def create_mass_spectrum():
'''parse transient data from Bruker into a mass spectrum class object
Parameters
----------
file_location: str
The full path of the *.d data folder
Returns
-------
MassSpecfromFreq() class
(See MassSpecfromFreq class for more details)
'''
file_location = Path.cwd() / "tests/tests_data/ESI_NEG_SRFA.d/"
bruker_reader = ReadBrukerSolarix(file_location)
bruker_transient = bruker_reader.get_transient()
MSParameters.mass_spectrum.threshold_method = 'auto'
MSParameters.mass_spectrum.noise_threshold_std = 3
MSParameters.ms_peak.peak_min_prominence_percent = 0.01
mass_spectrum = bruker_transient.get_mass_spectrum(plot_result=False,
auto_noise=True,
auto_process=True,
keep_profile=True)
return mass_spectrum
def get_mass_spectrum(file_location):
bruker_reader = ReadBrukerSolarix(file_location)
bruker_transient = bruker_reader.get_transient()
return bruker_transient.get_mass_spectrum(plot_result=False,
auto_process=True)
def test_create_mass_spectrum():
file_location = Path.cwd() / "tests/tests_data/ESI_NEG_SRFA.d/"
bruker_reader = ReadBrukerSolarix(file_location)
TransientSetting.apodization_method = 'Hamming'
bruker_transient = bruker_reader.get_transient()
TransientSetting.apodization_method = 'Blackman'
TransientSetting.number_of_truncations = 1
bruker_transient = bruker_reader.get_transient()
mass_spectrum_obj = bruker_transient.get_mass_spectrum(plot_result=False,
auto_process=True)
MassSpectrumSetting.threshold_method = 'signal_noise'
mass_spectrum_obj = bruker_transient.get_mass_spectrum(plot_result=False,
auto_process=True)
MassSpectrumSetting.threshold_method = 'relative_abundance'
mass_spectrum_obj = bruker_transient.get_mass_spectrum(plot_result=False,
auto_process=True)
mass_spectrum_obj.freq_exp
mass_spectrum_obj.dir_location
mass_spectrum_obj.resolving_power
mass_spectrum_obj.signal_to_noise
mass_spectrum_obj.max_abundance
mass_spectrum_obj.filter_by_mz(200, 1000)
mass_spectrum_obj.reset_indexes()
mass_spectrum_obj.filter_by_abundance(0, 1000)
mass_spectrum_obj.reset_indexes()
mass_spectrum_obj.filter_by_max_resolving_power(12, 3)
mass_spectrum_obj.reset_indexes()
mass_spectrum_obj.filter_by_min_resolving_power(15, 3)
mass_spectrum_obj.reset_indexes()
mass_spectrum_obj.filter_by_noise_threshold()
mass_spectrum_obj.reset_indexes()
mass_spectrum_obj.get_mz_and_abundance_peaks_tuples()
mass_spectrum_obj.get_masses_count_by_nominal_mass()
mass_spectrum_obj.resolving_power_calc(12, 1)
mass_spectrum_obj._f_to_mz()
mass_spectrum_obj.number_average_molecular_weight(profile=True)
mass_spectrum_obj.reset_cal_therms(mass_spectrum_obj.Aterm,
mass_spectrum_obj.Bterm,
mass_spectrum_obj.Cterm)
mass_spectrum_obj.reset_indexes()
kendrick_group_index = mass_spectrum_obj.kendrick_groups_indexes()
mass_spectrum_obj.reset_indexes()
return mass_spectrum_obj, kendrick_group_index
def get_mass_spectrum(self, scan_number):
bruker_reader = ReadBrukerSolarix(self.lcms.file_location)
bruker_transient = bruker_reader.get_transient(scan_number)
mass_spec = bruker_transient.get_mass_spectrum(plot_result=False,
auto_process=self.auto_process,
keep_profile=self.keep_profile,
auto_noise=self.auto_noise)
return mass_spec
def test_import_transient():
# from corems.structure.input.MidasDatFile import ReadMidasDatFile
file_location = Path.cwd() / "tests/tests_data/ESI_NEG_SRFA.d/"
MSParameters.transient.apodization_method = "Hanning"
MSParameters.transient.number_of_truncations = 0
MSParameters.transient.number_of_zero_fills = 1
with ReadBrukerSolarix(file_location) as bruker_transient:
MSParameters.mass_spectrum.threshold_method = 'relative_abundance'
MSParameters.mass_spectrum.relative_abundance_threshold = 10
MSParameters.ms_peak.peak_min_prominence_percent = 1
mass_spectrum_obj = bruker_transient.get_mass_spectrum(
plot_result=False, auto_process=True)
mass_spectrum_obj.plot_profile_and_noise_threshold()
#pyplot.show()
print(len(mass_spectrum_obj))
print(mass_spectrum_obj.mspeaks[0].mz_exp,
mass_spectrum_obj.mspeaks[-1].mz_exp)
def test_mspeaks_fit():
from matplotlib import pyplot
file_location = Path.cwd() / "tests/tests_data/ftms/ESI_NEG_SRFA.d/"
bruker_reader = ReadBrukerSolarix(file_location)
bruker_transient = bruker_reader.get_transient()
mass_spectrum_obj = bruker_transient.get_mass_spectrum(plot_result=False,
auto_process=True)
i = 0
mass_spectrum_obj[3].plot_simulation()
mass_spectrum_obj[3].plot_simulation(sim_type="gaussian",
oversample_multiplier=10)
mass_spectrum_obj[3].plot_simulation()
def create_mass_spectrum():
file_location = Path.cwd() / "tests/tests_data/ESI_NEG_SRFA.d/"
bruker_reader = ReadBrukerSolarix(file_location)
bruker_transient = bruker_reader.get_transient()
mass_spectrum_obj = bruker_transient.get_mass_spectrum(plot_result=False,
auto_process=True)
# polariy need to be set if reading a text file
#polariy = -1
