PXD021889

PXD021889 is an original dataset announced via ProteomeXchange.

Title	Capillary zone electrophoresis-tandem mass spectrometry as an alternative to liquid chromatography-tandem mass spectrometry for top-down proteomics of histones with the identification of over 1000 histone proteoforms
Description	Top-down proteomics (TDP) is an ideal approach for deciphering the histone code and it routinely employs reversed-phase liquid chromatography (RPLC)-tandem mass spectrometry (MS/MS). Here we present capillary zone electrophoresis (CZE)-MS/MS via the electro-kinetically pumped sheath-flow CE-MS interface for large-scale top-down delineation of histone proteoforms. CZE-MS/MS identified 80% more proteoforms than RPLC-MS/MS (589 vs. 322) from a calf histone sample with more than 30-fold less sample consumption (75-ng vs. 3 µg), indicating its substantially higher sensitivity. The electrophoretic mobility (µef) of unmodified histone proteoforms can be predicted accurately (R2=0.98) with an optimized semi-empirical model based on our recent work, and we revealed that N-terminal acetylation had minimal effect on histone proteoforms’ µef. We identified 1108 histone proteoforms from the calf histone sample using two-dimensional size-exclusion chromatography (SEC)-CZE-MS/MS with less than 300-ng proteins consumed. We achieved delineation of histone proteoforms regarding post-translational modifications (PTMs) and their combinations, relative abundance among different proteoforms of the same protein, as well as the frequency of PTM occurrence on histone proteoforms. We identified histone proteoforms carrying various PTMs, e.g., acetylation, methylation (mono-, di-, and tri-), phosphorylation, and succinylation. We revealed that different histone proteins had drastically different patterns of PTMs. The results render CZE-MS/MS as a useful tool for deciphering the histone code in a proteoform-specific manner and on a global scale.
HostingRepository	PRIDE
AnnounceDate	2022-05-25
AnnouncementXML	Submission_2022-05-25_09:09:54.895.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Liangliang Sun
SpeciesList	scientific name: Bos taurus (Bovine); NCBI TaxID: 9913;
ModificationList	phosphorylated residue; acetylated residue; monohydroxylated residue; deamidated residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-10-08 01:02:46	ID requested
⏵ 1	2022-05-25 09:09:57	announced

Chen D, Yang Z, Shen X, Sun L, Capillary Zone Electrophoresis-Tandem Mass Spectrometry As an Alternative to Liquid Chromatography-Tandem Mass Spectrometry for Top-down Proteomics of Histones. Anal Chem, 93(10):4417-4424(2021) [pubmed]

submitter keyword: intact histone proteoforms/mobility prediction/top-down proteomics/ histone postlational modifications/calf histone

Liangliang Sun
contact affiliation	Michigan State University
contact email	lsun@chemistry.msu.edu
lab head
Liangliang Sun
contact affiliation	Michigan State University
contact email	lsun@chemistry.msu.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD021889
     1. Label: PRIDE project
     2. Name: Capillary zone electrophoresis-tandem mass spectrometry as an alternative to liquid chromatography-tandem mass spectrometry for top-down proteomics of histones with the identification of over 1000 histone proteoforms