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Noble-Lab / casanovo

De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model
https://casanovo.readthedocs.io
Apache License 2.0
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WARNING: Skipped spectra with invalid precursor info #326

Closed lutfia95 closed 4 months ago

lutfia95 commented 4 months ago

Hey,

in which cases are the spectra skipped due to invalid precursor info? I have dataset which contains some not cleaned data and not sure if there is any way to clean/pre-process it.

Best, Ahmad

wsnoble commented 4 months ago

Casanovo will skip spectra for two reasons:

  1. The charge state is larger than the maximum allowed charge state (as per max_charge), or

  2. The spectrum itself is misformatted and can't be parsed.

We are working on adding a threshold for the minimum number of peaks configurable here and on giving more details about the skipped spectra.