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Spectrum Fundamentals

Spectrum Fundamentals is a package we use in our rescoring pipeline. It was created to be able to handle spectra from different files.

Features

  • 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.).

Installation

Install with:

pip install git+https://github.com/wilhelm-lab/spectrum_fundamentals

Usage

Annotation Pipeline

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)