The First Pilot Project of the Consortium for Top-down Proteomics: a Status Report

Overview

Journal Proteomics

Date 2014 Mar 20

PMID 24644084

Citations 48

Authors

Xibei Dang

Jenna Scotcher

Si Wu

Rosalie K Chu

Nikola Tolic

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 Borchers

Jennifer S Brodbelt

Jeffery N Agar

Ljiljana Pasa-Tolic

Neil L Kelleher

Nicolas L Young

Affiliations

Soon will be listed here.

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.

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