Open AccessA uniform proteomics MS/MS analysis platform utilizing open XML file formats
Author(s) -
Keller Andrew,
Eng Jimmy,
Zhang Ning,
Li Xiaojun,
Aebersold Ruedi
Publication year - 2005
Publication title -
molecular systems biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 8.523
H-Index - 148
ISSN - 1744-4292
DOI - 10.1038/msb4100024
Subject(s) - computer science , file format , pipeline (software) , mascot , xml , proteomics , mass spectrometry , tandem mass spectrometry , database , raw data , identification (biology) , peptide , computational biology , data mining , biology , operating system , chemistry , chromatography , programming language , biochemistry , botany , political science , law , gene
The analysis of tandem mass (MS/MS) data to identify and quantify proteins is hampered by the heterogeneity of file formats at the raw spectral data, peptide identification, and protein identification levels. Different mass spectrometers output their raw spectral data in a variety of proprietary formats, and alternative methods that assign peptides to MS/MS spectra and infer protein identifications from those peptide assignments each write their results in different formats. Here we describe an MS/MS analysis platform, the Trans‐Proteomic Pipeline, which makes use of open XML file formats for storage of data at the raw spectral data, peptide, and protein levels. This platform enables uniform analysis and exchange of MS/MS data generated from a variety of different instruments, and assigned peptides using a variety of different database search programs. We demonstrate this by applying the pipeline to data sets generated by ThermoFinnigan LCQ, ABI 4700 MALDI‐TOF/TOF, and Waters Q‐TOF instruments, and searched in turn using SEQUEST, Mascot, and COMET.