An overview of technologies for MS-based proteomics-centric multi-omics

Andrew T. Rajczewski, Pratik D. Jagtap, Timothy J. Griffin

Research output: Contribution to journalReview articlepeer-review

6 Scopus citations


Introduction: Mass spectrometry-based proteomics reveals dynamic molecular signatures underlying phenotypes reflecting normal and perturbed conditions in living systems. Although valuable on its own, the proteome has only one level of moleclar information, with the genome, epigenome, transcriptome, and metabolome, all providing complementary information. Multi-omic analysis integrating information from one or more of these other domains with proteomic information provides a more complete picture of molecular contributors to dynamic biological systems. Areas Covered: Here, we discuss the improvements to mass spectrometry-based technologies, focused on peptide-based, bottom-up approaches that have enabled deep, quantitative characterization of complex proteomes. These advances are facilitating the integration of proteomics data with other ‘omic information, providing a more complete picture of living systems. We also describe the current state of bioinformatics software and approaches for integrating proteomics and other ‘omics data, critical for enabling new discoveries driven by multi-omics. Expert Commentary: Multi-omics, centered on the integration of proteomics information with other ‘omic information, has tremendous promise for biological and biomedical studies. Continued advances in approaches for generating deep, reliable proteomic data and bioinformatics tools aimed at integrating data across ‘omic domains will ensure the discoveries offered by these multi-omic studies continue to increase.

Original languageEnglish (US)
Pages (from-to)165-181
Number of pages17
JournalExpert Review of Proteomics
Issue number3
StatePublished - 2022

Bibliographical note

Funding Information:
Support for this work was provided from the National Cancer Institute’s Informatics Technology for Cancer Research (ITCR) grant 1U24CA199347 awarded to T.J.G.; A.T.R. was supported by Biotechnology Training Grant T32GM008347 from the National Institute of General Medical Sciences, an operating division of the National Institutes of Health.

Publisher Copyright:
© 2022 Informa UK Limited, trading as Taylor & Francis Group.


  • bioinformatics
  • bottom-up proteomics
  • Mass spectrometry
  • multi-omics
  • proteogenomics

PubMed: MeSH publication types

  • Journal Article
  • Research Support, N.I.H., Extramural


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