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.

journal_name

Nat Protoc

journal_title

Nature protocols

authors

Villanueva J,Philip J,DeNoyer L,Tempst P

doi

10.1038/nprot.2007.57

subject

Has Abstract

pub_date

2007-01-01 00:00:00

pages

588-602

issue

3

eissn

1754-2189

issn

1750-2799

pii

nprot.2007.57

journal_volume

2

pub_type

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