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
The official documentation can be found at https://spectrum-fundamentals.readthedocs.io
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