Tuesday, May 24, 2016

Proteomics peptide data in the Feature Viewer

The Protein Feature Viewer in UniProt is an interactive representation of all protein sequence features in one compact view. It now provides a new track displaying proteomics peptide identification data for UniProt Knowledgebase entries.

UniProt runs an analysis pipeline to map data from publicly available proteomics resources to UniProtKB sequences. So far these data were available as a download from the UniProt FTP site. Now these data are also displayed in the Protein Feature Viewer which can be accessed through the ‘Feature viewer’ link on the left hand side of the entry view page.

The proteomics track currently displays mass spectrometry peptide data mapped from PeptideAtlas, EPD and MaxQB to UniProtKB protein sequences and more mass spectrometry proteomics resources will be added in the future. The track can be further expanded to see unique and non-unique mapped peptides, as shown in the example screenshot below.

Unicity of peptides is evaluated according to gene groups underlying the UniProtKB reference proteomes where we group  protein sequences based on the gene(s) encoding them. Each gene group is constituted by one or more UniProtKB protein isoform sequences. A peptide is considered unique if it belongs to only one gene group. Two types of peptides are therefore identified: unique and non-unique.

In the future, we also plan to also add post-translational modification-specific proteomics data sets (initially phosphorylation sites) to the mappings to UniProtKB sequences.