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freejstone / CONGA

Implementation of the CONGA algorithm for a combined open and narrow search between experimental spectra and a peptide database.
MIT License
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Feature request: Make it work with Comet #3

Closed wsnoble closed 1 year ago

wsnoble commented 2 years ago

I think, if it's not too much effort, it would be excellent to ensure that Groupwalk works with Comet, ideally both the standalone version and the one that is packaged with Crux.

freejstone commented 2 years ago

Hi Bill,

I spent a little bit familiarising myself with Comet. The user needs to obtain target-decoy pairs (which are obtained via tide-index). I suppose the workflow for Comet users could be to use tide-index first, then to use Comet, using the ocncantenated target-decoy FASTA file and the target-decoy pairs produced by tide-index. But is this the usual workflow? Indeed the FAQ section says the following:

"Tide converts your FASTA file to an index (either as part of tide-search or by using tide-index), whereas Comet does searching directly from the FASTA file."

Which makes me think that the usual approach is to directly use Comet, in which case, one would be without the target-decoy pairs.

Is there a way to obtain these target-decoy pairs without tide-index? And if not, is it still worth Group-walk works with Comet (particularly for the standalone version outside of Crux)?

wsnoble commented 2 years ago

Comet uses reversed peptide decoys, so I don't think you actually need the target-decoy pair listing.

http://comet-ms.sourceforge.net/parameters/parameters_202101/decoy_search.php

freejstone commented 2 years ago

Comet (in crux) has been integrated. I just need to check that the search files in comet standalone are the same as comet in crux.

wsnoble commented 2 years ago

Alas, the column names in standalone Comet do indeed differ from those in Crux. This is something that has been causing Andy headaches recently, and in retrospect I wish we had just retained the same column names in both versions. I think we were trying to make crux comet and crux tide-search more consistent with one another.

freejstone commented 2 years ago

Standalone Comet is now integrated. Thankfully it wasn't too painful for me with how I set things up and given the fact that open groupwalk just returns the same format regardless of input.

freejstone commented 1 year ago

Closing this now since Standalone Comet is now supported.