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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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Extract PTM descriptions from Unimod #24

Open wsnoble opened 1 year ago

wsnoble commented 1 year ago

Bo pointed out that we could extract candidate PTM identifications from Unimod based on the observed delta mass. This would make CONGA much more useful to the end user.

mriffle commented 1 year ago

Not saying you shouldn't do this, but Limelight will basically do this for you--it links out to Unimod for open mod masses (rounded to some scale). Part of the challenge w/ unimod is that, depending on the scale of your rounding, you will match multiple, different mods. And with open mod masses, since they include the error from the ID (entire delta mass being considered a mod), you won't ever exactly match anything in unimod.

freejstone commented 1 year ago

Yes I had wondered if Limelight did this already anyhow, but have been meaning to ask you about that Mike. Thanks!