PyOpenMS

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:

1. Load and process raw data
2. Detect features
3. Align retention times across samples
4. Link features to consensus map
5. 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