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PXD008009-2

PXD008009 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.
HostingRepositoryPRIDE
AnnounceDate2017-10-26
AnnouncementXMLSubmission_2017-10-26_07:58:28.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterJoao Paulo
SpeciesList scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationListTMT6plex-126 reporter+balance reagent acylated residue; iodoacetamide derivatized residue
InstrumentOrbitrap Fusion Lumos; Orbitrap Fusion
Dataset History
RevisionDatetimeStatusChangeLog Entry
02017-10-20 03:06:46ID requested
12017-10-26 03:15:44announced
22017-10-26 07:58:30announcedUpdated project metadata.
32024-10-22 04:28:43announced2024-10-22: Updated project metadata.
Publication List
Paulo JA, O'Connell JD, Gygi SP, A Triple Knockout (TKO) Proteomics Standard for Diagnosing Ion Interference in Isobaric Labeling Experiments. J Am Soc Mass Spectrom, 27(10):1620-5(2016) [pubmed]
Keyword List
curator keyword: Technical
submitter keyword: MS standard, MuiltiNotch, TMT, Orbitrap Fusion, Lumos, ion interference
Contact List
Joao A. Paulo
contact affiliationCell Biology, Harvard Medical School
contact emailjoao_paulo@post.harvard.edu
lab head
Joao Paulo
contact affiliationHarvard Medical School
contact emailjoao_paulo@post.harvard.edu
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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