articleNature CommunicationsJan 21, 2026GOLD OA

Community benchmarking and evaluation of human unannotated microprotein detection by mass spectrometry based proteomics

AWAaron WacholderEWEric W. DeutschLWLeron W. KokJTJip T. van DinterJLJiwon Lee

University of Pittsburgh · Institute for Systems Biology · +25 more institutions

PubMed
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Abstract

Thousands of short open reading frames (sORFs) are translated outside of annotated coding sequences. Recent studies have pioneered searching for sORF-encoded microproteins in mass spectrometry (MS)-based proteomics and peptidomics datasets. Here, we assessed literature-reported MS-based identifications of unannotated human proteins. We find that studies vary by three orders of magnitude in the number of unannotated proteins they report. Of nearly 10,000 reported sORF-encoded peptides, 96% were unique to a single study, and 12% mapped to annotated proteins or proteoforms. Manual curation of a benchmark dataset of 406 manually evaluated spectra from 204 sORF-encoded proteins revealed large variation in…

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Topics
Keywords
  • Proteomics
  • Benchmarking
  • Workflow
  • Benchmark (surveying)
  • Quantitative proteomics
  • Protein methods
UN Sustainable Development Goals
  • Quality Education
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