Semi-specific digest, search and reporting

[DoerigC]

Is your feature request related to a problem? Please describe. Due to its high specificity, trypsin is the enzyme of choice in shotgun proteomics. Nonetheless, several publications do report the identification of semi-tryptic peptides: peptides which were cleaved at the C-Terminal side of R and K by trypsin at one end but not the other. These peptides are also important for a handful of specialized workflows such as LiP-MS (https://doi.org/10.1038/nprot.2017.100)

Describe the solution you'd like It would be nice to have the option to set the specificity of the digest to semi-specific. As a consequence, the cleave_sequence function could generate sequences that match a trypsin digest on either the C- or N-term of the peptide – but not necessarily both.

Ideally, these sequences would then not only be searched for, but their specificity (fully, specific-N-term or specific-C-term) could also be reported in the output tables. As an example report I added a screenshot of such a report from Spectronaut.

Describe alternatives you've considered Alternatively, one could use the already implemented unspecific search and then filter the identified peptides in the downstream analysis by matching them to the fasta and determine the specificity.

Additional context Attached screenshot of a sample report (see above)

[straussmaximilian]

Great suggestion. We are currently busy making a documentation revision, but potentially, this could be one item for the next releases.

[straussmaximilian]

Closed for inactivity. Feel free to comment in case.