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pFindStudio / pFind3

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"Specific only" broken or misleading #22

Closed heuselm closed 5 years ago

heuselm commented 5 years ago

Dear pFind team,

Some peptides are erroneously labeled as specific, even though they map to multiple entries in the .fasta reference sequence database. Specific should (I assume) indicate proteotypicity which, in the context of the considered sequence space, means mapping to one parent sequence (AC) only.

I noticed a bug when visualizing results, specifically protein sequence view with aligned detected peptides. Limiting the view to "only specific" leaves peptides in the view which map to and may have originated from multiple different parent sequences (ACs).

This is highly misleading as to the quality and frequency of evidence for a target protein of interest. Hope you can make this a high priority bug fix.

Best, mh

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jalew188 commented 5 years ago

@heuselm "Specific Flag" = "S" means it is a specifically digested peptide, not for proteins.

heuselm commented 5 years ago

Alright, thanks for the clarification. I would have anticipated specificity to stand for specificity of a peptide sequence for the given protein entry, which is often of interest. Therefore, please consider it a feature suggestion - It would be nice to remove non-proteotypic peptides (that could also have been generated from another protein entry in the .fasta) for visualization purposes (Especially the nice sequence alignments!). Thanks & best, Moritz