How you can help:

We have assembled a short guide on how to enter your experimental information and batch upload your protein termini, cleavages, cleavage sites or inhibition. Please contact us if there are any questions or you want to enquire about other options for batch data import (e.g. when you already have your data in a structured form, or for example in a database)

Step 1: Create Evidence

Please fill out and save the following document describing the source of the contributed information.

Click Here to Download Form

Step 2: Create Excel File

Please create a comma separated (.csv) file including a header line. You can contribute five kinds of data:

1. Proteases cleaving a native protein
Headerline: protease, position, substrate
Protease: UniProt ID (ex. Q9BYF1)
Position: Cleavage site position in the form 222-223
Substrate: UniProt ID (ex. Q9BYF1)

2. Proteases cleaving a peptide
Headerline: protease, peptide
Protease: UniProt ID (ex. Q9BYF1)
Peptide: Peptide sequence with the cleavage site indicated by a colon (ex. GA:GQCVFA)

3. Proteases inhibited by protein inhibitors
Headerline: protease, inhibitor
Protease: UniProt ID (ex. Q9BYF1)
Peptide: UniProt ID (ex. Q9BYF1)

4&5. Protein N-termini/C-termini
Headerline: protein, position, modification, confidence, confidence_type
Protein: UniProt ID (ex. Q9BYF1)
Position: Last amino acid relative to UniProt full length protein sequence (ex. 221)
Modification: Name of the modification of the first amino acid according to TopFIND (ex. acetylation)
Confidence: A confidence measurement if applicable (e.g. when based on peptide identification by mass spectrometry)
Confidence type: The type of the confidence value given (any of: 'unkown', 'probability', 'MASCOT score', 'X! Tandem score', 'PeptideProphet probability')

Step 3: Submit Files

In order to submit your data, we request that you email both your evidence file and .csv file to topfind.clip@msl.ubc.ca. We will confirm when we have received your data, and let you know if your data meets the criteria for addition to the TopFIND database after curation by our team.

Please contact Peter Bell in case of problems or further questions.