Spectrum IO: File / Data Conversion for Mass Spec data within the Oktoberfest ecosystem
spectrum_io is a package primarily developed for usage within the rescoring and spectral library generation pipeline oktoberfest (https://github.com/wilhelm-lab/oktoberfest).
- It provides the following functionalities:
read search results from different search engines (MaxQuant, MSFragger, Sage, Xisearch) or a generic csv format and transform them to the internal format for rescoring with oktoberfest
extraction of MS2 level spectra from .RAW files and conversion to to mzML for rescoring with oktoberfest
spectra extraction from .d folders, conversion to .hdf5 format, and aggregation to MS2 level with metadata from a MaxQuant search for timsTOF rescoring with oktoberfest
in-silico digestion of a fasta file with various configuration options (protease, missed cleavages, length of peptides, fragmentation, …) for spectral library generation with oktoberfest
write spectral libraries in dlib, msp, or spectronaut(csv) format
parquet file creation for peptide prediction model development and refinement within DLOmix
Documentation
The official documentation is available at https://spectrum-io.readthedocs.io/
How to Cite
Please always cite the main publication:
Oktoberfest: Picciani M, Gabriel W, Giurcoiu VG et al. (2023), Oktoberfest: Open-source spectral library generation and rescoring pipeline based on Prosit, Proteomics
Metadata
Release files for spectrum-io 0.9.0
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
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| spectrum_io-0.9.0.tar.gz | 147.8 kB | With provenance | Details for spectrum_io-0.9.0.tar.gz |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| spectrum_io-0.9.0-py3-none-any.whl | Python 3 | none | any | Details for spectrum_io-0.9.0-py3-none-any.whl |
Total release size: 309.9 kB
Release files / spectrum_io-0.9.0.tar.gz
| Download URL | spectrum_io-0.9.0.tar.gz |
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| Size | 147.8 kB |
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| Size | 162.2 kB |
| Tags | Python 3 |
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