Multiplexed quantitative phosphoproteomics of cell line and tissue samples

Post-translational modifications (PTMs) of proteins increase a biological system's repertoire of regulatory tools to control cellular mechanisms. Protein phosphorylation is the most studied PTM and known to be dysregulated in many diseases, including cancer, and protein kinases are among the most important drug targets. Many proteins across the eukaryotic proteome are phosphorylated, and more than 50,000 unique protein phosphorylation sites have been identified in a single human cell line. Understanding the vast biological networks directed by protein phosphorylation requires deep quantitative mapping of the phosphoproteome across many samples. Multiplexed proteomics using isobaric labeling reagents to barcode proteome samples for simultaneous quantification has greatly increased the throughput of mass spectrometry-based proteomics and enabled the number of analyses required to understand complex biological systems. We are presenting a detailed protocol to use multiplexed proteomics for mapping phosphoproteomes in samples from cell culture experiments and in tissue samples. The protocol includes phosphopeptide enrichment with TiO₂ and phosphotyrosine antibody technology. We are using tandem mass tag (TMT) reagents for barcoding the samples allowing parallel quantification of up to 11 samples. The mass spectrometry method is based on the MultiNotch MS3 method to generate quantitative data of high accuracy and reproducibility. Tandem mass spectrometry (MS2) based on regular collision-induced dissociation (CID) and higher-energy collisional dissociation (HCD) is used to maximize the number of quantified phosphopeptides. The protocol typically enables the quantification of more than 20,000 unique phosphoforms (unique patterns of peptide phosphorylations) from proteome samples of human origin requiring less than 8h of mass spectrometry time per sample.