PXD044397

PXD044397 is an original dataset announced via ProteomeXchange.

Title	Adapting an isobaric tag-labeled yeast peptide standard to develop targeted proteomics assays
Description	Quantitative targeted proteomics strategies present a streamlined hypothesis-driven approach to analyze specific sets of pathways and/or disease related proteins. goDig is a targeted tandem mass tag (TMT)-based assay that can measure the expression differences for hundreds of proteins directly from unfractionated mixtures. Specific protein groups or entire pathways of up to 200 proteins can be selected for quantitative profiling, while leveraging sample multiplexing permits the simultaneous analysis of up to 18 samples. Despite these benefits, implementing goDig is not without challenges as it requires access to an instrument application programming interface (iAPI), an elution order and spectral library, a web-based method builder, and dedicated companion software. In addition, the absence of an example test assay may dissuade a researcher from testing or implementing goDig. Here, we repurpose the TKO11 standard - which is commercially available but may also be assembled in-lab – and establish it as a de facto test assay for goDig. We build a proteome-wide goDig yeast library, quantify protein expression across several gene ontology (GO) categories, and compare results to a fully-fractionated yeast gold-standard data set. Essentially, we provide a guide detailing the goDig-based quantification of TKO11, which can be used also as a template for user-defined assays in other species.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:18:59.548.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; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2023-08-06 08:55:58	ID requested
1	2023-12-28 11:20:21	announced
⏵ 2	2024-10-22 06:19:01	announced	2024-10-22: Updated project metadata.

Dong KD, Schmid EW, Bomgarden RD, Choi JH, Gygi SP, Yu Q, Paulo JA, Adapting an Isobaric Tag-Labeled Yeast Peptide Standard to Develop Targeted Proteomics Assays. J Proteome Res, 23(1):142-148(2024) [pubmed]

10.1021/acs.jproteome.3c00493;

submitter keyword: TMTpro, TMT, API,targeted assay, TKO, GoDig

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

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/2023/12/PXD044397

PRIDE project URI

• PRIDE
  1. PXD044397
     1. Label: PRIDE project
     2. Name: Adapting an isobaric tag-labeled yeast peptide standard to develop targeted proteomics assays