spectrum-io 0.9.0

IO related functionalities for oktoberfest.

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