PXD012744

PXD012744 is an original dataset announced via ProteomeXchange.

Title	DIA data analysis with unambiguously determined precursor mass
Description	Proteomics research today no longer simply seeks exhaustive protein identification; now, robust, large-scale quantitative information is sought. For this purpose, data-independent acquisition (DIA) has emerged as a promising strategy largely owing to the developments in advanced mass spectrometers and sophisticated data analysis methods. However, the highly complex multiplexed MS/MS spectra produced by DIA remain challenging to interpret. Here, we present a novel strategy to analyze DIA data, based on unambiguous precursor mass assignment through the mPE-MMR (multiplexed post-experimental monoisotopic mass refinement) procedure, and combined with complementary multi-stage database searching. Compared to conventional spectral library searching, the accuracy and sensitivity of peptide identification were effectively increased by assigning precise precursor masses to DIA data. Additional peptides absent from spectral libraries, including sample-specific mutated peptides and post-translationally-modified peptides, were identified by MS-GF+ and MODa/MODi multi-stage database searching with the precursor masses determined. This first use of unambiguously-determined precursor masses to mine DIA data demonstrates considerable potential for further exploitation of this rich experimental data.
HostingRepository	PRIDE
AnnounceDate	2019-08-19
AnnouncementXML	Submission_2019-08-19_00:49:01.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Dong-Gi Mun
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	dihydroxylated residue; monomethylated residue; dehydrated residue; phosphorylated residue; formylated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-02-18 01:22:05	ID requested
⏵ 1	2019-08-19 00:49:02	announced

Mun DG, Nam D, Kim H, Pandey A, Lee SW, Accurate Precursor Mass Assignment Improves Peptide Identification in Data-Independent Acquisition Mass Spectrometry. Anal Chem, 91(13):8453-8460(2019) [pubmed]

curator keyword: Technical

submitter keyword: DIA, Precursor mass

Sang-Won Lee
contact affiliation	Department of Chemistry, Korea University
contact email	cacagong@korea.ac.kr
lab head
Dong-Gi Mun
contact affiliation	Korea University
contact email	cacagong@korea.ac.kr
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/2019/08/PXD012744

PRIDE project URI

• PRIDE
  1. PXD012744
     1. Label: PRIDE project
     2. Name: DIA data analysis with unambiguously determined precursor mass