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A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS.

Author information

Affiliations

  • 1. LabKey Software, Seattle, WA 98109, USA.
      Authors
    • Bellew M 1
    (1 author)

ORCIDs linked to this article

Bioinformatics (Oxford, England), 09 Jun 2006, 22(15):1902-1909
https://doi.org/10.1093/bioinformatics/btl276 PMID: 16766559 

Abstract 

Motivation

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.

Availability

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/.

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Read article at publisher's site: https://doi.org/10.1093/bioinformatics/btl276

Read article for free, from open access legal sources, via Unpaywall: https://academic.oup.com/bioinformatics/article-pdf/22/15/1902/670089/btl276.pdfUnpaywall

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