PXD005797-1

PXD005797 is an original dataset announced via ProteomeXchange.

Title	Extensive Peptide Fractionation and y1 Ion-based Interference Detection Enable Accurate Quantification by Isobaric Labeling and Mass Spectrometry
Description	Isobaric labeling quantification by mass spectrometry (MS) has emerged as a powerful technology for multiplexed large-scale protein profiling, but measurement accuracy in complex mixtures is confounded by the interference from co-isolated ions, resulting in ratio compression. Here we report that the ratio compression can be essentially resolved by the combination of pre-MS peptide fractionation, MS2-based interference detection and post-MS computational interference correction. We pooled tandem mass tag (TMT) labeled E. coli peptides at 1 : 3 : 10 ratios, and added in ~20-fold more rat peptides as background, followed by the analysis of two dimensional liquid chromatography (LC)-MS/MS. The quantitative interference was systematic investigated and the interference in MS2 scans were estimated by the intensity of contaminated y1 product ions. An algorithm was thus developed to correct reporter ion ratios of tryptic peptides.
HostingRepository	PRIDE
AnnounceDate	2022-02-28
AnnouncementXML	Submission_2022-02-28_02:24:59.925.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	xusheng wang
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-01-28 03:44:37	ID requested
⏵ 1	2022-02-28 02:25:02	announced
2	2023-11-14 08:49:24	announced	2023-11-14: Updated project metadata.

Niu M, Cho JH, Kodali K, Pagala V, High AA, Wang H, Wu Z, Li Y, Bi W, Zhang H, Wang X, Zou W, Peng J, Ion-Based Interference Detection Method for Enabling Accurate Quantification by Isobaric Labeling and Mass Spectrometry. Anal Chem, 89(5):2956-2963(2017) [pubmed]

curator keyword: Technical

submitter keyword: proteomics, mass spectrometry, LC-MS/MS, isobaric labeling, TMT, iTRAQ, and ratio compression

Junmin Peng, PhD
contact affiliation	Structural Biology MS 311, Room D1034C St. Jude Children's Research Hospital 262 Danny Thomas Place Memphis, TN 38105-3678
contact email	junmin.peng@stjude.org
lab head
xusheng wang
contact affiliation	Proteomics
contact email	xushengwang78@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD005797
     1. Label: PRIDE project
     2. Name: Extensive Peptide Fractionation and y1 Ion-based Interference Detection Enable Accurate Quantification by Isobaric Labeling and Mass Spectrometry