The mass spectrometry-based ‘omics’ sub-discipline that focuses on comprehensive, often exploratory, analyses of endogenous peptides involved in cell-to-cell communication is oftentimes referred to as peptidomics. Although the progress in bioanalytical technology development for peptide discovery has been tremendous, perhaps the largest advances have involved robust quantitative mass spectrometric approaches and data mining algorithms. These efforts have accelerated the discovery and validation of biomarkers, functionally important posttranslational modifications, and unexpected molecular interactions, information that aids drug development. In this article we outline the current approaches used in quantitative peptidomics and the technical challenges that stimulate new advances in the field, while also reviewing the newest literature on functional characterizations of endogenous peptides using quantitative mass spectrometry.
