Methods, tools and current perspectives in proteogenomics

Kelly V. Ruggles, Karsten Krug, Xiaojing Wang, Karl R. Clauser, Jing Wang, Samuel H. Payne, David Fenyö, Bing Zhang, D. R. Mani

Research output: Contribution to journalReview articlepeer-review

110 Scopus citations


With combined technological advancements in highthroughput next-generation sequencing and deep mass spectrometry-based proteomics, proteogenomics, i.e. the integrative analysis of proteomic and genomic data, has emerged as a new research field. Early efforts in the field were focused on improving protein identification using sample-specific genomic and transcriptomic sequencing data. More recently, integrative analysis of quantitative measurements from genomic and proteomic studies have identified novel insights into gene expression regulation, cell signaling, and disease. Many methods and tools have been developed or adapted to enable an array of integrative proteogenomic approaches and in this article, we systematically classify published methods and tools into four major categories, (1) Sequence-centric proteogenomics; (2) Analysis of proteogenomic relationships; (3) Integrative modeling of proteogenomic data; and (4) Data sharing and visualization. We provide a comprehensive review of methods and available tools in each category and highlight their typical applications.

Original languageEnglish (US)
Pages (from-to)959-981
Number of pages23
JournalMolecular and Cellular Proteomics
Issue number6
StatePublished - Jun 2017
Externally publishedYes

ASJC Scopus subject areas

  • Analytical Chemistry
  • Molecular Biology
  • Biochemistry


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