Comparative proteomic analysis of database search engines on massive amount of tandem mass spectra for non-halal pork-based food products

Shotgun proteomics is a high-throughput proteomic studies that commonly used to establish the peptide markers. Massive amounts of tandem mass spectra will be produced after an LC-MS/MS acquisition, as a consequence of thousands of proteins from several biological samples is digested by an enzyme. Manual interpretation for these massive mass spectra is unfeasible; instead, database search engine is used to match the spectra with sequence information contained in the database. Each search engine has a unique algorithm to provide a list of the best matching peptide sequences, as well as a score that related to the confidence level for an individual tandem mass spectrum. In this study, three proteomic database search engines namely Comet, X! Tandem, and ProteinProspector are used against 45 types of pork-based food products with triplicate each for halal analysis. The ability of each database search engine is compared and discussed in term of detected spectra, matched peptide-spectrum, and inferred proteins. A false-discovery rate is also presented and discussed in respect of database searching. A combined database search engine is proposed to leverage the information contained in the database during interpretation of massive amounts of tandem mass spectra.