Proteome wide screening using peptide affinity capture

MS-based strategies are key technologies for identifying proteins in proteomic research. Despite significant improvements in recent years efficient fractionation processes of target analytes remain major bottlenecks in MS-based protein analysis. Immunoaffinity-based sample fractionation strategies have shown their potential for the enrichment of analyte peptides of interest, but only small numbers of analytes can be quantified in one experiment. The lack of appropriate capture reagents limits the application of immunoaffinity-based approaches and only biased biomarker discovery approaches are possible. This perspective discusses the current status of immunoaffinity MS-based approaches and introduces a novel concept that uses group specific anti-peptide antibodies - Triple X Proteomics Antibodies - for the enrichment of signature peptides. Classes of peptides with identical termini can be fractionated based on TXP immunoaffinity enrichment steps and can subsequently be identified using established tandem MS procedures. Based on bioinformatic algorithms minimal sets of TXP epitopes can be specified, that cover a wide range of given proteome landscapes of one or even several different species. This opens the possibility to use a minimal number of TXP antibodies as a universal toolbox for general immunoaffinity-based approaches in proteome analysis.