PXD010571 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 | 2019-01-07 |
AnnouncementXML | Submission_2019-01-07_08:18:54.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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2018-07-26 03:23:18 | ID requested | |
⏵ 1 | 2019-01-07 08:18:55 | announced | |
Publication List
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] |
Keyword List
curator keyword: Technical, Biological |
submitter keyword: Method development, DIWA, MSMS, TMT |
Contact List
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 | |
Full Dataset Link List
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/2019/01/PXD010571 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD010571
- Label: PRIDE project
- Name: Evaluation of a Dual Isolation Width Acquisition (DIWA) method for isobaric labelling ratio decompression