Functional profiling of normal and cancer cells.

The advent of molecular biology and molecular profiling in clinical medicine has transformed our understanding of the molecular basis of human cancer. As a result, we are increasingly improving the classification of human tumors based on their specific genetic and molecular mechanisms of pathogenesis. However, currently only a small number of mutant alleles guide treatment decisions, while most observed mutations remain of unknown pathologic and clinical significance. In addition, even for recently approved drugs, such as those targeting activated kinase signaling, clinical efficacy is highly varied, with no currently satisfactory means to identify molecular markers of response and resistance. Quantitative measurements of the abundance of proteins and stoichiometry of their regulatory post-translational modifications can be used to determine activation states of pathways and cells.

Quantifying biochemical regulation.

Cells often control protein activity altering their concentration and post-translational chemical modification (PTM). To independently determine these two factors for any given protein, the amounts of modified and unmodified peptides spanning critical regulatory sites can be independently measured to determine differential PTM stoichiometry, and peptides from non-modified domains are quantified to determine variations in protein concentration (Cifani and Kentsis, MCP, 2017) Integration of this quantitative data across multiple nodes of biochemical pathways informs specific activation of cellular processes, even in the absence of evident genetic lesions.

The Quantitative Cancer Proteomic Atlas.

QCPA is a panel of quantitative mass spectrometry assays for the analysis of activities of signaling and regulatory pathways in cancer cells. Its current version is focused on molecular targets and pathogenic signaling pathways known to mediate cancer pathogenesis and therapy response, such as most known oncogenic receptor tyrosine kinases, apoptosis mediators, master transcription factors, chemotherapy metabolizing enzymes, and regulators of cell growth and quiescence. For most proteins included in QCPA, two independent peptides are quantified to determine differential protein abundance, and stoichiometry of functional chemical modifications is measured for at least one regulatory site. Proteins and regulatory sites in QCPA were selected based on literature and on the contribution of expert collaborators.