PXD000274

PXD000274 is an original dataset announced via ProteomeXchange.

Title	Redox proteomics in NO-mediated protection on hypoxic cardiomyocyte
Description	We 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.
HostingRepository	PRIDE
AnnounceDate	2024-10-07
AnnouncementXML	Submission_2024-10-07_08:56:54.479.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000274
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Kuan-Ting Pan
SpeciesList	scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue; adenylated residue; deamidated residue
Instrument	LTQ Orbitrap Velos Pro

Revision	Datetime	Status	ChangeLog Entry
0	2013-05-31 02:32:08	ID requested
1	2016-06-27 07:57:12	announced
⏵ 2	2024-10-07 08:56:59	announced	2024-10-07: Updated project metadata.

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]

curator keyword: Technical, Biological, Biomedical

submitter keyword: S-nitrosylation, mass spectrometry, hypoxia, redox cysteine modifications,Redox-proteomics

Kay-Hooi Khoo
contact affiliation	Institute of Biological Chemistry, Academia Sinica, Taiwan
contact email	kkhoo@gate.sinica.edu.tw
lab head
Kuan-Ting Pan
contact affiliation	Institute of Biological Chemistry
contact email	kuanting@gate.sinica.edu.tw
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD000274

PRIDE project URI

• PRIDE
  1. PXD000274
     1. Label: PRIDE project
     2. Name: Redox proteomics in NO-mediated protection on hypoxic cardiomyocyte