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bzhanglab / PepQuery

PepQuery: a targeted peptide search engine
http://pepquery.org
GNU General Public License v3.0
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Peptide abundance from the standalone tool #61

Open emilyhmwong-vir opened 3 months ago

emilyhmwong-vir commented 3 months ago

Hi Bo,

I was using the standalone tool to identify/validate a novel peptide. How do I know the abundance of that peptide in different samples?

best, Emily

wenbostar commented 3 months ago

Hi Emily,

I think the best way is probably to add the novel peptide passed PepQuery validation into a database with known reference proteins and then run FragPipe/TMT-Integrator workflow on the customized database and the corresponding MS/MS files.

Bo

emilyhmwong-vir commented 2 months ago

Thanks Bo. May I know how you constructed the customized database? Could you please give an example?

wenbostar commented 1 month ago

May I know how you constructed the customized database? Could you please give an example?

Hi @emilyhmwong-vir , I'd like to recommemd you to ask the developers of FragPipe for help on this.

fcyu commented 1 month ago

@emilyhmwong-vir this is Fengchao from FragPipe team.

To make a fully supported FASTA file, it’d be better to make the protein header follow the UniProt rule.

Best,

Fengchao