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

Area of Science:

• Proteomics
• Biochemistry
• Molecular Biology

Background:

• Targeted proteomics offers a hypothesis-driven method for analyzing specific protein sets or pathways.
• goDig is a quantitative, targeted tandem mass tag (TMT)-based assay for measuring relative protein abundance differences in unfractionated mixtures.
• Implementing goDig presents challenges including required software, libraries, and the lack of a readily available test assay.

Purpose of the Study:

• To establish a standardized test assay for the goDig targeted proteomics platform.
• To create a proteome-wide goDig yeast library for quantitative profiling.
• To provide a guide for goDig implementation using the TKO11 standard.

Main Methods:

• Repurposing the commercially available TKO11 standard as a goDig test assay.
• Building a proteome-wide goDig yeast library.
• Quantifying protein expression across Gene Ontology (GO) categories and comparing to a gold-standard dataset.

Main Results:

• Successfully established the TKO11 standard as a functional goDig test assay.
• Generated a comprehensive goDig yeast library enabling quantification of hundreds of proteins.
• Demonstrated goDig's utility by comparing yeast protein expression data to a gold-standard dataset.

Conclusions:

• The TKO11 standard serves as an effective goDig test assay, simplifying implementation.
• The developed yeast library and quantification guide provide a template for goDig assays in other species.
• This work lowers the barrier for researchers to adopt and utilize goDig for targeted proteomics studies.