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peterblattmann / SWATH2stats

https://peterblattmann.github.io/SWATH2stats/
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Have filter_proteotypic_peptides() identify proteotypic peptides by looking for unique peptide-protein mappings instead of looking for the string "1/" in the protein name #4

Open dpanyard opened 3 years ago

dpanyard commented 3 years ago

Hi there, thanks for developing this package. I'd like to suggest an enhancement to the filter_proteotypic_peptides() function. As I understand the function currently, it identifies proteotypic peptides solely by looking for the string "1/" at the start of the protein identifier. It would be helpful if the function identified proteotypic peptides itself by looking at which peptides map uniquely to one protein rather than relying on this string in the ProteinName column.

peterblattmann commented 3 years ago

Dear Daniel, thank you very much for this comment and suggestion. Yes, you are right it infers proteotypic peptides based on the string and I did this easier solution as I thought that the identification if a peptide is proteotypic would need to be solved/addressed while designing the SWATH/DIA-library. But you are right that it could be useful to do a check afterwards by comparing to a provided fasta file. I will think about it but cannot promise if I find time to do this. If you (or someone else) want to contribute a function feel free. Thank you in any case for your comment!