title: Automated identification of SUMOylation sites using mass spectrometry and SUMmOn pattern recognition software.
abstract: Tandem mass spectrometry (MS/MS) allows for the rapid identification of many types of post-translational modifications (PTMs), especially those that can be detected by a diagnostic mass shift in one or more peptide fragment ions (for example, phosphorylation). But some PTMs (for example, SUMOs and other ubiquitin-like modifiers) themselves produce multiple fragment ions; combined with fragments from the modified target peptide, a complex overlapping fragmentation pattern is thus generated, which is uninterpretable by standard peptide sequencing software. Here we introduce SUMmOn, an automated pattern recognition tool that detects diagnostic PTM fragment ion series within complex MS/MS spectra, to identify modified peptides and modification sites within these peptides. Using SUMmOn, we demonstrate for the first time that human SUMO-1 multimerizes in vitro primarily via three N-terminal lysines, Lys7, Lys16 and Lys17. Notably, our method is theoretically applicable to any type of modification or chemical moiety generating a unique fragment ion pattern.
authors.affiliation: Institute for Systems Biology, 1441 N. 34th Street, Seattle, Washington 98103, USA.
authors.forename: Patrick G A
authors.initials: PG
authors.lastname: Pedrioli
authors.forename: Brian
authors.initials: B
authors.lastname: Raught
authors.forename: Xiang-Dong
authors.initials: XD
authors.lastname: Zhang
authors.forename: Richard
authors.initials: R
authors.lastname: Rogers
authors.forename: John
authors.initials: J
authors.lastname: Aitchison
authors.forename: Michael
authors.initials: M
authors.lastname: Matunis
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001331:Automation / Q000379:methods*; D006801:Humans; D008239:Lysine / Q000737:chemistry* / Q000235:genetics*; D013058:Mass Spectrometry / Q000379:methods*; D008969:Molecular Sequence Data; D011499:Protein Processing, Post-Translational / Q000235:genetics*; D016415:Sequence Alignment; D025841:Small Ubiquitin-Related Modifier Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012984:Software
chemical_list: D025841:Small Ubiquitin-Related Modifier Proteins; D008239:Lysine