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PXD015257

PXD015257 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleA Triple Knockout (TKO) Proteomics Standard for Diagnosing Ion Interference in Isobaric Labeling Experiments
DescriptionIsobaric 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)
HostingRepositoryMassIVE
AnnounceDate2019-09-03
AnnouncementXMLSubmission_2019-09-03_08:28:09.xml
DigitalObjectIdentifier
ReviewLevelNon peer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterMeena Choi
SpeciesList scientific name: Saccharomyces cerevisiae; common name: baker's yeast; NCBI TaxID: 4932;
ModificationListTMT6plex-126 reporter+balance reagent acylated residue; iodoacetamide derivatized residue
InstrumentOrbitrap Fusion
Dataset History
RevisionDatetimeStatusChangeLog Entry
02019-08-30 15:27:47ID requested
12019-09-03 08:28:09announced
Publication List
no publication
Keyword List
submitter keyword: TMT, Controlled mixture, Triple Knockout (TKO), Proteomics
Contact List
Joao A. Paulo
contact affiliationCell Biology, Harvard Medical School
contact emailjoao_paulo@post.harvard.edu
lab head
Meena Choi
contact affiliationNortheastern University
contact emailmnchoi67@gmail.com
dataset submitter
Full Dataset Link List
MassIVE dataset URI
Dataset FTP location
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