bigbio
Inclusion of the MSFragger search engine and open search feature
Description of feature
I'm aiming to integrate the MSFragger search engine into the QuantMS workflow. It should be included as an option for the closed search, alongside a completely new open modification search feature. The roadmap and workarounds (licencing of MSFragger) suggested by @ypriverol for the inclusion are as follows:
- Require msfragger to be added to the
binfolder of the pipeline with no container in the middle. - Execute msfragger search always from the
binlike a normal java tool. No container needed - For CI/CD put the msfragger version into a private place (github repo) or other authenticated system, add the keys to the secrets in quantms repo, and pull the msfragger before testing
- Put all the other tools needed that are free into conda packages.
- Implement the msfragger steps as a new search engine (for closed search)
- Implement a pipeline (with no comet or msgf+) for open search based on msfragger
- Testing both pipelines and integration into quantms with some data
- Run in the existing datasets and see how it goes in both pipelines (multi-closed-search) and (open search) to detect new modifications
@tillenglert If there are licensing issues at play, you could also consider using Sage instead of MSFragger.
Sage is an open source & MIT-licensed search engine that uses MSFragger's ion indexing approach, runs up to 5x faster on open (and narrow) searches, and supports RT prediction, integrated linear discriminant analysis, PEP calculation, and TMT quantification.
@lazear can you give me a contact to call you and talk. We are really interested in integrating Sage in quantms. I have tried to reach you over twitter or scripps but can't find an email.
