-
Notifications
You must be signed in to change notification settings - Fork 17
How to prepare a protein database
Proteomics pipelines and toolkits like Philosopher rely on properly formatted protein sequence databases to correctly identify peptides. Here are some tips on how to prepare a protein database for your experiment.
Run Philosopher from the command line to download one from UniProt by executing the following two commands:
philosopher workspace --init
philosopher database --reviewed --contam --id UP000005640
This will generate a human UniProt/SwissProt (i.e. reviewed sequences only) database, with common contaminants and decoys added (with a default decoy prefix rev_). If you would like to use the full UniProt, remove the --reviewed
tag.
For mouse, for example, use the proteome ID UP000000589. To find the proteome ID for other organisms, search within the UniProt proteomes.
Add decoys and contaminants and format it for FragPipe using the following commands:
philosopher workspace --init
philosopher database --custom <file_name> --contam
Reformat it for FragPipe using the following commands:
philosopher workspace --init
philosopher database --annotate <file_name> --prefix <prefix>
If you need to run the --custom
or the --annotate
command, you may manually inspect the formatted files to ensure it will be compatible with Philosopher, it should follow one of these formats:
Generic means a simple: >proteinID
If you are adding you own decoys, they also need to follow a specific formatting; sequences need to be formatted as a whole protein string in FASTA file with a decoy (e.g. rev_ or DECOY_) added at the beginning.
Examples of compatible formats:
- >rev_tr|J3KNE0|J3KNE0_HUMAN
- >DECOY_tr|J3KNE0|J3KNE0_HUMAN
Examples of incompatible formats:
- >tr_REVERSED|J3KNE0|J3KNE0_HUMAN
- >tr|fake_J3KNE0|J3KNE0_HUMAN RanBP2-like
- >tr|J3KNE0_DECOY|J3KNE0_HUMAN