spectrum_utils

Efficient MS/MS spectrum processing and visualization in Python.

Features

• Spectrum processing
  • Precursor & noise peak removal
  • Intensity filtering
  • Intensity scaling
  • Peak annotations
    • Modification-aware (static & variable) peptide fragments
    • SMILES-based molecules
    • Custom strings
• Spectrum plotting
  • Fully customizable individual spectrum plots
  • Mirror plot of matching spectra
  • Interactive spectrum plots

Installation

spectrum_utils can easily be installed using conda:

conda install -c bioconda spectrum_utils

Dependencies

spectrum_utils has the following dependencies:

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

Missing dependencies will be automatically installed when you install spectrum_utils.

Alternative installation options

The recommended way to install spectrum_utils is using conda. Alternatively spectrum_utils can also be installed using pip:

pip install spectrum_utils

To install the basic spectrum_utils version. Or:

pip install spectrum_utils[iplot]

To include the interactive plotting functionality (requires Pandas and Altair).

When installing using pip it is recommended to explicitly install any dependencies (listed above or in the environment file) in advance. Any missing dependencies will be automatically installed from PyPI when you install spectrum_utils, except RDKit. Please refer to the RDKit installation notes for information on how to install RDKit.

In contrast, when installing spectrum_utils using conda all dependencies will be automatically installed, including RDKit.

Example

import spectrum_utils.plot as sup
import spectrum_utils.spectrum as sus


# Initialize spectrum information first...

spectrum = sus.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'
spectrum = (spectrum.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=50)
            .annotate_peptide_fragments(fragment_tol_mass, fragment_tol_mode,
                                        ion_types='aby'))

# Plot the MS/MS spectrum.
sup.spectrum(spectrum, grid=False)

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.