Common errors in mass spectrometry-based analysis of post-translational modifications

Min Sik Kim, Jun Zhong, Akhilesh Pandey

Research output: Contribution to journalReview article

38 Scopus citations

Abstract

Mass spectrometry (MS) is a powerful tool to analyze complex mixtures of proteins in a high-throughput fashion. Proteome analysis has already become a routine task in biomedical research with the emergence of proteomics core facilities in most research institutions. Post-translational modifications (PTMs) represent a mechanism by which complex biological processes are orchestrated dynamically at the systems level. MS is rapidly becoming popular to discover new modifications and novel sites of known PTMs, revolutionizing the current understanding of diverse signaling pathways and biological processes. However, MS-based analysis of PTMs has its own caveats and pitfalls that can lead to erroneous conclusions. Here, we review the most common errors in MS-based PTM analyses with the goal of adopting strategies that maximize correct interpretation in the context of biological questions that are being addressed. Finally, we provide suggestions that should help mass spectrometrists, bioinformaticians and biologists to perform and interpret MS-based PTM analyses more accurately.

Original languageEnglish (US)
Pages (from-to)700-714
Number of pages15
JournalProteomics
Volume16
Issue number5
DOIs
StatePublished - Mar 1 2016
Externally publishedYes

Keywords

  • Immonium
  • Localization
  • PTM
  • Signature
  • SUMO
  • Technology
  • Ubiquitin

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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