Scientific Skill: 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:

```bash
uv uv pip install pyopenms
```

Verify installation:

```python
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:

```python
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:

```python
# 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.

```python
# 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:

```python
# 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

```python
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:

```python
# 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:

```python
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