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kusterlab / prosit

Prosit offers high quality MS2 predicted spectra for any organism and protease as well as iRT prediction. When using Prosit is helpful for your research, please cite "Gessulat, Schmidt et al. 2019" DOI 10.1038/s41592-019-0426-7
https://www.proteomicsdb.org/prosit/
Apache License 2.0
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API for Prosit predictions #64

Closed MarcIsak closed 3 years ago

MarcIsak commented 3 years ago

Hello,

I wonder if it is possible to use some sort of API to send / retrieve jobs from the Prosit server(s)? That would make my life much easier when submitting several jobs ;).

Thank you for the amazing Prosit tool!

Best,

Marc

LLautenbacher commented 3 years ago

Hi Marc,

we do not offer and do not plan an API for Prosit since our server-infrastructure would not be able to handle the number of requests we expect to get.

I am sorry for not being able to help you more with this.

Best, Ludwig

kevinkovalchik commented 3 years ago

Hi @MarcIsak. I also am interested in an API to the tool. I don't know if it would be useful to you, but I have been doing a little work on a programmatic interface to the Prosit models (run locally, not connecting with the online server): https://github.com/kevinkovalchik/my_prosit

I have not had to change much from the original Prosit code. Mainly I migrated it to Tensorflow 2 and added a "Predictor" class which lets you use the Prosit models without interfacing with the online server or running a local server. Also some convenience functions like calculating the normalized spectral contrast angle between an observed spectrum (from mzml) and a predicted.

It is not very well tested or documented and probably not the most robust implementation at this point, but perhaps it could be of interest. If you have questions or suggestions feel free to post an issue there.

@LLautenbacher, as Marc said, thank you for the very nice tool!

Kevin