pyopenms

SKILL.md

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 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

Basic identification workflow:

# Load identification data
protein_ids = []
peptide_ids = []
ms.IdXMLFile().load("identifications.idXML", protein_ids, peptide_ids)

# Apply FDR filtering
fdr = ms.FalseDiscoveryRate()
fdr.apply(peptide_ids)

For detailed workflows: See references/identification.md

5. Metabolomics Analysis

Perform untargeted metabolomics preprocessing and analysis.

Typical workflow:

Load and process raw data

Detect features

Align retention times across samples

Link features to consensus map

Annotate with compound databases

For complete metabolomics workflows: See references/metabolomics.md

Data Structures

PyOpenMS uses these primary objects:

MSExperiment: Collection of spectra and chromatograms

MSSpectrum: Single mass spectrum with m/z and intensity pairs

MSChromatogram: Chromatographic trace

Feature: Detected chromatographic peak with quality metrics

FeatureMap: Collection of features

PeptideIdentification: Search results for peptides

ProteinIdentification: Search results for proteins

For detailed documentation: See references/data_structures.md

Common Workflows

Quick Start: Load and Explore Data

import pyopenms as ms

# Load mzML file
exp = ms.MSExperiment()
ms.MzMLFile().load("sample.mzML", exp)

# Get basic statistics
print(f"Number of spectra: {exp.getNrSpectra()}")
print(f"Number of chromatograms: {exp.getNrChromatograms()}")

# Examine first spectrum
spec = exp.getSpectrum(0)
print(f"MS level: {spec.getMSLevel()}")
print(f"Retention time: {spec.getRT()}")
mz, intensity = spec.get_peaks()
print(f"Peaks: {len(mz)}")

Parameter Management

Most algorithms use a parameter system:

# Get algorithm parameters
algo = ms.GaussFilter()
params = algo.getParameters()

# View available parameters
for param in params.keys():
    print(f"{param}: {params.getValue(param)}")

# Modify parameters
params.setValue("gaussian_width", 0.2)
algo.setParameters(params)

Export to Pandas

Convert data to pandas DataFrames for analysis:

import pyopenms as ms
import pandas as pd

# Load feature map
fm = ms.FeatureMap()
ms.FeatureXMLFile().load("features.featureXML", fm)

# Convert to DataFrame
df = fm.get_df()
print(df.head())

Integration with Other Tools

PyOpenMS integrates with:

Pandas: Export data to DataFrames

NumPy: Work with peak arrays

Scikit-learn: Machine learning on MS data

Matplotlib/Seaborn: Visualization

R: Via rpy2 bridge

Resources

Official documentation: https://pyopenms.readthedocs.io

OpenMS documentation: https://www.openms.org

GitHub: https://github.com/OpenMS/OpenMS

References

references/file_io.md - Comprehensive file format handling

references/signal_processing.md - Signal processing algorithms

references/feature_detection.md - Feature detection and linking

references/identification.md - Peptide and protein identification

references/metabolomics.md - Metabolomics-specific workflows

references/data_structures.md - Core objects and data structures