A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS.
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/.
Bellew
Matthew
M
LabKey Software, Seattle, WA 98109, USA.
Coram
Marc
M
Fitzgibbon
Matthew
M
Igra
Mark
M
Randolph
Tim
T
Wang
Pei
P
May
Damon
D
Eng
Jimmy
J
Fang
Ruihua
R
Lin
Chenwei
C
Chen
Jinzhi
J
Goodlett
David
D
Whiteaker
Jeffrey
J
Paulovich
Amanda
A
McIntosh
Martin
M
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
D045424:Complex Mixtures; D011506:Proteins