title: A large synthetic peptide and phosphopeptide reference library for mass spectrometry-based proteomics.
abstract: We present a peptide library and data resource of >100,000 synthetic, unmodified peptides and their phosphorylated counterparts with known sequences and phosphorylation sites. Analysis of the library by mass spectrometry yielded a data set that we used to evaluate the merits of different search engines (Mascot and Andromeda) and fragmentation methods (beam-type collision-induced dissociation (HCD) and electron transfer dissociation (ETD)) for peptide identification. We also compared the sensitivities and accuracies of phosphorylation-site localization tools (Mascot Delta Score, PTM score and phosphoRS), and we characterized the chromatographic behavior of peptides in the library. We found that HCD identified more peptides and phosphopeptides than did ETD, that phosphopeptides generally eluted later from reversed-phase columns and were easier to identify than unmodified peptides and that current computational tools for proteomics can still be substantially improved. These peptides and spectra will facilitate the development, evaluation and improvement of experimental and computational proteomic strategies, such as separation techniques and the prediction of retention times and fragmentation patterns.
authors.affiliation: Technische Universität München, Freising, Germany.
authors.forename: Harald
authors.initials: H
authors.lastname: Marx
authors.forename: Simone
authors.initials: S
authors.lastname: Lemeer
authors.forename: Jan Erik
authors.initials: JE
authors.lastname: Schliep
authors.forename: Lucrece
authors.initials: L
authors.lastname: Matheron
authors.forename: Shabaz
authors.initials: S
authors.lastname: Mohammed
authors.forename: Jürgen
authors.initials: J
authors.lastname: Cox
authors.forename: Matthias
authors.initials: M
authors.lastname: Mann
authors.forename: Albert J R
authors.initials: AJ
authors.lastname: Heck
authors.forename: Bernhard
authors.initials: B
authors.lastname: Kuster
mesh_terms: D000465:Algorithms; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D019151:Peptide Library; D010455:Peptides / Q000138:chemical synthesis / Q000235:genetics*; D010748:Phosphopeptides / Q000138:chemical synthesis / Q000235:genetics*; D010766:Phosphorylation; D040901:Proteomics / Q000379:methods* / Q000592:standards; D012015:Reference Standards; D012984:Software
chemical_list: D019151:Peptide Library; D010455:Peptides; D010748:Phosphopeptides