title: The first pilot project of the consortium for top-down proteomics: a status report.
abstract: 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.
authors.affiliation: 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.
authors.forename: Xibei
authors.initials: X
authors.lastname: Dang
authors.forename: Jenna
authors.initials: J
authors.lastname: Scotcher
authors.forename: Si
authors.initials: S
authors.lastname: Wu
authors.forename: Rosalie K
authors.initials: RK
authors.lastname: Chu
authors.forename: Nikola
authors.initials: N
authors.lastname: Tolić
authors.forename: Ioanna
authors.initials: I
authors.lastname: Ntai
authors.forename: Paul M
authors.initials: PM
authors.lastname: Thomas
authors.forename: Ryan T
authors.initials: RT
authors.lastname: Fellers
authors.forename: Bryan P
authors.initials: BP
authors.lastname: Early
authors.forename: Yupeng
authors.initials: Y
authors.lastname: Zheng
authors.forename: Kenneth R
authors.initials: KR
authors.lastname: Durbin
authors.forename: Richard D
authors.initials: RD
authors.lastname: Leduc
authors.forename: Jeremy J
authors.initials: JJ
authors.lastname: Wolff
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Thompson
authors.forename: Jingxi
authors.initials: J
authors.lastname: Pan
authors.forename: Jun
authors.initials: J
authors.lastname: Han
authors.forename: Jared B
authors.initials: JB
authors.lastname: Shaw
authors.forename: Joseph P
authors.initials: JP
authors.lastname: Salisbury
authors.forename: Michael
authors.initials: M
authors.lastname: Easterling
authors.forename: Christoph H
authors.initials: CH
authors.lastname: Borchers
authors.forename: Jennifer S
authors.initials: JS
authors.lastname: Brodbelt
authors.forename: Jeffery N
authors.initials: JN
authors.lastname: Agar
authors.forename: Ljiljana
authors.initials: L
authors.lastname: Paša-Tolić
authors.forename: Neil L
authors.initials: NL
authors.lastname: Kelleher
authors.forename: Nicolas L
authors.initials: NL
authors.lastname: Young
mesh_terms: D002853:Chromatography, Liquid / Q000379:methods; D016000:Cluster Analysis; D006367:HeLa Cells; D006657:Histones / Q000032:analysis / Q000737:chemistry; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods; D010865:Pilot Projects; D011499:Protein Processing, Post-Translational; D040901:Proteomics / Q000379:methods*; D012984:Software
chemical_list: D006657:Histones
keywords: Human histone H4; PTM analysis; Technology; Top-down proteomics