PXD017803

PXD017803 is an original dataset announced via ProteomeXchange.

Title	A Triple KnockOut Isobaric-labelling Quality Control Platform in an Integrated On-line Database Search
Description	Sample multiplexing using isobaric tagging is a powerful strategy for proteome-wide protein quantification. One major caveat of isobaric tagging is ratio compression that results from the isolation, fragmentation, and quantification of co-eluting, near-isobaric peptides, a phenomenon typically referred to as “ion interference.” A robust platform to ensure quality control, optimize parameters, and enable comparisons across samples is essential as new instrumentation and analytical methods evolve. Here, we introduce TKO-iQC, an integrated platform consisting of the Triple Knock-Out (TKO) yeast digest standard and an automated web-based database search and protein profile visualization application. We highlight two new TKO standards based on the TMTpro reagent (TKOpro9 and TKOpro16), as well as an updated TKO Viewing Tool, TVT2.0. TKO-iQC greatly facilitates the comparison of instrument performance with a straightforward and streamlined workflow.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:01:42.099.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joao Paulo
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue
Instrument	Orbitrap Fusion Lumos; Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2020-03-02 00:47:06	ID requested
1	2020-03-31 01:32:46	announced
⏵ 2	2024-10-22 05:01:50	announced	2024-10-22: Updated project metadata.

Gygi JP, Ramin Rad, Navarrete-Perea J, Younesi S, Gygi SP, Paulo JA, A Triple Knockout Isobaric-Labeling Quality Control Platform with an Integrated Online Database Search. J Am Soc Mass Spectrom, 31(7):1344-1349(2020) [pubmed]

10.1021/jasms.0c00029;

submitter keyword: TKO standard

ion interference

TMT

iTRAQ

SPS-MS3

TVT

Shiny application

Joao A. Paulo
contact affiliation	Cell Biology Harvard Medical School Boston, MA 02115
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

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://ftp.pride.ebi.ac.uk/pride/data/archive/2020/03/PXD017803

PRIDE project URI

• PRIDE
  1. PXD017803
     1. Label: PRIDE project
     2. Name: A Triple KnockOut Isobaric-labelling Quality Control Platform in an Integrated On-line Database Search