The Cleavage Atlas collects proteolytic cleavage sites observed in public mass-spectrometry proteomics data (PRIDE/ProteomeXchange). Each identifier names a single peptide bond in a UniProtKB protein, independent of which protease cleaves it: the UniProtKB accession, an optional isoform number, and the P1 residue position (Schechter-Berger numbering on the full precursor sequence, Met1 = 1). The bond named is the one between residue P1 and residue P1+1.

Comment

The accession + P1 key formalises what MEROPS, TopFIND and TermineR already use internally to join cleavage records, so a MEROPS cleavage, a TopFIND cleavage, a UniProt "Site" cleavage feature and an atlas observation map to the same identifier. Unlike those keys it does not include the protease. P1 = 0 and P1 = sequence length are protein termini, not bonds, and are not valid. No isoform suffix means the UniProt canonical isoform.

Prefix

cleavageatlas

Keywords

mass spectrometry proteomics

License

CC0-1.0

Links

Homepage Request Discussion

Pattern for Local Unique Identifiers

Local unique identifiers in Cleavage Atlas should match this regular expression:
^([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2})(-[0-9]+)?_[1-9][0-9]*$

Example Local Unique Identifiers

P01009_382   Resolve
P15692-4_26   Resolve
P15692-9_141   Resolve
Q8N2S1-2_20   Resolve

Pattern for CURIES

Compact URIs (CURIEs) constructed from Cleavage Atlas should match this regular expression:
^cleavageatlas:([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2})(-[0-9]+)?_[1-9][0-9]*$

Example CURIEs

cleavageatlas:P01009_382
cleavageatlas:P15692-4_26
cleavageatlas:P15692-9_141
cleavageatlas:Q8N2S1-2_20

Contact

Rens de Groot   0000-0002-1044-9499   rensdg-code

Contributor

creator Rens de Groot   0000-0002-1044-9499   rensdg-code

Reviewer

Charles Tapley Hoyt   0000-0003-4423-4370   cthoyt

A provider turns a local unique identifiers from a resource into a URI. Many providers are also resolvable as URLs (i.e., they can be used in a web browser).

The local unique identifier P01009_382 is used to demonstrate the providers available for Cleavage Atlas. Some providers may use a different example, which is displayed in the table below. A guide for curating additional providers can be found here.