emzed.ms2 package

Submodules

• emzed.ms2.attach_ms2_spectra module
  • LookupMS2
    • LookupMS2.find_spectra()
  • attach_ms2_spectra()
  • print_report()
• emzed.ms2.merge_spectra module
  • merge_spectra()
• emzed.ms2.sirius_export module
  • export_sirius_files()

Module contents

emzed.ms2.attach_ms2_spectra(peak_table, mode='union', mz_tolerance=0.0013, print_final_report=True)

takes peak_table with columns “rtmin”, “rtmax”, “mzmin”, “mzmax” and “peakmap” and extracts the ms2 spectra for these peaks.

the peak_table is modified in place, an extra column “ms2_spectra” is added. the content of such a cell in the table is always a list of spectra. for modes “union” and “intersection” this list contains one single spectrum.

modes:

• “all”: extracts a list of ms2 spectra per peak

• “max_range”: extracts spec with widest m/z range

• “max_signal”: extrats spec with maximal energy

• “union”: merges all ms2 spectra from one peak to one spectrum containing all peaks

• “intersection”: merges all ms2 spectra from one peak to one spectrum containing peaks which appear in all ms2 spectra.

mz_tolerance: only needed for modes “union” and “intersection”.

print_final_report: prints some final report with diagnosis messages for testing

if mz_tolerance parameter fits, you shoud set this parameter to True if you are not sure if mz_tolerance fits to your machines resolution.

emzed.ms2.export_sirius_files(peak_table, output_folder, abs_min_intensity=0.0, rel_min_intensity=0.0, *, overwrite=False)

exports peaks with attached ms2 spectra as sirius .ms files to the specified folder.

Parameters:

• peak_table – peak table with column spectra_ms2. Columns rt and id can be helpful to identify results in sirius, but are optional.

• output_folder – folder to write sirius files to.

• abs_min_intensity – filter ms2 spectra by absolute minimal intensity. if rel_min_intensity is also specified peaks compliant to both criteria are exported.

• rel_min_intensity – filter ms2 spectra by relatie minimal intensity compared to highest ms2 peak. if abs_min_intensity is also specified peaks compliant to both criteria are exported.

• overwrite – set to True when the output folder already contains .ms files and you take the risk to potentially overwrite existing files.

emzed.ms2.merge_spectra(spectra, mz_binning_width, is_ppm=False)

merges spectra.

Parameters:

• spectra – list of Spectrum objects or PeakMap or PeakMap.spectra attribute, must be of same ms leve..

• mz_binning_width – tolerance parameter for matching m/z values

• is_ppm – indicates if mz_binning_width is in Da or ppm.

Returns:

merged spectrum, return None if spectra is empty.