Python for High Resolution Mass Spectrometry

Learn to code, code to learn.

An initial search for python packages to analyze high resolution mass spectrometry data, I found a few that seem rather useful. I will quickly explore them below.

molmass

The molmass package can be installed from the Python package index: https://pypi.org/project/molmass/.

Warning

The latest version of molmass requires Python version 3.8.

import molmass 
import numpy as np 
import pandas as pd 
import sys

You can check your version of a package with the .__version__ attribute. The latest version is ‘2022.12.9’.

print(sys.version)
3.10.18 (main, Jun  4 2025, 04:04:42) [GCC 13.3.0]
print(molmass.__version__)
2025.4.14

Let’s explore the properties of caffeine as detailed in the code example.

from molmass import Formula
f = Formula('C8H10N4O2')  # Caffeine
f
Formula('C8H10N4O2')

And look up the average, nominal and monoisotopic mass.

f.mass  # average mass
194.19095199999998
f.nominal_mass  # == f.isotope.massnumber in previous package version
194
f.monoisotopic_mass  # == f.isotope.mass in previous package version
194.08037557916
f.composition().dataframe()
Count Relative mass Fraction
Element
C 8 96.085920 0.494801
H 10 10.079410 0.051905
N 4 56.026812 0.288514
O 2 31.998810 0.164780

Next, let’s compute the mass spectrum for caffeine for all the different isotope combinations.

df = f.spectrum().dataframe()
df
Relative mass Fraction Intensity % m/z
Mass number
194 194.080376 8.988278e-01 1.000000e+02 194.080376
195 195.082873 9.262511e-02 1.030510e+01 195.082873
196 196.084968 8.021964e-03 8.924917e-01 196.084968
197 197.087214 5.004776e-04 5.568114e-02 197.087214
198 198.089410 2.370420e-05 2.637235e-03 198.089410
199 199.091577 9.094718e-07 1.011842e-04 199.091577
200 200.093769 2.738857e-08 3.047143e-06 200.093769
201 201.095939 6.190814e-10 6.887653e-08 201.095939
202 202.098016 1.031659e-11 1.147783e-09 202.098016
203 203.099952 1.265261e-13 1.407679e-11 203.099952
204 204.101915 1.092906e-15 1.215924e-13 204.101915
205 205.104365 4.529557e-18 5.039404e-16 205.104365

Let’s plot the the mass spectrum…

import matplotlib.pyplot as plt
Code 
fig, ax = plt.subplots()
ax.scatter(df['Relative mass'], df['Fraction'])
ax.set_xlabel('Monoisotopic mass (u)')
ax.set_ylabel('Mass fraction')
ax.set_title('Caffeine mass spectrum');

Here is also the mass spectrum for the different isotopes of iron.

Fe = Formula('Fe')
Fe.spectrum().dataframe()
Relative mass Fraction Intensity % m/z
Mass number
54 53.939609 0.05845 6.370294 53.939609
56 55.934936 0.91754 100.000000 55.934936
57 56.935393 0.02119 2.309436 56.935393
58 57.933274 0.00282 0.307344 57.933274 
CH2 = Formula('CH2')
CH2.monoisotopic_mass
14.01565006446

pyhrms

Need to look into this.

See: https://pypi.org/project/pyhrms/

pymzml

Need to look into this.

See: https://pypi.org/project/pymzml/

This seems to be an important package. Here is the documentation: https://pymzml.readthedocs.io/en/latest/