Data analysis of assorted serum peptidome profiles Journal Article

  


Authors: Villanueva, J.; Philip, J.; DeNoyer, L.; Tempst, P.
Article Title: Data analysis of assorted serum peptidome profiles
Abstract: Discovery of biomarker patterns using proteomic techniques requires examination of large numbers of patient and control samples, followed by data mining of the molecular read-outs (e.g., mass spectra). Adequate signal processing and statistical analysis are critical for successful extraction of markers from these data sets. The protocol, specifically designed for use in conjunction with MALDI-TOF-MS-based serum peptide profiling, is a data analysis pipeline, starting with transfer of raw spectra that are interpreted using signal processing algorithms to define suitable features (i.e., peptides). We describe an algorithm for minimal entropy-based peak alignment across samples. Peak lists obtained in this way, and containing all samples, all peptide features and their normalized MS-ion intensities, can be evaluated, and results validated, using common statistical methods. We recommend visual inspection of the spectra to confirm all results, and have written freely available software for viewing and color-coding of spectral overlays.
Keywords: methodology; mass spectrometry; biological marker; biological markers; blood proteins; bayes theorem; gene expression profiling; validation study; peptide; algorithms; information processing; proteomics; statistical analysis; data interpretation, statistical; algorithm; data analysis; matrix assisted laser desorption ionization time of flight mass spectrometry; computer program; liquid chromatography; signal processing; mathematical computing; analytical error; plasma protein; sample size; spectrometry, mass, matrix-assisted laser desorption-ionization; peptide analysis; principal component analysis; electrospray mass spectrometry; entropy; data mining
Journal Title: Nature Protocols
Volume: 2
Issue: 3
ISSN: 1754-2189
Publisher: Nature Publishing Group  
Date Published: 2007-03-01
Start Page: 588
End Page: 602
Language: English
DOI: 10.1038/nprot.2007.57
PUBMED: 17406620
PROVIDER: scopus
DOI/URL:

http://www.scopus.com/inward/record.url?eid=2-s2.0-34347266569&partnerID=40&md5=b8554ff5be0063f9b41403958b9c040f
Notes: --- - "Cited By (since 1996): 17" - "Export Date: 17 November 2011" - "Source: Scopus"
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MSK Authors
  1. Jose Villanueva
    24 Villanueva
  2. Paul J Tempst
    324 Tempst
  3. John Philip
    48 Philip
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