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PXD000274

PXD000274 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleRedox proteomics in NO-mediated protection on hypoxic cardiomyocyte
DescriptionWe developed a mass spectrometry (MS)-based quantitative approach using a set of novel iodoacetyl-based cysteine-reactive isobaric tags (iodoTMT) endowed with unique irreversible Cys-reactivities to differentially quantify the multiple redox-modified forms of a Cys site in the original cellular context. The established method was than applied to map global Cys-redoxomic regulation in NO-mediated ischemic cardioprotection. Upon cell lysis, iodoacetamide was first added to the cell lysates to block free thiols. Reversible Cys modifications were then selectively reduced and labeled by different isobaric sets of iodoTMT. After tryptic digestion, the iodoTMT-labeled peptides were immuno-enriched, and analyzed by LTQ-Orbitrap Velos (Thermo Fisher Scientific) coupled with nanoACQUITY (Waters). All MS and MS/MS raw data were processed with Proteome Discoverer version 1.3 (Thermo Fisher Scientific), and the peptides were identified from the MS/MS spectra searched against the UniProtKB/Swiss-Prot database using the Mascot 2.3.02 (Matrix Science) with the following constraints: only tryptic peptides with up to two missed cleavage sites; taxonomy: Rattus; and mass accuracy of 10 ppm for the parent ion and 0.05 Da for the fragment ions. iodoTMT labeled (C), carbamidomethyl (C), deamidation (NQ), oxidation (M), and acetyl (protein N-term) were specified as dynamic modifications. False discovery rates were calculated by target-decoy strategy with or without using Mascot Percolator. All peptide hits were filtered with a 1% FDR cutoff.
HostingRepositoryPRIDE
AnnounceDate2024-10-07
AnnouncementXMLSubmission_2024-10-07_08:56:54.479.xml
DigitalObjectIdentifierhttps://dx.doi.org/10.6019/PXD000274
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterKuan-Ting Pan
SpeciesList scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116;
ModificationListacetylated residue; monohydroxylated residue; iodoacetamide derivatized residue; adenylated residue; deamidated residue
InstrumentLTQ Orbitrap Velos Pro
Dataset History
RevisionDatetimeStatusChangeLog Entry
02013-05-31 02:32:08ID requested
12016-06-27 07:57:12announced
22024-10-07 08:56:59announced2024-10-07: Updated project metadata.
Publication List
10.6019/PXD000274;
10.1089/ars.2013.5326;
Pan KT, Chen YY, Pu TH, Chao YS, Yang CY, Bomgarden RD, Rogers JC, Meng TC, Khoo KH, Mass spectrometry-based quantitative proteomics for dissecting multiplexed redox cysteine modifications in nitric oxide-protected cardiomyocyte under hypoxia. Antioxid Redox Signal, 20(9):1365-81(2014) [pubmed]
Keyword List
curator keyword: Technical, Biological, Biomedical
submitter keyword: S-nitrosylation, mass spectrometry, hypoxia, redox cysteine modifications,Redox-proteomics
Contact List
Kay-Hooi Khoo
contact affiliationInstitute of Biological Chemistry, Academia Sinica, Taiwan
contact emailkkhoo@gate.sinica.edu.tw
lab head
Kuan-Ting Pan
contact affiliationInstitute of Biological Chemistry
contact emailkuanting@gate.sinica.edu.tw
dataset submitter
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Dataset FTP location
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PRIDE project URI
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