Spectrum processing

See the quickstart for a brief introduction to how to start using spectrum_utils. Here we will describe the spectrum processing functionality provided by spectrum_utils in more detail.

Peak annotations

Fragment ions can be annotated as follows:

  • Using MsmsSpectrum.annotate_peptide_fragments(...) to annotate a, b, c, x, y, or z ions for peptide spectra.

  • Using MsmsSpectrum.annotate_molecule_fragment(...) using SMILES strings to annotate peaks with molecule (sub)structures.

  • Using MsmsSpectrum.annotate_mz_fragment(...) to annotate peaks with their m/z value.

Peak annotations can be visualized using the spectrum_utils plotting functionality.

The example in the quickstart shows how spectrum peaks can be annotated with peptide fragments.

The following example shows how spectrum peaks can be annotated with their m/z values:

import matplotlib.pyplot as plt
import pandas as pd
import spectrum_utils.spectrum as sus
import spectrum_utils.plot as sup
import urllib.parse

usi = 'mzspec:GNPS:GNPS-LIBRARY:accession:CCMSLIB00000840351'
peaks = pd.read_csv(
    f'https://metabolomics-usi.ucsd.edu/csv/?usi={urllib.parse.quote(usi)}')
precursor_mz = 633.2680
precursor_charge = 1
spectrum = sus.MsmsSpectrum(usi, precursor_mz, precursor_charge,
                            peaks['mz'].values, peaks['intensity'].values)
spectrum.filter_intensity(0.05)

tol_mass, tol_mode = 0.5, 'Da'
annotate_fragment_mz = [133.102, 147.080, 195.117, 237.164, 267.174, 295.170,
                        313.181, 355.192, 377.172, 391.187, 451.209, 511.231,
                        573.245, 633.269]
for fragment_mz in annotate_fragment_mz:
    spectrum.annotate_mz_fragment(fragment_mz, tol_mass, tol_mode)

fig, ax = plt.subplots(figsize=(12, 6))
sup.spectrum(spectrum, ax=ax)
plt.show()
plt.close()

Resulting in the following spectrum plot:

_images/annotations.png

Peptide modifications

When annotating peptide spectra the masses of the fragment ions will be automatically calculated to annotate the corresponding peaks. This functionality is modification-aware: you can specify static modifications to globally change the mass of specific amino acid residues and variable modifications to modify amino acids in specific positions for a given peptide.

Static modifications

Static modifications can be set as follows:

sus.static_modification('C', 57.02146)

To, for example, set a static carbamidomethylation of cysteine.

Modification mass differences can be either positive or negative.

All static modifications can be reset:

sus.reset_modifications()

Variable modifications

Variable modifications can be set for an individual spectrum and peptide by specifying the amino acid index and corresponding mass difference for each modification.

Modification positions can be the following:

  • The index of the amino acid where the modification is present (0-based).

  • ‘N-term’ for N-terminal modifications.

  • ‘C-term’ for C-terminal modifications.

For example, for a spectrum corresponding to peptide ‘DLTDYLMK’ with an oxidated methionine:

peptide = 'DLTDYLMK'
modifications = {6: 15.994915}

spectrum = sus.MsmsSpectrum(
    identifier, precursor_mz, precursor_charge, mz, intensity,
    peptide=peptide, modifications=modifications)

Neutral losses

Besides the canonical a, b, c, x, y, and z ions, each of these ions can also be automatically annotated with a neutral loss (or gain). Neutral losses need to be specified by their identifier (molecular formula) and their mass difference:

spectrum.annotate_peptide_fragments(0.05, 'Da', ion_types='aby',
                                    neutral_losses={'NH3': -17.026549,
                                                    'H2O': -18.010565})

The above example will consider all peaks with an optional ammonia (NH3) or water (H2O) neutral loss.

Common neutral losses to consider are:

Neutral loss/gain Molecular formula Mass difference
Hydrogen H 1.007825
Ammonia NH3 17.026549
Water H2O 18.010565
Carbon monoxide CO 27.994915
Carbon dioxide CO2 43.989829
Formamide HCONH2 45.021464
Formic acid HCOOH 46.005479
Methanesulfenic acid CH4OS 63.998301
Sulfur trioxide SO3 79.956818
Metaphosphoric acid HPO3 79.966331
Mercaptoacetamide C2H5NOS 91.009195
Mercaptoacetic acid C2H4O2S 91.993211
Phosphoric acid H3PO4 97.976896

Note that typically the neutral loss mass difference should be negative.