What are PeptideAtlas and PASSEL?
The PeptideAtlas project, at the Institute of Systems Biology (ISB, Seattle, USA), annotates genome sequences of different organisms with peptides and proteins derived mainly from MS/MS data.
All data in PeptideAtlas are reprocessed using the Trans Proteomics Pipeline (TPP). PeptideAtlas is organised into species-specific or sample-specific ‘builds’, which represent all peptides mapped to a single reference Ensembl genome.
What is PASSEL?
The Peptide Atlas SRM Experiment Library (PASSEL) is a component of the PeptideAtlas project that is designed to allow submission, dissemination, and reuse of selected reaction monitoring (SRM) experimental results from analysis of biological samples.
Figure 3. The PASSEL web interface.
The raw data are automatically processed in a uniform manner and the results are stored in a database. They can be downloaded or browsed via a web interface that includes a chromatogram viewer (Figure 3).
PASSEL allows the cross-analysis of SRM data, supports optimisation of SRM data collection, and facilitates the review of SRM data.
PASSEL is the initial submission point in the ProteomeXchange consortium for SRM data.
In this course, we focus on submission of MS/MS data to PRIDE. For help submitting SRM data to the Proteomexchange consortium via PASSEL, we recommend that you visit the PeptideAtlas website.