Search2: Mass Spectrometry Data Analysis

Search2 (the Spectral Elementaly-Altered Compound Highlighter, or SEArCH) is a Python tool for analyzing LC/MS mass spectrometry data, by identifying molecules with a specific mass difference (e.g., SO₃, gain/loss of functional groups, isotope labeling). It supports single .mzML files, lists of files, or entire directories, and provides flexible output options including CSV, heatmaps, and consensus feature maps.

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Features

• Automated search for mass differences (default: SO₃, 79.9569 Da)
• Supports single files, file lists, or directories
• Flexible filtering by retention time, relative intensity, and mass
• Optional feature map analysis using pyOpenMS
• Export results as CSV (single experiment), TSV (combined results), heatmaps, and consensusXML
• MS2 spectra analysis
• Comprehensive logging

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Requirements

• Python 3.8+ (tested on 3.12.10)
• pyOpenMS
• numpy
• matplotlib
• tqdm

Install dependencies with:

pip install pyopenms numpy matplotlib tqdm

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Usage

Run the main script from the command line:

python Search.py [options] <filename>

Arguments

• filename : Path to a .mzML file, a .txt file with file paths, or a directory containing .mzML files.

Options

Option	Description	Default
-l, --lower	Lower retention time limit in seconds.	30
-u, --upper	Upper retention time limit in seconds.	3000
-t, --tolerance	Mass tolerance for matching peaks (Da).	0.001
-c, --cutoff	Minimum intensity threshold for peaks.	0.05
-m, --mass	Mass difference to search for (Da).	79.9569
-o, --csvoff	Disable CSV output for candidate pairs.	(enabled)
-g, --graph	Enable heatmap output. Use twice for helper lines.	(disabled)
-n, --minmass	Minimum m/z value for unsulfated species.	0
-d, --deisotopingdisable	Disable deisotoping of spectra.	(enabled)
-e, --merger	Enable merging of spectra before analysis.	(disabled)
-s, --subfolder	Name of subfolder for output files.	None
-r, --retlim	Disable retention time limit for sulfated species.	(enabled)
-q, --combine	Export combined TSV summary of all experiments.	(disabled)
-j, --msmsOn	Enable MS2 spectra analysis.	(disabled)
-f, --featuremap	Use pyOpenMS feature map algorithm instead of standard SEARCH.	(disabled)
-p, --scope	Comparison scope for the SEARCH algorithm.	1

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Output

• CSV files: Candidate pairs found in each experiment.
• Heatmaps: Visual representation of retention times.
• Combined TSV: Summary of all experiments (if enabled).
• ConsensusXML: Consensus feature map (if enabled).
• MS2 TSV: MS2 analysis results (if enabled).
• Log files: Full record of arguments, progress, and results.

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Example

python Search.py data/example.mzML -n 100 -u 1200 -s Example_Data -gg -q 

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Project Structure

Search2/
├── Search.py
├── search/
│   ├── __init__.py
│   ├── analyse.py
│   ├── export.py
│   ├── setup.py
│   ├── misc_functions.py
│   ├── logs/
├── search_output/

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License

MIT License

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Note: This tool is intended for research use. Please validate results before using in production or clinical settings.