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lazear / sage

Proteomics search & quantification so fast that it feels like magic
https://sage-docs.vercel.app
MIT License
201 stars 38 forks source link

Bruker tdf integration #91

Closed sander-willems-bruker closed 8 months ago

sander-willems-bruker commented 8 months ago

This PR adds the option to identify peptides directly from Bruker ddaPASEF raw data (i.e. a .d folder containing analysis.tdf and analysis.tdf_bin files) instead of converting to mzml first.

lazear commented 8 months ago

Super exciting, thanks! I will test and review when I am back from vacation!

lazear commented 8 months ago

I have tested on a couple data sets and everything seems to work well (and it's fast!) - I think it's ready to merge in, with the only remaining thing being access to MS1 frames or psuedo/merged spectra (could also be implemented on Sage's side?)

sander-willems-bruker commented 8 months ago

I updated to timsrust 0.2.0 which includes the error forwarding instead of panicking (still assuming the files are actually parsable). Furthermore there is now a read ms1 and read ms2 option available. By splitting this, it also is twice as fast as ms1 frames are not read anymore when reading spectra.

lazear commented 8 months ago

Excellent, thank you. I will go ahead and rebase/squash so that CI/testing can get set up, and we can continue working on further integration!

sander-willems-bruker commented 8 months ago

Turns out I forgot to put those options into the filereader itself, apologies. Timsrust 0.2.1 should now be available to avtually do this