Spectrum Fundamentals is a package we use in our rescoring pipeline. It was created to be able to handle spectra from different files.
- Annotate Spectra.
- Modify peptide sequence to follow one of the recommended notations of ProForma.
- Generate features than can be used by percoltor for rescoring (spectral angle, cosine similarity, Pearson's correlation, Spearman's correlation, etc.).
Install with:
pip install git+https://github.com/wilhelm-lab/spectrum_fundamentals
The annotation script can be found in the package in annotation/annotation.py.
- Install and import the function:
from spectrum_fundamentals.annotation.annotation import annotate_spectra
- Apply the function on any given dataframe with peptides meta data, raw intensities and mz:
annotate_spectra(dataframe)