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Sven Nahnsen, Timo Sachsenberg, and Oliver Kohlbacher (2013)

PTMeta: Increasing Identification Rates of Modified Peptides Using Modification Pre-scanning and Meta-analysis

Proteomics, 13(6):1042-51.

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 pre-scanning 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.
23335442
10.1002/pmic.201200315