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How to define CE and charge state for spectral library generation workflow #126
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This is currently hardcoded in the digest function in spectrum-io. I will separate the digestion from writing the output file and add a configuration file section for library generation options containing:
Requires:
This is a breaking change in spectrum-io. |
Hi @picciama, what is the status quo here? Is it possible to def. a CE paramter in specLib generation workflow? I can't see any corresponding change in the online docu. Best, |
How urgent is it? I was pretty busy with some higher prio stuff, see release history. But given that we also have another issue in that regard (#157) I can do this next. |
Hmmm...I would say depends on Ludwig. I personally think we need it for the Koina manuscript. |
Hey Tobi, the current development branch of oktoberfest now has the new spectral library generation workflow. Please check if this is working for you. Also please look at the newest documentation because the config has changed: https://oktoberfest.readthedocs.io/en/latest/jobs.html#b-spectral-library-generation I will also merge the generic model support branch soonish and release this together to have a working version for the koina manuscript. I also optimized the workflow so you should see extreme runtime improvements. I tested this already on ~1.7 Mio peptides. This works within less than 10 minutes for both spectronaut and msp compared to more than an hour and the library size went from 16 GB to 4.5 GB and 4.6 GB to 1.5 GB for spectronaut and msp, respectively, due to the following changes:
Please try it out and tell me if this makes sense in terms of default values and if you have additional suggestions that might be helpful. |
Hi @picciama, NICE! 🥳 will test asap. A question regarding the For the example config file:
These following lines can be deleted when starting from a FASTA DB?
|
Yes, the intensity < minIntensity will be filtered out, intensity >= minIntensity will be in the file. If you really want all, you need to set minIntensity to 0. Koina adds a very small epsilon at around 1e-8 to "negative" or zero peaks according to Ludwig, but since it is rounded to 4 digits, you will see 0.0000 in these cases. The search results are indeed not necessary for spectral library generation. I will remove it from the config examples in the documentation. |
Question
Dear oktoberfest maintainers,
I tried the
SpectralLibraryGeneration
workflow starting from a complete reference proteome ("library_input_type": "fasta"
) and the job finished successfully. Nice! But it seems like the default settings for the workflow are predicting charges 2, 3, 4 at NCE 30:How can I reduce the charge states (2 and 3 or only 2) or select a specific NCE? My settings were:
Best,
Tobi
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