Nature Methods 3, 533 - 539 (2006)
Published online: 21 June 2006; | doi:10.1038/nmeth891
Automated identification of SUMOylation sites using mass spectrometry and SUMmOn pattern recognition softwarePatrick G A Pedrioli1, 5, Brian Raught2, 5, Xiang-Dong Zhang3, Richard Rogers1, John Aitchison1, Michael Matunis3
& Ruedi Aebersold1, 41
Institute for Systems Biology, 1441 N. 34th Street, Seattle, Washington 98103, USA. 2
University Health Network, Ontario Cancer Institute and McLaughlin Centre for Molecular Medicine, MaRS TMDT 9-805, 101 College Street, Toronto, Ontario M5G 1L7, Canada. 3
Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Maryland 21205, USA. 4
Institute for Molecular Systems Biology, Swiss Federal Institute of Technology, ETH Hönggerberg HPT E 78, CH-8093 Zürich, Switzerland and Faculty of Natural Sciences, University of Zurich, Switzerland. 5
These authors contributed equally to this work.
Correspondence should be addressed to Brian Raught brian.raught@uhnres.utoronto.ca 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.
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