matchms

name	matchms
description	Parse MSP (mass spectrometry) files and count spectral data: spectrum count, peak count per spectrum, and total peak count. Use when users ask about mass spectrometry data parsing, spectral counting, or MSP file analysis.

Matchms: Mass Spectrometry Data Parsing

Overview

Matchms is a Python library for mass spectrometry data processing. This skill focuses on loading MSP (NIST Mass Spectral Library) files and extracting spectral information.

Loading MSP Files

from matchms.importing import load_from_msp

# Load MSP file
spectra = list(load_from_msp("/root/input.msp"))

Accessing Spectrum Data

Each spectrum has accessible properties. The MSP Name: field is stored in the compound_name metadata field:

for spectrum in spectra:
    # IMPORTANT: Use 'compound_name' not 'name' for MSP 'Name:' field
    name = spectrum.get("compound_name", "Unknown")
    peaks_mz = spectrum.peaks.mz          # Array of m/z values
    peaks_intensities = spectrum.peaks.intensities  # Array of intensities
    num_peaks = len(spectrum.peaks.mz)    # Number of peaks

Counting Spectra and Peaks

# Total number of spectra
total_spectra = len(spectra)

# Find spectrum with most peaks
max_peaks = 0
spectrum_with_most = None
for spectrum in spectra:
    peak_count = len(spectrum.peaks.mz)
    if peak_count > max_peaks:
        max_peaks = peak_count
        # Use 'compound_name' for the MSP Name: field
        spectrum_with_most = spectrum.get("compound_name", "Unknown")

# Total peaks across all spectra
total_peaks = sum(len(spectrum.peaks.mz) for spectrum in spectra)

Key Reference

• load_from_msp(filename) — Load MSP format files
• spectrum.peaks.mz — m/z values array
• spectrum.peaks.intensities — intensity values array
• spectrum.get("compound_name") — spectrum name from MSP Name: field
• spectrum.get("name") — may return None for MSP files, use compound_name instead