Abstract:
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.
