Preprocessing mzMLs

[bsphinney]

Hi casanovo team! Is it possible to preprocess mzML files before it searches them with the GPU. The reason I ask is that the gpu nodes are in high demand here and from what I can tell cassanovo spends a lot of time pre-processing the mzMLs . At least I think that's what it's doing as takes about 30 minutes to start searching compared to the MGF's I have tried to search before which start almost instantaneously.

On a related question is there any advantages to using using mzML's over MGF's ? Should I just be using MGF's instead?

[bsphinney]

nevermind, I think there is something going on with my clusters GPU nodes. However do you have any advice about using mzML's vs MGFs for casanovo? Do you see a major difference in the output?

Thanks!!

[wsnoble]

I would certainly hope that the results are identical irrespective of the format of the input file, though I don't think we have specifically tested that. Parsing the files should not take very much time either way.

[bsphinney]

I'll let you know if I see any differences!