than could be analyzed directly by MS, thus allowing lower concentrations to be measured. In practice, assay sensitivity can be improved by 1,000-10,000-fold by this approach. By removing the unbound (non-target) peptides present in the sample digest, the sample presented to the mass spectrometer is drastically simplified, thus reducing the need for peptide separation by liquid chromatography prior to MS analysis. In some cases liquid chromatography has been eliminated entirely, resulting in MS cycle times of 7-20 sec rather than 5–40 minutes required in typical unfractionated digest protocols involving extensive chromatographic separation. By virtue of the extreme specificity of mass spectrometric detection, SISCAPA assays can be combined into multiplex panels without cross-assay interference. Panels combining 22, 50, and 150 assays into a single operation have been demonstrated. SISCAPA’s use of proteolytic digestion as a first step eliminates the protein:protein complexes (including complexes of a target protein with auto-antibodies) that cause “interferences” in protein capture assays, including conventional immunoassays (e.g., ELISA assays). Elimination of such autoantibody interferences drove the adoption of SISCAPA as an alternative to immunoassays for clinical measurement of thyroglobulin as a marker of thyroid cancer recurrence in patients who exhibit anti-thyroglobulin autoantibodies. A limitation of the specific peptide capture approach is the requirement for a specially-developed antibody against the selected peptide. To date several hundred anti-peptide antibody reagents have been developed for enrichment of tryptic peptides from sample digests, mainly for established clinical biomarkers (,) and cancer research targets, but these do not yet cover a majority of protein targets of interest in non-cancer research or clinical contexts. A variety of MS instrument types have been used for quantitation of the enriched peptides, including most frequently triple quadrupole mass spectrometers implementing the “multiple reaction monitoring” (MRM) method (a format sometimes referred to as “immuno-MRM”), and MALDI-ToF (a format sometimes referred to as iMALDI). Related methods Alternative specific enrichment methods include MSIA (“mass spectrometric immunoassay”,) in which antibodies are used to enrich target proteins, which are analyzed intact by MS; and hybrid methods in which antibodies are used to enrich target proteins, which are then digested prior to peptide detection by MS. References Protein methods