Writers and controlled vocabulary manager for PSI-MS's mzML and mzIdentML standards
Project description
psims
Prototype work for a unified API for writing Proteomics Standards Initiative standardized formats for mass spectrometry:
- mzML
- mzIdentML
- mzMLb
See the Documenation for more information
Installation
With pip:
pip install psims
With conda:
conda install -c bioconda -c conda-forge -c defaults psims
mzML Minimal Example
from psims.mzml.writer import MzMLWriter # Load the data to write scans = get_scan_data() with MzMLWriter(open("out.mzML", 'wb'), close=True) as out: # Add default controlled vocabularies out.controlled_vocabularies() # Open the run and spectrum list sections with out.run(id="my_analysis"): spectrum_count = len(scans) + sum([len(products) for _, products in scans]) with out.spectrum_list(count=spectrum_count): for scan, products in scans: # Write Precursor scan out.write_spectrum( scan.mz_array, scan.intensity_array, id=scan.id, params=[ "MS1 Spectrum", {"ms level": 1}, {"total ion current": sum(scan.intensity_array)} ]) # Write MSn scans for prod in products: out.write_spectrum( prod.mz_array, prod.intensity_array, id=prod.id, params=[ "MSn Spectrum", {"ms level": 2}, {"total ion current": sum(prod.intensity_array)} ], # Include precursor information precursor_information={ "mz": prod.precursor_mz, "intensity": prod.precursor_intensity, "charge": prod.precursor_charge, "scan_id": prod.precursor_scan_id, "activation": ["beam-type collisional dissociation", {"collision energy": 25}], "isolation_window": [prod.precursor_mz - 1, prod.precursor_mz, prod.precursor_mz + 1] })
Citing
If you use psims
in an academic project, please cite:
Klein, J. A., & Zaia, J. (2018). psims - A declarative writer for mzML and mzIdentML for Python. Molecular & Cellular Proteomics, mcp.RP118.001070. https://doi.org/10.1074/mcp.RP118.001070
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