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lazear / sage

Proteomics search & quantification so fast that it feels like magic
https://sage-docs.vercel.app
MIT License
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Support modification of amino acids at peptide or protein termini #63

Closed mvaudel closed 1 year ago

mvaudel commented 1 year ago

Hi,

Thanks for leading this exciting project. Some common modifications target amino acids at peptide or protein termini. Examples: https://www.thegpm.org/TANDEM/api/pqp.html https://www.thegpm.org/TANDEM/api/pqa.html

Last time I checked, this was not supported. It would be great to have it implemented - or some pointers on how we can help with this :-)

Many thanks,

Marc

lazear commented 1 year ago

Hi Marc,

Currently there is support for peptide/protein-terminal modifications that are not specific for certain AAs. I think it should be pretty straightforward to extend the modification syntax and allow specificity, thanks for the reminder!

Best, Mike

lazear commented 1 year ago

Marc,

I've added support for modifications of amino acids at peptide/protein termini:

"variable_mods": {
    "M": [15.9949],
    "^Q": -17.026549,
    "^E": -18.010565,
    "[": 42.010565
}

You can also now specify multiple modifications for a single amino acid/terminus. SearchGUI/PeptideShaker came in handy while developing this - super easy to run X!Tandem/Comet and drop in the Sage results to compare 😃.