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Nesvilab / MSFragger

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics
https://msfragger.nesvilab.org
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Use a pre-digested database for close/open search #299

Closed yonghanyu closed 8 months ago

yonghanyu commented 8 months ago

Hi,

I am wondering whether there is a way to use a predigested peptide database when conducting close or open search with msfragger?

fcyu commented 8 months ago

Yes, you can. Just prepare your own fasta file and make sure that the header is in good format.

Best,

Fengchao

yonghanyu commented 8 months ago

Yes, you can. Just prepare your own fasta file and make sure that the header is in good format.

Best,

Fengchao

Hi Fengchao,

Thank you for your quick reply. However, the msfragger will always perform in silico digestion even with philosopher pre annotated database. Is there a way to avoid such behaviour as my peptide database is pre-digested.

fcyu commented 8 months ago

You could set the enzyme cuts to something like X so that there is no sites to cut (assuming there are no X in your proteins).

Best,

Fengchao

yonghanyu commented 8 months ago

You could set the enzyme cuts to something like X so that there is no sites to cut (assuming there are no X in your proteins).

Best,

Fengchao

Thank you very much! I will give it a shot.