title: Resources for Assignment of Phosphorylation Sites on Peptides and Proteins.
abstract: Reversible protein phosphorylation is a key regulatory posttranslational modification that plays a significant role in major cellular signaling processes. Phosphorylation events can be systematically identified, quantified, and localized on protein sequence using publicly available bioinformatic tools. Here we present the software tools commonly used by the phosphoproteomics community, discuss their underlying principles of operation, and provide a protocol for large-scale phosphoproteome data analysis using the MaxQuant software suite.
authors.affiliation: Proteome Center Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany.
authors.forename: Vaishnavi
authors.initials: V
authors.lastname: Ravikumar
authors.affiliation: Proteome Center Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany. boris.macek@uni-tuebingen.de.
authors.forename: Boris
authors.initials: B
authors.lastname: Macek
authors.affiliation: Department of Systems and Synthetic Biology, Chalmers University of Technology, Kemivägen 10, 412 96, Göteborg, Sweden. ivan.mijakovic@chalmers.se.
authors.forename: Ivan
authors.initials: I
authors.lastname: Mijakovic
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology; D030562:Databases, Protein; D006801:Humans; D010748:Phosphopeptides / Q000737:chemistry* / Q000378:metabolism; D010750:Phosphoproteins / Q000737:chemistry* / Q000378:metabolism; D010766:Phosphorylation; D011499:Protein Processing, Post-Translational; D040901:Proteomics / Q000379:methods*; D012984:Software; D057188:Workflow
chemical_list: D010748:Phosphopeptides; D010750:Phosphoproteins
keywords: Bioinformatics; MaxQuant; Phosphorylation site identification