Meta-analysis defines principles for the design and analysis of co-fractionation mass spectrometry experiments

Michael A. Skinnider, Leonard J. Foster

Research output: Contribution to journalArticlepeer-review

31 Scopus citations

Abstract

Co-fractionation mass spectrometry (CF-MS) has emerged as a powerful technique for interactome mapping. However, there is little consensus on optimal strategies for the design of CF-MS experiments or their computational analysis. Here, we reanalyzed a total of 206 CF-MS experiments to generate a uniformly processed resource containing over 11 million measurements of protein abundance. We used this resource to benchmark experimental designs for CF-MS studies and systematically optimize computational approaches to network inference. We then applied this optimized methodology to reconstruct a draft-quality human interactome by CF-MS and predict over 700,000 protein–protein interactions across 27 eukaryotic species or clades. Our work defines new resources to illuminate proteome organization over evolutionary timescales and establishes best practices for the design and analysis of CF-MS studies.

Original languageEnglish (US)
Pages (from-to)806-815
Number of pages10
JournalNature Methods
Volume18
Issue number7
DOIs
StatePublished - Jul 2021
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Biochemistry
  • Biotechnology
  • Cell Biology

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