PXD038382

PXD038382 is an original dataset announced via ProteomeXchange.

Title	Enriching cysteine-containing peptides using a sulfhydryl-reactive alkylating reagent with a phosphonic acid group, and immobilized metal affinity chromatography
Description	The reduction of disulfide bonds and their subsequent alkylation is commonplace in typical proteomics workflows. Here, we highlight a sulfhydryl-reactive alkylating reagent with a phosphonic acid group (iodoacetamido-LC-phosphonic acid, 6C-CysPAT) that facilitates the enrichment of cysteine-containing peptides for isobaric tag-based proteome abundance profiling. Specifically, we profile the proteome of SH-SY5Y cells following 24 hr treatments with two proteasome inhibitors (bortezomib and MG-132) in a TMTpro9-plex experiment. We acquired three datasets - 1) Cys-enriched, 2) Cys-depleted, and 3) non-depleted - and compared the peptides and proteins quantified in each dataset, with emphasis on Cys-containing peptides. The data show that enrichment using 6C-CysPAT quantified over 38,000 Cys-containing peptides in 5 hr with >90% specificity. In addition, our combined dataset provides the research community with a resource of over 9,900 protein abundance profiles that exhibit the effects of two different proteosome inhibitors. Overall, the seamless incorporation of alkylation by 6C-CysPAT into a current TMT-based workflow permits the enrichment of a Cys-containing peptide subproteome. The acquisition of this “Mini-Cys” dataset can be used to preview and assess the quality of a deep, fractionated dataset.
HostingRepository	PRIDE
AnnounceDate	2023-12-28
AnnouncementXML	Submission_2023-12-28_11:18:58.025.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joao Paulo
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2022-11-26 03:54:36	ID requested
⏵ 1	2023-12-28 11:18:58	announced

10.1021/acs.jproteome.2c00806;

Liu X, Rossio V, Gygi SP, Paulo JA, Enriching Cysteine-Containing Peptides Using a Sulfhydryl-Reactive Alkylating Reagent with a Phosphonic Acid Group and Immobilized Metal Affinity Chromatography. J Proteome Res, 22(4):1270-1279(2023) [pubmed]

submitter keyword: FAIMS, TMTpro,CysPAT, Fe3+-NTA, Orbitrap Eclipse, isobaric tagging

Joao A. Paulo
contact affiliation	Department of Cell Biology Harvard Medical School Boston, MA, USA
contact email	joao_paulo@post.harvard.edu
lab head
Joao Paulo
contact affiliation	Harvard Medical School
contact email	joao_paulo@post.harvard.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD038382
     1. Label: PRIDE project
     2. Name: Enriching cysteine-containing peptides using a sulfhydryl-reactive alkylating reagent with a phosphonic acid group, and immobilized metal affinity chromatography