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