spectrum_utils

Simple MS/MS spectrum preprocessing and visualization in Python.

Features

• Spectrum (pre)processing
  • Precursor & noise peak removal
  • Intensity filtering
  • Intensity scaling
  • Modification-aware fragment ion annotating (powered by Pyteomics)
• Spectrum plotting
  • Single spectrum with annotated ions
  • Mirror plot of matching spectra
  • Interactive spectrum plots

Example

import matplotlib.pyplot as plt

from spectrum_utils import plot
from spectrum_utils import spectrum


# Initialize spectrum information first...

spec = spectrum.MsmsSpectrum(identifier, precursor_mz, precursor_charge,
                             mz, intensity, retention_time=retention_time,
                             peptide=peptide)

# Preprocess the MS/MS spectrum.
fragment_tol_mass = 10
fragment_tol_mode = 'ppm'
spec = (spec.set_mz_range(min_mz=100, max_mz=1400)
            .remove_precursor_peak(fragment_tol_mass, fragment_tol_mode)
            .filter_intensity(min_intensity=0.05, max_num_peaks=150)
            .scale_intensity(scaling='root')
            .annotate_peaks(fragment_tol_mass, fragment_tol_mode,
                            ion_types='aby'))

# Plot the MS/MS spectrum.
plot.spectrum(spec)

plt.show()
plt.close()

(Condensed example. See here for the full code to generate the figure below.)

Installation

spectrum_utils can be installed easily via pip:

pip install spectrum_utils

Or via conda:

conda install -c bioconda spectrum_utils

Dependencies

spectrum_utils has the following dependencies:

• Altair
• Matplotlib
• Numba
• NumPy
• Pandas
• Pyteomics

Missing dependencies will be automatically installed when you install spectrum_utils.

API documentation

You can find the API documentation here.

Contact

For more information you can visit the official code website or send an email to wout.bittremieux@uantwerpen.be.