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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

Quantitation #45

Closed lgatto closed 1 year ago

lgatto commented 1 year ago

Could you clarify whether sage does TMT MS2 quantitation (none in our result files)? Re-reading the README file, it looks like it's only MS3.

Thank you in advance.

lazear commented 1 year ago

There is support for MS2 quantitation in the codebase, but it's not enabled as a CLI flag yet. Let me push out a release that enables this.

I haven't tested MS2 quant, but I have extensively validated the MS3 quant against Proteome Discoverer (across 100s of files). MS2 quant uses the same quantitation code, so it should be fine, but let me know if there are any issue once it's live.

lazear commented 1 year ago

OK - v0.8.1 has a configuration flag quant.tmt_level that can be set to 2 (defaults to 3). Sage is currently also pre-processing MS2 spectra for search (fragment_min_mz, deisotope options), so make sure to set these to reasonable values (126, false) so that MS2 quantitation can proceed smoothly

lgatto commented 1 year ago

Thank you! Will test and report back here.

lgatto commented 1 year ago

All working as expected here. We haven't been able to compare the quantitation data against other software yet, but the distributions look as expected.

lazear commented 1 year ago

Great! I will close the issue for now, please re-open if anything looks wonky!