PXD015257
PXD015257 is an original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
---|---|---|---|
0 | 2019-08-30 15:27:47 | ID requested | |
⏵ 1 | 2019-09-03 08:28:09 | announced |
Publication List
no publication |
Keyword List
submitter keyword: TMT, Controlled mixture, Triple Knockout (TKO), Proteomics |
Contact List
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 |
Full Dataset Link List
MassIVE dataset URI |
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://massive.ucsd.edu/MSV000084263/ |