These authors contributed equally to this work.
PTMeta: Increasing identification rates of modified peptides using modification prescanning and meta-analysis
Article first published online: 11 MAR 2013
© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
Special Issue: Analysis of Post-translational Modifications
Volume 13, Issue 6, pages 1042–1051, March 2013
How to Cite
Nahnsen, S., Sachsenberg, T. and Kohlbacher, O. (2013), PTMeta: Increasing identification rates of modified peptides using modification prescanning and meta-analysis. Proteomics, 13: 1042–1051. doi: 10.1002/pmic.201200315
- Issue published online: 11 MAR 2013
- Article first published online: 11 MAR 2013
- Accepted manuscript online: 20 JAN 2013 04:19AM EST
- Manuscript Accepted: 9 JAN 2013
- Manuscript Revised: 6 DEC 2012
- Manuscript Received: 24 JUL 2012
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.