA 98109, USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: Bellew
authors.forename: Marc
authors.initials: M
authors.lastname: Coram
authors.forename: Matthew
authors.initials: M
authors.lastname: Fitzgibbon
authors.forename: Mark
authors.initials: M
authors.lastname: Igra
authors.forename: Tim
authors.initials: T
authors.lastname: Randolph
authors.forename: Pei
authors.initials: P
authors.lastname: Wang
authors.forename: Damon
authors.initials: D
authors.lastname: May
authors.forename: Jimmy
authors.initials: J
authors.lastname: Eng
authors.forename: Ruihua
authors.initials: R
authors.lastname: Fang
authors.forename: Chenwei
authors.initials: C
authors.lastname: Lin
authors.forename: Jinzhi
authors.initials: J
authors.lastname: Chen
authors.forename: David
authors.initials: D
authors.lastname: Goodlett
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Whiteaker
authors.forename: Amanda
authors.initials: A
authors.lastname: Paulovich
authors.forename: Martin
authors.initials: M
authors.lastname: McIntosh
mesh_terms: D000465:Algorithms; D002853:Chromatography, Liquid / Q000379:methods*; D045424:Complex Mixtures / Q000032:analysis; D003196:Computer Graphics; D013058:Mass Spectrometry / Q000379:methods*; D010449:Peptide Mapping / Q000379:methods*; D011506:Proteins / Q000032:analysis* / Q000737:chemistry*; D012984:Software; D018511:Systems Integration; D014584:User-Computer Interface
chemical_list: D045424:Complex Mixtures; D011506:Proteins