Databases: The PRF maintains up-to-date versions of the SwissProt database for commonly used organisms (human, mouse, etc.). However, any protein database, including custom databases, can be used provided they are available in the FASTA format. A list of common Repository of Adventitious Proteins (cRAP) are appended to all databases. False Discovery Rate (FDR) is estimated by searching the data against "reverse protein sequences" of all proteins in the relevant database.
Other available software:
MaxQuant – Available on a dedicated computer for data search and analysis.
Byonic – Useful for identifying intact glycopeptides and conducting wildcard searches for unknown modifications (cannot be done with X!Tandem/TPP or PD).
Advanced data analysis: The PRF works closely with Dr. Alexey Nesvizhskii, Associate Professor at the Department of Pathology, who is a leader in the field of proteome informatics. His research interests are in the fields of bioinformatics, proteomics and systems biology, with a focus on the development of computational methods for processing and extracting biological information from complex biological data sets. His laboratory has developed numerous programs for the qualitative and quantitative analysis of proteomic datasets which can be accessed through the link below.