pyopenms

PyOpenMS

Overview

PyOpenMS provides Python bindings to the OpenMS library for computational mass spectrometry, enabling analysis of proteomics and metabolomics data. Use for handling mass spectrometry file formats, processing spectral data, detecting features, identifying peptides/proteins, and performing quantitative analysis.

Installation

Install using uv:

uv uv pip install pyopenms

Verify installation:

import pyopenms
print(pyopenms.__version__)

Core Capabilities

PyOpenMS organizes functionality into these domains:

1. File I/O and Data Formats

Handle mass spectrometry file formats and convert between representations.

Supported formats: mzML, mzXML, TraML, mzTab, FASTA, pepXML, protXML, mzIdentML, featureXML, consensusXML, idXML

Basic file reading:

import pyopenms as ms

# Read mzML file
exp = ms.MSExperiment()
ms.MzMLFile().load("data.mzML", exp)

# Access spectra
for spectrum in exp:
    mz, intensity = spectrum.get_peaks()
    print(f"Spectrum: {len(mz)} peaks")

For detailed file handling: See references/file_io.md

2. Signal Processing

Process raw spectral data with smoothing, filtering, centroiding, and normalization.

Basic spectrum processing:

# Smooth spectrum with Gaussian filter
gaussian = ms.GaussFilter()
params = gaussian.getParameters()
params.setValue("gaussian_width", 0.1)
gaussian.setParameters(params)
gaussian.filterExperiment(exp)

For algorithm details: See references/signal_processing.md

3. Feature Detection

Detect and link features across spectra and samples for quantitative analysis.

# Detect features
ff = ms.FeatureFinder()
ff.run("centroided", exp, features, params, ms.FeatureMap())

For complete workflows: See references/feature_detection.md

4. Peptide and Protein Identification

Integrate with search engines and process identification results.

Supported engines: Comet, Mascot, MSGFPlus, XTandem, OMSSA, Myrimatch