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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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Feature Request: add peptide start/end position to report #131

Closed kaisengit closed 3 years ago

kaisengit commented 3 years ago

Hello there and thanks for the great software!

I was wondering whether it would be feasible for you to add the peptide start (and optionally also end) position in relation to the fasta sequence? Spectronaut and Skyline both allow you to add this to their reports and it would really help my workflow if DiaNN included this too.

Thanks in any case!

vdemichev commented 3 years ago

Hi, this might be possible to implement, but what to do with peptides that map to several different proteins?

kaisengit commented 3 years ago

Good question. I am not sure how other software handles it as in my workflow I work with single proteins and have not encountered the problem yet. One possible approach could be to output peptide start in a list form in accordance with the Protein.Ids column so that the first start position matches the first protein in Protein.Ids and so on

DarioS commented 3 years ago

Oh, that would be convenient! May it assign ambiguous peptides based on distinctive peptides, like R.S.E.M. for RNA-seq does?

vdemichev commented 3 years ago

Visualisation of peptide positions is now possible with https://github.com/MannLabs/alphamap

kaisengit commented 3 years ago

Unfortunately I cannot get AlphaMap to work. It says

The columns necessary for further analysis cannot be extracted from the first experimental file. Please check the data uploading instructions for a particular software tool.

The correct columns are in the file however (and I am definitely using the correct report.tsv) and it does parse my sample names. Just the upload does not work. I guess however this should be a separate bug report for AlphaMap and not your tool.

In any case it would be neat to directly have the peptide start column in the report without the need of another tool as it would help (at least me) with downstream analysis using python/R.