Bioinformatics

Databases

The Proteomics Resource Facility 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 (Thermo Fisher Scientific): Used for database searching and downstream analysis of proteomics data, including qualitative and quantitative workflows.
• FragPipe / MSFragger: Used for database searching and analysis of DDA and DIA proteomics data, with MSFragger serving as the primary search engine for many of our DIA database-search workflows. FragPipe provides an integrated computational platform for peptide and protein identification, quantification, and downstream proteomic data analysis.
• PEAKS X Studio: Available on a dedicated computer for additional database searching and proteomic data 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 are available on a collaboration model. Please contact Dr. Nesvizhskii.

Data Dissemination

The Proteomic Resources Facility will retain the raw/result files as long as possible, but will also transfer the data via Dropbox or equivalent service, if requested. The PRF will provide assistance in uploading the data files to public repositories such as ProteomeXchange, as needed.