Automated identification of SUMOylation sites using mass spectrometry and SUMmOn pattern recognition software

Patrick G A Pedrioli, Brian Raught, Xiang Dong Zhang, Richard Rogers, John Aitchison, Michael J Matunis, Ruedi Aebersold

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)533-539
Number of pages7
JournalNature Methods
Volume3
Issue number7
DOIs
StatePublished - Jul 2006

Fingerprint

Sumoylation
Mass Spectrometry
Software
Post Translational Protein Processing
Ions
Peptides
Automated Pattern Recognition
Peptide Fragments
Ubiquitin
Tandem Mass Spectrometry
Lysine
Phosphorylation

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Biology
  • Cell Biology

Cite this

Pedrioli, P. G. A., Raught, B., Zhang, X. D., Rogers, R., Aitchison, J., Matunis, M. J., & Aebersold, R. (2006). Automated identification of SUMOylation sites using mass spectrometry and SUMmOn pattern recognition software. Nature Methods, 3(7), 533-539. https://doi.org/10.1038/nmeth891

Automated identification of SUMOylation sites using mass spectrometry and SUMmOn pattern recognition software. / Pedrioli, Patrick G A; Raught, Brian; Zhang, Xiang Dong; Rogers, Richard; Aitchison, John; Matunis, Michael J; Aebersold, Ruedi.

In: Nature Methods, Vol. 3, No. 7, 07.2006, p. 533-539.

Research output: Contribution to journalArticle

Pedrioli, PGA, Raught, B, Zhang, XD, Rogers, R, Aitchison, J, Matunis, MJ & Aebersold, R 2006, 'Automated identification of SUMOylation sites using mass spectrometry and SUMmOn pattern recognition software', Nature Methods, vol. 3, no. 7, pp. 533-539. https://doi.org/10.1038/nmeth891
Pedrioli, Patrick G A ; Raught, Brian ; Zhang, Xiang Dong ; Rogers, Richard ; Aitchison, John ; Matunis, Michael J ; Aebersold, Ruedi. / Automated identification of SUMOylation sites using mass spectrometry and SUMmOn pattern recognition software. In: Nature Methods. 2006 ; Vol. 3, No. 7. pp. 533-539.
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