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Title: The first pilot project of the consortium for top-down proteomics: A status report

Pilot Project #1—the identification and characterization of human histone H4 proteoforms by top-down MS—is the first project launched by the Consortium for Top-Down Proteomics (CTDP) to refine and validate top-down MS. Within the initial results from seven participating laboratories, all reported the probability-based identification of human histone H4 (UniProt accession P62805) with expectation values ranging from 10-13 to 10-105. Regarding characterization, a total of 74 proteoforms were reported, with 21 done so unambiguously; one new PTM, K79ac, was identified. Inter-laboratory comparison reveals aspects of the results that are consistent, such as the localization of individual PTMs and binary combinations, while other aspects are more variable, such as the accurate characterization of low-abundance proteoforms harboring >2 PTMs. An open-access tool and discussion of proteoform scoring are included, along with a description of general challenges that lie ahead including improved proteoform separations prior to mass spectrometric analysis, better instrumentation performance, and software development.
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  1. Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee FL USA; Department of Chemistry and Biochemistry, Florida State University, Tallahassee FL USA
  2. Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee FL USA
  3. Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland WA USA
  4. Departments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston IL USA
  5. NIH/NCRR Mass Spectrometry Resource, Washington University in St. Louis, St. Louis MO USA
  6. Bruker Daltonics, Billerica MA USA
  7. UVic-Genome BC Proteomics Centre, Department of Biochemistry and Microbiology, University of Victoria, Victoria BC Canada
  8. Department of Chemistry, University of Texas, Austin TX USA
  9. Departments of Chemistry and Pharm. Sci., Barnett Institute, Northeastern University, Boston MA USA
Publication Date:
OSTI Identifier:
Report Number(s):
Journal ID: ISSN 1615-9853; 48211; KP1704020
DOE Contract Number:
Resource Type:
Journal Article
Resource Relation:
Journal Name: Proteomics; Journal Volume: 14; Journal Issue: 10
Research Org:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org:
Country of Publication:
United States
59 BASIC BIOLOGICAL SCIENCES Environmental Molecular Sciences Laboratory