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bigbio / quantms

Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
https://quantms.org
MIT License
34 stars 37 forks source link

Add Multiple or Custom Enzymes #273

Open jackrogan opened 1 year ago

jackrogan commented 1 year ago

Description of feature

Is it possible to run a search with multiple enzymes, or to add a custom enzyme (in this case with the appropriate cleaving locations expected for a 2-enzyme digestion?)

If it helps, the digestions I'm interested in running are Trypsin + Asp-N and Trypsin + Glu-C.

Thanks!

ypriverol commented 1 year ago

@jackrogan this is not supported. Yet, we will give priority for next release. Can you let me know which dataset do you have in mind that can help us to test.

jpfeuffer commented 1 year ago

Yes, it is a bit complicated. In theory, we need to model any order of enzymes and add an option to allow for simultaneous application. While e.g. Comet supports this, many other search engines do not. We could probably release a Comet-only version of this feature earlier than a general one.

ypriverol commented 1 year ago

I know already that when I'm using enzymes different that Trypsin, I need to enable only Comet, this is already happening because, examples Trypsin/P doesn't work properly with multi search engine.

As you said similar approach can be followed for multiple enzymes, only allow Comet when multiple enzymes is needed.

jackrogan commented 1 year ago

@jackrogan this is not supported. Yet, we will give priority for next release. Can you let me know which dataset do you have in mind that can help us to test.

I don't have any data yet - I'm still working out how to analyse a planned experiment.

jpfeuffer commented 1 year ago

I know already that when I'm using enzymes different that Trypsin, I need to enable only Comet, this is already happening because, examples Trypsin/P doesn't work properly with multi search engine.

As you said similar approach can be followed for multiple enzymes, only allow Comet when multiple enzymes is needed.

Trypsin/P should work. Please open another issue for this.