def run_thermo(file_location): MSParameters.mass_spectrum.threshold_method = 'relative_abundance' MSParameters.mass_spectrum.relative_abundance_threshold = 1 MSParameters.mass_spectrum.threshold_method = 'auto' MSParameters.mass_spectrum.s2n_threshold = 6 parser = rawFileReader.ImportMassSpectraThermoMSFileReader(file_location) transient_time_list = parser.get_icr_transient_times() print(transient_time_list) # sums all the mass spectra mass_spectrum = parser.get_average_mass_spectrum_in_scan_range() # sums scans in selected range mass_spectrum = parser.get_average_mass_spectrum_in_scan_range( first_scan=1, last_scan=5) scans_list = [1, 4, 6, 9] # sums scans in selected range mass_spectrum = parser.get_average_mass_spectrum_by_scanlist(scans_list) return mass_spectrum
def run_thermo_reduce_profile(file_location, corems_params_path, first_scan, last_scan): from corems.mass_spectra.input import rawFileReader parser = rawFileReader.ImportMassSpectraThermoMSFileReader(file_location) mass_spectrum = parser.get_average_mass_spectrum_in_scan_range( first_scan=1, last_scan=5) return mass_spectrum
def run_thermo(file_location): MSParameters.mass_spectrum.threshold_method = 'auto' MSParameters.mass_spectrum.s2n_threshold = 6 parser = rawFileReader.ImportMassSpectraThermoMSFileReader(file_location) # mass_spectrum = transient.get_mass_spectrum(plot_result=False, auto_process=True) mass_spectrum = parser.get_average_mass_spectrum_in_scan_range() return mass_spectrum, 3
def run_thermo(file_location): MSParameters.mass_spectrum.threshold_method = 'relative_abundance' MSParameters.mass_spectrum.relative_abundance_threshold = 0.1 #MSParameters.mass_spectrum.threshold_method = 'auto' #MSParameters.mass_spectrum.s2n_threshold = 6 parser = rawFileReader.ImportMassSpectraThermoMSFileReader(file_location) parser.chromatogram_settings.start_scan = -1 parser.chromatogram_settings.end_scan = -1 tic_data, ax = parser.get_tic(ms_type='MS', plot=True) plt.show() print(parser.get_all_filters()) transient_time_list = parser.get_icr_transient_times() print(transient_time_list) # sums all the mass spectra mass_spectrum = parser.get_average_mass_spectrum_in_scan_range() # sums scans in selected range parser.chromatogram_settings.start_scan = 1 parser.chromatogram_settings.end_scan = 10 mass_spectrum = parser.get_average_mass_spectrum_in_scan_range() scans_list = [1] # sums scans in selected range mass_spectrum = parser.get_average_mass_spectrum_by_scanlist(scans_list) return mass_spectrum
from corems.molecular_id.search.priorityAssignment import OxygenPriorityAssignment from corems.molecular_id.search.molecularFormulaSearch import SearchMolecularFormulas from corems.encapsulation.factory.parameters import MSParameters #set file here file_location = "tests/tests_data/icpms/rmb_161221_kansas_h2o_2" #Set peak detection threshold method MSParameters.mass_spectrum.threshold_method = 'relative_abundance' MSParameters.mass_spectrum.relative_abundance_threshold = 1 MSParameters.mass_spectrum.threshold_method = 'auto' MSParameters.mass_spectrum.s2n_threshold = 10 #Parser for thermo RAW files. parser = rawFileReader.ImportMassSpectraThermoMSFileReader(file_location) t_ion_chromatogram = parser.get_tic() t_ion_subset = t_ion_chromatogram[(t_ion_chromatogram["Time"] > 8) & (t_ion_chromatogram["Time"] < 9)] #print(t_ion_chromatogram['Time']) #print(parser.start_scan) #print(parser.end_scan) #Function for obtaining extracted ion chromatogram def get_EIC(parser, mass, dmz, scanrange): EIC = np.zeros((len(scanrange), 3)) ## scan, time, eic