Comments (4)
bittremieux
commented on July 23, 2024
This hasn't really been completed though?
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melihyilmaz
commented on July 23, 2024
We have
Casanovo can predict peptide sequences for MS/MS spectra in mzML, mzXML, and MGF files. This will write peptide predictions for the given MS/MS spectra to the specified output file in mzTab format
in the Getting Started page
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bittremieux
commented on July 23, 2024
Yes, but I think @wsnoble also wanted a brief description of what the output mzTab file looks like. So explain what information is included in the metadata and PSM sections.
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wsnoble
commented on July 23, 2024
Yes. I think it would be helpful to explain what the various columns mean. If possible, please also include pointers to descriptions of the mzML, mzXML, MGF and mzTab format specifications.
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Related Issues (20)
- Exclude some PTMs for prediction? HOT 2
- Question about tracking spectra from MGF files in output HOT 1
- Using HDF5 file as train/val dataset leads to index out of bound error HOT 9
- No Models Saved, No Validation Loss Reported HOT 3
- Save final model HOT 1
- how to train casanovo v4 on huge dataset like massive-kb from scratch? HOT 3
- What is the criteria of saving the top k models in Casanovo version 4? HOT 1
- add additional inputs to encoder and decoder HOT 1
- Add contrastive loss term
- Implement bidirectional decoding HOT 1
- Add rotary embeddings
- mzTab validation
- Automate mzTab validation HOT 7
- More information about the train/val/test split HOT 2
- WARNING: Skipped spectra with invalid precursor info HOT 1
- Export casanovo to torchscript/onnx HOT 1
- ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all() HOT 3
- Make Casanovo produce Skyline compatible output
- 9-Species Benchmark Set: Data Preprocessing Step? HOT 5
- Migrating PeptideMass, PeptideDecoder, and PeptideEncoder from depthcharge v0.2.3 to casanovo HOT 3
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