Mass spectrometry-based protein identification in proteomics—a review

Zainab Noor, Seong Beom Ahn, Mark S. Baker, Shoba Ranganathan, Abidali Mohamedali*

*Corresponding author for this work

Research output: Contribution to journalReview articlepeer-review

43 Citations (Scopus)


Statistically, accurate protein identification is a fundamental cornerstone of proteomics and underpins the understanding and application of this technology across all elements of medicine and biology. Proteomics, as a branch of biochemistry, has in recent years played a pivotal role in extending and developing the science of accurately identifying the biology and interactions of groups of proteins or proteomes. Proteomics has primarily used mass spectrometry (MS)-based techniques for identifying proteins, although other techniques including affinity-based identifications still play significant roles. Here, we outline the basics of MS to understand how data are generated and parameters used to inform computational tools used in protein identification. We then outline a comprehensive analysis of the bioinformatics and computational methodologies used in protein identification in proteomics including discussing the most current communally acceptable metrics to validate any identification.

Original languageEnglish
Pages (from-to)1620-1638
Number of pages19
JournalBriefings in Bioinformatics
Issue number2
Publication statusPublished - 22 Mar 2021


  • bioinformatics tools
  • mass spectrometry
  • protein characterization
  • protein identification
  • proteome
  • proteomics


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