PXD000994

PXD000994 is an original dataset announced via ProteomeXchange.

Title	TurboRAW2MGF: Removing isobaric-related ions improves the peptide/protein identification
Description	Isobaric labelling technique coupled with high resolution mass spectrometry has been widely employed in the proteomics workflows requiring relative quantification. For each high resolution tandem mass spectrum (MS/MS), it can be used not only to quantify the peptide from different samples by reporter ions，but also to identify the peptide it derived from. Since isobaric related ions act as noises in database searching, the MS/MS spectrum should be preprocessed before peptide/protein identification. In this paper, we demonstrated that there were a lot of high frequency, high abundance isobaric related ions in MS/MS spectrum. By combining removing isobaric related ions with deisotoping and deconvolution in MS/MS preprocessing procedure, the peptide/protein identification sensitivity improved significantly. A user-friendly software TurboRaw2MGF (v2.0) has been implemented for converting raw TIC data files to mascot generic format files which can be downloaded for free from https://github.com/shengqh/RCPA.Tools/releases as part of the software suite ProteomicsTools.
HostingRepository	PRIDE
AnnounceDate	2015-01-30
AnnouncementXML	Submission_2015-01-30_06:23:39.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000994
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Quanhu Sheng
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116;
ModificationList	monohydroxylated residue; iTRAQ8plex-116 reporter+balance reagent acylated residue; iodoacetamide derivatized residue; iTRAQ4plex-116 reporter+balance reagent acylated residue; TMT6plex-126 reporter+balance reagent acylated residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2014-05-21 02:56:27	ID requested
⏵ 1	2015-01-30 06:23:40	announced

Sheng Q, Li R, Dai J, Li Q, Su Z, Guo Y, Li C, Shyr Y, Zeng R, Preprocessing significantly improves the peptide/protein identification sensitivity of high-resolution isobarically labeled tandem mass spectrometry data. Mol Cell Proteomics, 14(2):405-17(2015) [pubmed]

curator keyword: Biomedical

submitter keyword: isobaric labelling, iTRAQ, preprocessing, peptide identification, LTQ-Orbitrap

Quanhu Sheng
contact affiliation	Shanghai Institutes for Biological Sciences
contact email	qhsheng@sibs.ac.cn
lab head
Quanhu Sheng
contact affiliation	Vanderbilt University
contact email	shengqh@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD000994
     1. Label: PRIDE project
     2. Name: TurboRAW2MGF: Removing isobaric-related ions improves the peptide/protein identification