title: PTMeta: increasing identification rates of modified peptides using modification prescanning and meta-analysis.
abstract: 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.
authors: Quantitative Biology Center, University of Tuebingen, Tuebingen, Germany. sven.nahnsen@uni-tuebingen.de
authors: Sven
authors: S
authors: Nahnsen
authors: Timo
authors: T
authors: Sachsenberg
authors: Oliver
authors: O
authors: Kohlbacher
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D029968:Escherichia coli Proteins / Q000737:chemistry; D006801:Humans; D015201:Meta-Analysis as Topic; D008970:Molecular Weight; D010446:Peptide Fragments / Q000737:chemistry*; D010449:Peptide Mapping / Q000379:methods*; D011499:Protein Processing, Post-Translational; D020543:Proteome / Q000737:chemistry; D057386:Search Engine; D012984:Software
chemical_list: D029968:Escherichia coli Proteins; D010446:Peptide Fragments; D020543:Proteome