MSFragger / FragPipe integration about alphamap

[ibludau]

Thanks for the suggestion to include FragPipe output.
We're still expanding on the input formats and can certainly aim to incorporate that for the next release!

[hcadre]

Purrfect! Thanks!

[ibludau]

Hey, could you maybe share an example combined_peptide.tsv with us so we can look into the integration? We would only need a handful of proteins including some PTMs.

[hcadre]

Enclosed, please find excerpts from the combined_peptide.tsv as well as from the combined_protein.tsv files. Hope this helps!
combined_protein_alphamap.txt
combined_peptide_alphamap.txt

[ibludau]

Thanks a lot for providing the example files. I realised that the site positions of observed PTMs are not annotated in the sequence. Is there an additional output file that contains this information? Otherwise AlphaMap cannot show them.

[hcadre]

Oh yes, I should have known better: Unfortunately, FragPipe / MSFRagger currently does not provide PTM positional information on the protein level. According to Alexey Nesvizhskii this is due to Philosopher, which does not generate site-level reports and that there is a need for parsers / tools that would do the job. Fragpipe however generates a peptide.tsv file per each raw file, which contains information about the position of a PTM relative to the sequence of the peptide, in which the PTM is present. But that would not help a lot, would it? I attach an example anyway.
peptide_alphamap.txt

[ibludau]

This table actually contains the necessary information, but this means that you could only upload single runs at a time I assume? That is slightly suboptimal.
Options are therefore the following:

1. enable combined_peptide.tsv as input format and ​and neglect PTM information at this point
2. enable the peptide.tsv file import for individual runs including PTM information (but being limited to a single run per trace)

Do you have a preference for your applications?

[EugeniaVoytik]

Thank you for suggesting this feature! We've integrated two options that Isabell mentioned in the previous comment. You may read more about it in the instructions for the import of FragPipe output files in AlphaMap in GUI directly or in the README.md file.