Open emilyhmwong-vir opened 6 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
Thanks Bo. May I know how you constructed the customized database? Could you please give an example?
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.
@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
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