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Rappsilber-Laboratory / build-xiview

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display 'monolinks' (linker modified peptides) #19

Closed colin-combe closed 5 years ago

colin-combe commented 6 years ago

as xiNET at crosslinkviewer.org does

colin-combe commented 5 years ago

further user requests for this. (Not having it blocks people from moving from xiNET to xiView.)

colin-combe commented 5 years ago

also https://github.com/Rappsilber-Laboratory/XiSearch/issues/43

lutzfischer commented 5 years ago

How do you detect "mono-links"?

colin-combe commented 5 years ago

omit LinkPos2 in uploaded CSV, same as here http://crosslinkviewer.org/CLMS-CSV.php#productTypes

can you see any problems with this?

there's currently no way of doing it with mzId

i need to update documentation about CSV format on xiView website

colin-combe commented 5 years ago

loop links are not yet implemented as they were in http://crosslinkviewer.org/CLMS-CSV.php#productTypes

lutzfischer commented 5 years ago

Xi does not write a monolink as such but just writes the cross-linker as a modification into the file. So I was wondering if one could provide a list of modifications to display like that?

colin-combe commented 5 years ago

yes, its always been something that's used by people using search software other than xi

you should be able to include things displayed like that by providing CSV files in which there's no LinkPos2

colin-combe commented 5 years ago

i think i've misinterpreted you - you'll be asking for an automated way of doing it on basis of whats already in xi output?

lutzfischer commented 5 years ago

No. I am basically asking for some means to flag specific observed modifications.

Meaning to provide a lsit of modifications found in the CSV/mzIdentML and let the user select some to be flagged on the protein-sequence.

That could be usefull beyond monolinks