Isotope Distribution Analysis

Isotope distribution analysis enables determination of lipid double bond position through examination of the isotope distributions for putative OzID fragments from LC-OzID-MS data. This analysis is implemented in lipidoz.workflows.run_isotope_scoring_workflow().

Inputs

• OzID data in .mza format

• Lipid target list in .csv format † with the following columns:

  • lipid – lipid name in standard abbreviated format

  • adduct – MS ionization state

  • retention time – observed retention time

• Parameters controlling data extraction/interpretation:

  • RT tolerance – determines the size of the retention time window (around fitted retention time) that is used for extraction of precursor and OzID fragment MS1 spectra

  • RT extraction window – determines the size of the window (around target retention time) used for extraction of LC chromatograms for retention time fitting

  • m/z tolerance – m/z tolerance for extraction of LC chromatograms

  • deuterium label – count of deuteriums in labeled lipids (e.g., in SPLASH LipidoMIX standards)

  • deuterium label in NL – indicates whether the deuteriums in labeled lipids are present in the neutral loss from OzID fragmentation (and therefore must be accounted for in the fragment formulae)

† The target list is expected to have one header row, and rows beginning with “#” are treated as comments and skipped

Output

• LipidOz Analysis Results – Full analysis results including plots and scoring information for all lipid targets, organized in a hierarchical dictionary datastructure (see Structure of run_isotope_scoring_workflow Results for details). These results can be saved in a binary format for viewing later (use function: lipidoz.workflows.save_isotope_scoring_results()) or exported in tabular format as an Excel spreadsheet (use function: lipidoz.workflows.write_isotope_scoring_report_xlsx()).

Examples

example of isotope distribution analysis with labeled standards

from lipidoz.workflows import (
    run_isotope_scoring_workflow, save_isotope_scoring_results, write_isotope_scoring_report
)


def main():

    # OzID data file, in .mza format
    oz_data_file = 'data/SPLASH_d7_pos_Oz.mza'

    # target list in .csv format
    target_file = 'splash_d7_pos.csv'

    # setup parameters controlling data extraction/interpretation
    rt_tol = 0.2
    rt_ext_win = 1.5
    mz_tol = 0.01
    # these parameters are specific for describing deuterium labels
    d_label = 7
    d_label_in_nl = True

    # run the analysis
    results = run_isotope_scoring_workflow(oz_data_file, target_file,
                                           rt_tol, rt_ext_win, mz_tol,
                                           d_label=d_label, d_label_in_nl=d_label_in_nl)

    # when analysis is complete, save and export the results
    save_isotope_scoring_results(results, 'splash_d7_pos.loz')
    write_isotope_scoring_report_xlsx(results, 'splash_d7_pos_iso_scoring.xlsx')


if __name__ == '__main__':
    main()

example of isotope distribution analysis using the progress callback

from lipidoz.workflows import (
    run_isotope_scoring_workflow, save_isotope_scoring_results, write_isotope_scoring_report
)

def progcb(lipid_name, adduct, pos, tot):
    # simple callback function that just prints out info
    s = 'lipid: {} adduct: {} ({} of {})'
    print(s.format(lipid_name, adduct, pos, tot), flush=True)


def main():

    # OzID data file, in .mza format
    oz_data_file = 'data/total_lipids_1234_pos_Oz.mza'

    # target list in .csv format
    target_file = 'total_lipids_1234_pos.csv'

    # setup parameters controlling data extraction/interpretation
    rt_tol = 0.2
    rt_ext_win = 1.5
    mz_tol = 0.01

    # run the analysis
    # here we will use the progress callback to report on progress after each lipid target
    results = run_isotope_scoring_workflow(oz_data_file, target_file,
                                           rt_tol, rt_ext_win, mz_tol,
                                           progress_cb=progcb)

    # when analysis is complete, save and export the results
    save_isotope_scoring_results(results, 'total_lipids_1234_pos.loz')
    write_isotope_scoring_report_xlsx(results, 'total_lipids_1234_pos_iso_scoring.xlsx')


if __name__ == '__main__':
    main()