Dataset Information

Adapting an isobaric tag-labeled yeast peptide standard to develop targeted proteomics assays

ABSTRACT: 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.

INSTRUMENT(S): Orbitrap Eclipse

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Joao Paulo

LAB HEAD: Joao A. Paulo

PROVIDER: PXD044397 | Pride | 2023-12-28

REPOSITORIES: Pride

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Adapting an Isobaric Tag-Labeled Yeast Peptide Standard to Develop Targeted Proteomics Assays.

Dong Kevin D KD Schmid Ernst W EW Bomgarden Ryan D RD Choi Jae H JH Gygi Steven P SP Yu Qing Q Paulo Joao A JA

Journal of proteome research 20231127 1

Targeted proteomics strategies present a streamlined hypothesis-driven approach to analyze specific sets of pathways or disease related proteins. goDig is a quantitative, targeted tandem mass tag (TMT)-based assay that can measure the relative abundance 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 ...[more]

PMID: 38009700

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			Action	DRS
	Key.xlsx	Xlsx
	ea13731.raw	Raw
	ea13731_TKO11fxn_v22_DeamN.mzIdentML	Mzid
	ea13732.raw	Raw
	ea13732_TKO11fxn_v22_DeamN.mzIdentML	Mzid