emzed.ms2.sirius_export module

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

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.