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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