Data Analysis and Dissemination Pipeline
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.
Data Analysis Tools:
- Proteome Discoverer v 2.4 (ThermoFisher Scientific): This is the main software used for searching the raw data and providing results.
- PEAKS X Studio – Available on a dedicated computer for additional search and analysis.
Advanced Data Analysis: Dr. Alexey Nesvizhskii, Director of PRF, 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.
More complex/custom data analysis and advanced bioinformatics support is available on a collaboration model. Please contact Dr. Nesvizhskii.
Data Dissemination: PRF will retain the raw/result files as long as possible but also transfer the data via Dropbox or equivalent service, if requested. PRF will provide assistance in uploading the data files to public repositories such as ProteomeXchange, as needed.