Target class strategies in mass spectrometry-based proteomics

The cornerstone of proteomics resides in using traditional methods of protein chemistry, to extract and resolve complex mixtures, in concert with the powerful engines of mass spectrometry to decipher peptide and protein identities. The broad utility of proteomics technologies to map protein interactions, understand regulatory mechanisms and identify biomarkers associated with disease states and drug treatments necessitates a targeted biochemical approach tailored to the characteristics of the tissue, fluid or cellular extract being studied. The application of affinity methods in proteomic studies to focus on particular classes of molecules is being used with increasing frequency and comprises the subject of this review. An overview of successfully applied affinity methods is provided, along with speculation on the use of innovative approaches. Sample preparation and processing are critical for proteomics with affinity reagents, as only functional and active proteins can be isolated in most cases. Considerations for methods of sample preparation to optimize affinity capture and release are also discussed.