A large-scale targeted proteomics assay resource based on an in vitro human proteome

Area of Science:

• Proteomics
• Systems Biology
• Metabolomics

Background:

• Targeted proteomics enables accurate protein quantification.
• Scaling targeted proteomics requires robust, predefined assays.
• Previous methods lacked genome-wide applicability for absolute protein quantification.

Purpose of the Study:

• To develop a genome-wide targeted proteomics platform for absolute protein quantification.
• To apply this platform to study metabolic changes in human fibroblasts during oncogenic transformation.

Main Methods:

• Development of the in vitro proteome-assisted multiple reaction monitoring (MRM) for protein absolute quantification (iMPAQT) platform.
• Utilized over 18,000 human recombinant proteins and mass tag (mTRAQ)-labeled peptides.
• Mass spectrometry-based measurement of absolute protein abundance for predefined protein sets.

Main Results:

• Established iMPAQT for rapid, straightforward absolute protein quantification on a genome-wide scale.
• Applied iMPAQT to characterize the quantitative metabolic landscape of normal and transformed human fibroblasts.
• Observed global metabolic pathway alterations in transformed fibroblasts, including aerobic glycolysis (Warburg effect) and increased macromolecule synthesis.

Conclusions:

• iMPAQT enables large-scale, absolute protein quantification.
• Oncogenic transformation induces distinct metabolic reprogramming in fibroblasts.
• The iMPAQT platform is a valuable tool for quantitative biology and understanding cellular processes.