Development of a database and its use in the Investigation of Interferences in SRM assay design

Selected Reaction Monitoring (SRM), is a form of mass spectrometry that guarantees high throughput and also a high level of selectivity and specificity. Performing SRM experiments requires the development of assays to aid in peptide identification. This is a time consuming and expensive process thus biological researchers have come up with bioinformatics solutions for the design of SRM assay. The accuracy of these bioinformatics methods is quite high and the next step is to optimise the process by tackling the interference issue. As various analytes may have the same signals within an SRM experiment and thus interfere with each other’s signals, different solutions are being derived to tackle the issue. This thesis describes the development of a SRM transition database to store peptide and transition data, software to populate the database and also software to retrieve the data from the database. Finally the database is tested with the MRMaid transitions for the human proteome which were mined from the PRIDE database and the results analysed to investigate the transition interference issue. The database currently contains data for 20220 proteins and approximately 870,000 tryptic peptides from the human proteome.