ms1isotopes 0.4.0

Extract and evaluate MS1 isotope distributions from LC-MS/MS proteomics data

ms1isotopes

A Python package for extracting and evaluating MS1 isotope distributions from LC-MS/MS proteomics data.

What it does

Given an mzML file and a list of peptide identifications, ms1isotopes:

1. Extracts experimental isotope envelopes (m/z + intensity for up to 6 peaks) across the chromatographic elution window
2. Computes theoretical isotope distributions using the BRAIN algorithm (via brainpy)
3. Scores similarity between experimental and theoretical distributions using the spectral angle
4. Outputs annotated results in Excel, TSV, or hierarchical JSON

Installation

pip install ms1isotopes

Dependencies

• Python ≥ 3.9
• numpy, pandas, numba
• pyteomics (for mzML parsing)
• lxml (XML backend for pyteomics)
• brainpy (brain-isotopic-distribution)
• openpyxl (for Excel I/O)

Quick start

Command line

ms1isotopes extract \
    -m sample.mzML \
    -i identifications.xlsx \
    -o results \
    --tolerance 5

This produces results.xlsx, results.tsv, and results.json.

Python API

import ms1isotopes

# Load input list (Excel, CSV, or TSV)
input_list = ms1isotopes.read_input_list("identifications.xlsx")

# Run extraction
results = ms1isotopes.extract_ms1_isotope_distributions(
    mzml_path="sample.mzML",
    input_list=input_list,
    tolerance_ppm=5.0,
    n_isotopes=6,
)

# Save results
ms1isotopes.results_to_excel(results, "output.xlsx")
ms1isotopes.results_to_json(results, "output.json")

Computing isotope distributions without mzML data

import ms1isotopes
import numpy as np

# Peptide → atomic composition
comp = ms1isotopes.sequence_to_composition(
    "PEPTIDE", charge_state=2, n_carbamidomethyl=0
)
# → {'C': 34, 'H': 57, 'N': 7, 'O': 15, 'S': 0}

# Theoretical isotope distribution (via BRAIN)
mz_values, intensities = ms1isotopes.theoretical_isotope_distribution(comp, n_peaks=6)

# Spectral angle against experimental data
experimental = np.array([10000, 5500, 2000, 500, np.nan, np.nan])
sa = ms1isotopes.spectral_angle(intensities, experimental)

Input list format

The input list must contain these columns:

Column	Description
Peptide_Sequence	Amino acid sequence (single-letter codes)
Charge_State	Precursor charge state
Modifications	PTMs, e.g. C(57.0214)M(15.9949) or empty
RetentionTime	PSM retention time (seconds)
RetentionTimeWindowBefore	Extraction window before RT (seconds)
RetentionTimeWindowAfter	Extraction window after RT (seconds)

Optional columns: MZ (observed m/z), ErrorTolerance (ppm).

Output columns

The output DataFrame contains experimental isotope peaks, theoretical distributions from BRAIN, atomic composition, spectral angle, peak counts, and metadata. See the documentation for the full schema.

Testing

pip install ms1isotopes[dev]
pytest tests/

Citation

If you use ms1isotopes in your research, please cite:

[Work in progress]

License

GPLv3. See LICENSE for details.