PXD044397 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
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. |
Publication List
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; |
Keyword List
submitter keyword: TMTpro, TMT, API,targeted assay, TKO, GoDig |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD044397
- Label: PRIDE project
- Name: Adapting an isobaric tag-labeled yeast peptide standard to develop targeted proteomics assays