Affinity capture in bottom-up protein analysis – Overview of current status of proteolytic peptide capture using antibodies and molecularly imprinted polymers

Highlights: • Protein biomarker determination using peptide affinity capture. • Antibodies and molecularly imprinted polymers for sample clean-up prior to LC-MS. • Tools for determination of low-abundance biomarkers. • Determination of post-translational modifications by immuno-MS. • Recent progress in peptide affinity capture. Antibody-based affinity capture has become the gold standard in sample preparation for determination of low-abundance protein biomarkers in biological matrices prior to liquid chromatography-mass spectrometry (LC-MS) determination. This comprises both capture of intact proteins prior to the digestion step and capture of proteolytic peptides after digestion of the sample. The latter can be performed both using antibodies specifically developed to capture target proteolytic peptides, as well as by the less explored use of anti-protein antibodies to capture the proteolytic epitope peptide. Molecularly imprinted polymers (MIPs), also called plastic antibodies are another affinity-based approach emerging as sample preparation technique in LC-MS based protein biomarker analysis. The current review gives a critical and comprehensive overview of proteolytic peptide capture using antibodies and MIPs in LC-MS based protein biomarker determination during the last five years. The main emphasis is on capture of non-modified peptides, while a brief overview of affinity capture of peptides containing post-translational modifications (PTMs) is provided.