PXD015257-1

PXD015257 is an original dataset announced via ProteomeXchange.

Title	A Triple Knockout (TKO) Proteomics Standard for Diagnosing Ion Interference in Isobaric Labeling Experiments
Description	Isobaric labeling is a powerful strategy for quantitative mass spectrometry-based proteomic investigations. A complication of such analyses has been the co-isolation of multiple analytes of similar mass-to-charge resulting in the distortion of relative protein abundance measurements across samples. When properly implemented, triple-stage mass spectrometry and synchronous precursor selection (SPS-MS3) can reduce the occurrence of this phenomena, referred to as ion interference. However, no diagnostic tool is available currently to rapidly and accurately assess ion interference. To address this need, we developed a multiplexed TMT-based standard, termed the triple knockout (TKO). This standard is comprised of three yeast proteomes in triplicate, each from a strain deficient in a highly abundant protein (Met6, Pfk2, or Ura2). The relative abundance patterns of these proteins, which can be inferred from dozens of peptide measurements, are representative of ion interference in peptide quantification. We expect no signal in channels where the protein is knocked out, permitting maximum sensitivity for measurements of ion interference against a null background. Here, we emphasize the need to investigate further ion interference-generated ratio distortion and promote the TKO standard as a tool to investigate such issues. [dataset license: CC0 1.0 Universal (CC0 1.0)] Joao A. Paulo provided the raw file to Manuel Tzouros (Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Switzerland)
HostingRepository	MassIVE
AnnounceDate	2019-09-03
AnnouncementXML	Submission_2019-09-03_08:28:09.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Meena Choi
SpeciesList	scientific name: Saccharomyces cerevisiae; common name: baker's yeast; NCBI TaxID: 4932;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2019-08-30 15:27:47	ID requested
⏵ 1	2019-09-03 08:28:09	announced

no publication

submitter keyword: TMT, Controlled mixture, Triple Knockout (TKO), Proteomics

Joao A. Paulo
contact affiliation	Cell Biology, Harvard Medical School
contact email	joao_paulo@post.harvard.edu
lab head
Meena Choi
contact affiliation	Northeastern University
contact email	mnchoi67@gmail.com
dataset submitter

MassIVE dataset URI

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