PSI-MS的MZML和MZidentML标准的编写者和受控词汇管理器
psims的Python项目详细描述
psims
原型为一个用于编写psims标准化xml文档的统一api工作，目前只有mzml和mzidentml
有关详细信息，请参见Documenation。
mzml最小示例
frompsims.mzml.writerimportMzMLWriter# Load the data to writescans=get_scan_data()withMzMLWriter(open("out.mzML",'wb'))asout:# Add default controlled vocabulariesout.controlled_vocabularies()# Open the run and spectrum list sectionswithout.run(id="my_analysis"):spectrum_count=len(scans)+sum([len(products)for_,productsinscans])without.spectrum_list(count=spectrum_count):forscan,productsinscans:# Write Precursor scanout.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 scansforprodinproducts: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 informationprecursor_information={"mz":prod.precursor_mz,"intensity":prod.precursor_intensity,"charge":prod.precursor_charge,"scan_id":prod.precursor_scan_id})
引用
如果在学术项目中使用psims，请引用：
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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