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

Xibei Dang, Jenna Scotcher, Si Wu, Rosalie K. Chu, Nikola Tolić, Ioanna Ntai, Paul M. Thomas, Ryan T. Fellers, Bryan P. Early, Yupeng Zheng, Kenneth R. Durbin, Richard D. Leduc, Jeremy J. Wolff, Christopher J. Thompson, Jingxi Pan, Jun Han, Jared B. Shaw, Joseph P. Salisbury, Michael Easterling, Christoph H. BorchersJennifer S. Brodbelt, Jeffery N. Agar, Ljiljana Paša-Tolić, Neil L. Kelleher, Nicolas L. Young*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

61 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)1130-1140
Number of pages11
Issue number10
StatePublished - May 2014


  • Human histone H4
  • PTM analysis
  • Technology
  • Top-down proteomics

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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