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PTMeta: Increasing identification rates of modified peptides using modification prescanning and meta‐analysis
Author(s) -
Nahnsen Sven,
Sachsenberg Timo,
Kohlbacher Oliver
Publication year - 2013
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.201200315
Subject(s) - proteome , computational biology , pipeline (software) , database search engine , tandem mass spectrometry , computer science , posttranslational modification , chemistry , proteomics , identification (biology) , mass spectrometry , bioinformatics , biology , biochemistry , chromatography , search engine , information retrieval , programming language , enzyme , botany , gene
The analysis of peptides and proteins in complex biological systems has greatly improved over the last decade. State‐of‐the‐art mass spectrometric instruments combined with adequate software tools allow for more and more comprehensive proteome analyses. Most proteome‐wide studies focus on the analysis of unmodified proteins or look at selected modifications only. However, spectral information of protein modifications, chemically induced through sample preparation or post‐translationally attached in biological pathways is acquired as a significant, yet disregarded, fraction of tandem spectra in most discovery studies. We present a new computational pipeline, PTMeta, to uncover information of modifications attached to peptides. We use modification prescanning to pinpoint the most abundant potential modifications, followed by extensive database search and a statistical framework to combine results from database search runs with different modification settings.