PXD020342

PXD020342 is an original dataset announced via ProteomeXchange.

Title	Automated capillary isoelectric focusing-tandem mass spectrometry for top-down proteomics
Description	Mass spectrometry (MS)-based top-down proteomics (TDP) delineates proteoforms in cells and requires high-resolution proteoform separation. Herein, for the first time, we employed an automated capillary isoelectric focusing-tandem MS (cIEF-MS/MS) system for large-scale TDP of complex proteomes. Single-shot cIEF-MS/MS identified 771 proteoforms from an Escherichia coli (E. coli) proteome consuming only nanograms of proteins. Coupling two-dimensional size exclusion chromatography (SEC)-cIEF, named “gel-free 2D-PAGE”, to ESI-MS/MS enabled the identification of nearly 2000 proteoforms from the E. coli proteome. Label-free quantitative TDP of zebrafish male and female brains using the SEC-cIEF-MS/MS quantified thousands of proteoforms and revealed sex-dependent proteoform profiles in brains. We discovered several proteolytic proteoforms of pro-opiomelanocortin and prodynorphin with significantly higher abundance in male brains as potential endogenous hormone proteoforms. Multi-level quantitative proteomic analyses (TDP and bottom-up proteomics (BUP)) of the brains revealed that majority of proteoforms having statistically significant difference in abundance between genders (TDP) showed no abundance difference at the corresponding protein group level (BUP), which highlights the importance of delineating proteins in a proteoform-specific manner for accurately understanding protein function.
HostingRepository	PRIDE
AnnounceDate	2020-12-08
AnnouncementXML	Submission_2020-12-08_12:19:47.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Liangliang Sun
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Danio rerio (Zebrafish) (Brachydanio rerio); NCBI TaxID: 7955;
ModificationList	monomethylated residue; TMT6plex-126 reporter+balance reagent acylated residue; phosphorylated residue; acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-07-13 17:43:48	ID requested
⏵ 1	2020-12-08 12:19:48	announced

Xu T, Shen X, Yang Z, Chen D, Lubeckyj RA, McCool EN, Sun L, Automated Capillary Isoelectric Focusing-Tandem Mass Spectrometry for Qualitative and Quantitative Top-Down Proteomics. Anal Chem, 92(24):15890-15898(2020) [pubmed]

submitter keyword: endogenous hormone proteoforms/gel-free 2D-PAGE/multi-level proteomics/ sexual dimorphism/zebrafish brain

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. PXD020342
     1. Label: PRIDE project
     2. Name: Automated capillary isoelectric focusing-tandem mass spectrometry for top-down proteomics