PXD011654

PXD011654 is an original dataset announced via ProteomeXchange.

Title	A web-based search tool for visualizing instrument performance using the Triple Knockout (TKO) proteome standard
Description	Multiplexing strategies are at the forefront of mass spectrometry-based proteomics, with SPS-MS3 methods becoming increasingly commonplace. A known caveat of isobaric multiplexing is interference resulting from co-isolated and co-fragmented ions that do not originate from the selected precursor of interest. The triple knockout (TKO) standard was designed to benchmark data collection strategies to minimize interference. However, a limitation to its widespread use has been the lack of an automated analysis platform. Here, we present a TKO Visualization Tool (TVT). The TVT viewer allows for automated, web-based, database searching of the TKO standard, returning traditional figures of merit, such as peptide and protein counts, scan-specific ion accumulation times, as well as the TKO-specific metric, the IFI (interference-free index). Moreover, the TVT viewer allows for plotting of multiple TKO standards to assess protocol optimizations, compare instruments, or measure degradation of instrument performance over time. To showcase the TVT viewer, we investigated the selection of 1) stationary phase resin, 2) MS2 isolation window width, and 3) number of SPS ions for SPS-MS3 analysis. Using the TVT viewer will allow the proteomics community to search and compare TKO results to optimize user-specific data collection workflows.
HostingRepository	PRIDE
AnnounceDate	2018-12-04
AnnouncementXML	Submission_2018-12-04_08:12:03.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joao Paulo
SpeciesList	scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2018-11-12 02:12:19	ID requested
⏵ 1	2018-12-04 08:12:05	announced

Gygi JP, Yu Q, Navarrete-Perea J, Rad R, Gygi SP, Paulo JA, Web-Based Search Tool for Visualizing Instrument Performance Using the Triple Knockout (TKO) Proteome Standard. J Proteome Res, 18(2):687-693(2019) [pubmed]

curator keyword: Technical

submitter keyword: TKO

interference

TMT

iTRAQ

SPS-MS3

TVT

Shiny

Joao A. Paulo
contact affiliation	Cell Biology, Harvard Medical School, USA
contact email	joao_paulo@post.harvard.edu
lab head
Joao Paulo
contact affiliation	Harvard Medical School
contact email	joao_paulo@post.harvard.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD011654
     1. Label: PRIDE project
     2. Name: A web-based search tool for visualizing instrument performance using the Triple Knockout (TKO) proteome standard