Quantification of the novel peptide

[anuC]

Hi,

I am using standalone version for novel peptide identification/validation and I could identify the presence the novel peptide with 'yes' in the 'confident' column (I am with no experience in MS analysis). Now, I wonder whether the PepQery can provide any information about the quantity of the specific novel peptide in the MS sample or is there a way I can quantify the novel peptide from MS dataset.

Any help would be highly appreciated

Thanks in advance
Anu

[wenbostar]

Hi Anu, unfortunately not. I'd like to recommemd to use FragPipe pipeline for quantification. In brief, you could first validate your novel peptides using PepQuery and then create a new database by including both the novel peptides passed PepQuery validation and all reference proteins for FragPipe quantification.

[anuC]

Hi Bo, Thanks for the information.