Next-generation multiplexed targeted proteomics quantifies post-translational modifications in disease and compound-protein interactions with high throughput.

The GoDig platform enables sensitive, multiplexed targeted pathway proteomics without manual scheduling or synthetic standards. Here we present GoDig 2.0, which increases sample multiplexing to 35-fold, improves time efficiency and reduces scan delays for higher success rates, and allows flexible spectral and elution library generation from different mass spectrometry data types. GoDig 2.0 measures 2.4× more targets than GoDig 1.0, quantifying >99% of 800 peptides in a single run. We compile a library of 23,989 human phosphorylation sites from a phosphoproteomic dataset and use it to profile kinase signaling differences across cell lines. In human brain tissue, we establish a hyperphosphorylated tau assay including pTau127, revealing potential biomarkers for Alzheimer's disease. We also quantify diglycyl-lysine peptides to assess polyubiquitin branching. Finally, we build a library of 20,946 reactive cysteines and profile covalent compound-protein interactions spanning diverse pathways. GoDig 2.0 enables high-throughput analyses of site-specific protein modifications across many biological contexts.