PXD010571

PXD010571 is an original dataset announced via ProteomeXchange.

Title	Evaluation of a Dual Isolation Width Acquisition (DIWA) method for isobaric labelling ratio decompression
Description	Stable isotope labelling of peptides using isobaric reagents such as iTRAQ and TMT enables the multiplexed analysis of proteomes with deep quantitative coverage. Isobaric tagging demonstrates high precision but imperfect accuracy due to ratio underestimation caused by co-fragmentation of ions with mass-to-charge ratios within the isolation window of the targeted precursors. Prompted by empirical observations of isobaric-labelled peptide MS2 spectra, we argue that although a very narrow isolation window will result in severe loss of backbone fragment ions, rendering the spectra unsuitable for peptide identification, the reporter ion signals will remain intense enough to generate quantitative information for a significant portion of the spectra. Based on this assumption we have designed a Dual Isolation Width Acquisition (DIWA) method, in which each precursor is first fragmented with HCD using a standard isolation width for peptide identification and preliminary quantification followed by a concomitant MS2 HCD fragmentation using a much narrower isolation width for the acquisition of quantification-only spectra with reduced interference. We leverage the quantitative values obtained by the “narrow” scans to build linear regression models and apply these to decompress the fold-changes measured at the “standard” scans. Here, we evaluate the DIWA method using a two species TMT-6plex model and discuss the potential of this approach.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:47:09.480.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	James Wright
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2018-07-26 03:23:18	ID requested
1	2019-01-07 08:18:55	announced
⏵ 2	2024-10-22 04:47:10	announced	2024-10-22: Updated project metadata.

Roumeliotis TI, Weisser H, Choudhary JS, Evaluation of a Dual Isolation Width Acquisition Method for Isobaric Labeling Ratio Decompression. J Proteome Res, 18(3):1433-1440(2019) [pubmed]

10.1021/acs.jproteome.8b00870;

curator keyword: Technical, Biological

submitter keyword: Method development, TMT, MSMS, DIWA

Jyoti Choudhary
contact affiliation	The Institute of Cancer Research
contact email	jyoti.choudhary@icr.ac.uk
lab head
James Wright
contact affiliation	Functional Proteomics, Institute Cancer Research & Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute
contact email	jw13@sanger.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD010571
     1. Label: PRIDE project
     2. Name: Evaluation of a Dual Isolation Width Acquisition (DIWA) method for isobaric labelling ratio decompression