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Peptide abundance from the standalone tool #61

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emilyhmwong-vir opened this issue Apr 29, 2024 · 4 comments
Open

Peptide abundance from the standalone tool #61

emilyhmwong-vir opened this issue Apr 29, 2024 · 4 comments
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@emilyhmwong-vir
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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
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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
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Thanks Bo. May I know how you constructed the customized database? Could you please give an example?

@wenbostar
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wenbostar commented Jun 27, 2024

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
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fcyu commented Jun 27, 2024

@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

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