# load any type of mass list file, change the delimeter to read another type of file, i.e : "," for csv, "\t" for tabulated mass list, etc
#mass_list_reader = Read_MassList(file_location, )
#mass_spectrum_obj = mass_list_reader.get_mass_spectrum(polarity, auto_process=True)
return mass_spectrum_obj
def run_bruker_transient(file_location, corems_params_path):
with ReadBrukerSolarix(file_location) as transient:
transient.set_parameter_from_json(corems_params_path)
mass_spectrum = transient.get_mass_spectrum(plot_result=False,
auto_process=True)
return mass_spectrum
def run_bruker(file_location):
with ReadBrukerSolarix(file_location) as transient:
MSParameters.mass_spectrum.threshold_method = 'auto'
MSParameters.mass_spectrum.s2n_threshold = 6
mass_spectrum = transient.get_mass_spectrum(plot_result=False, auto_process=True)
# mass_spectrum.plot_profile_and_noise_threshold()
# plt.show()
return mass_spectrum, transient.transient_time
def run_bruker(file_location):
with ReadBrukerSolarix(file_location) as transient:
mass_spectrum = transient.get_mass_spectrum(plot_result=False,
auto_process=True)
# find_formula_thread = FindOxygenPeaks(mass_spectrum)
# find_formula_thread.run()
# mspeaks_results = find_formula_thread.get_list_found_peaks()
# calibrate = FreqDomain_Calibration(mass_spectrum, mspeaks_results)
# calibrate.ledford_calibration()
# mass_spectrum.clear_molecular_formulas()
return mass_spectrum
def run_bruker(file_location):
with ReadBrukerSolarix(file_location) as transient:
MSParameters.mass_spectrum.threshold_method = 'auto'
MSParameters.mass_spectrum.s2n_threshold = 6
mass_spectrum = transient.get_mass_spectrum(plot_result=False,
auto_process=True)
# mass_spectrum.plot_profile_and_noise_threshold()
# plt.show()
# find_formula_thread = FindOxygenPeaks(mass_spectrum)
# find_formula_thread.run()
# mspeaks_results = find_formula_thread.get_list_found_peaks()
# calibrate = FreqDomain_Calibration(mass_spectrum, mspeaks_results)
# calibrate.ledford_calibration()
# mass_spectrum.clear_molecular_formulas()
return mass_spectrum, transient.transient_time
def test_import_transient():
# from corems.structure.input.MidasDatFile import ReadMidasDatFile
# file_location = Path.cwd() / "tests/tests_data/SRFAII_20ppm_14Jul2020_IATp08_After_WebEx_1_01_54136.d/"
file_location = Path.cwd() / "tests/tests_data/ESI_NEG_SRFA.d"
MSParameters.transient.apodization_method = "Hanning"
MSParameters.transient.number_of_truncations = 0
MSParameters.transient.number_of_zero_fills = 1
with ReadBrukerSolarix(file_location) as bruker_transient:
#MSParameters.mass_spectrum.threshold_method = 'relative_abundance'
#MSParameters.mass_spectrum.relative_abundance_threshold = 1
#MSParameters.mass_spectrum.threshold_method = 'signal_noise'
#MSParameters.mass_spectrum.s2n_threshold = 50
MSParameters.mass_spectrum.threshold_method = 'auto'
MSParameters.mass_spectrum.noise_threshold_std = 3
MSParameters.ms_peak.peak_min_prominence_percent = 1
mass_spectrum_obj = bruker_transient.get_mass_spectrum(
plot_result=False, auto_process=True)
#from corems.encapsulation.constant import Labels
#from corems.mass_spectrum.input import numpyArray
#mass_spectrum_test = numpyArray.ms_from_array_profile(mz=mass_spectrum_obj.mz_exp_profile,
# abundance=mass_spectrum_obj.abundance_profile,
# dataname='test',
# polarity=-1,
# data_type=Labels.booster_profile,
# )
#mass_spectrum_test.plot_mz_domain_profile()
mass_spectrum_obj.plot_profile_and_noise_threshold()
pyplot.show()
from corems.transient.input.brukerSolarix import ReadBrukerSolarix
from corems.molecular_id.search.molecularFormulaSearch import SearchMolecularFormulas
from corems.mass_spectrum.output.export import HighResMassSpecExport
from matplotlib import pyplot
file_path= 'tests/tests_data/ftms/ESI_NEG_SRFA.d'
#Bruker Solarix class reader
bruker_reader = ReadBrukerSolarix(file_path)
#access the transient object
bruker_transient_obj = bruker_reader.get_transient()
#calculates the transient duration time
T = bruker_transient_obj.transient_time
#access the mass spectrum object
mass_spectrum_obj = bruker_transient_obj.get_mass_spectrum(plot_result=False, auto_process=True)
# - search monoisotopic molecular formulas for all mass spectral peaks
# - calculate fine isotopic structure based on monoisotopic molecular formulas found and current dynamic range
# - search molecular formulas of correspondent calculated isotopologues,
# - settings are stored at SearchConfig.json and can be changed directly on the file or inside the framework class
SearchMolecularFormulas(mass_spectrum_obj, first_hit=False).run_worker_mass_spectrum()
# iterate over mass spectral peaks objs
for mspeak in mass_spectrum_obj.sort_by_abundance():
# returns true if there is at least one molecular formula associated
# with the mass spectral peak
from matplotlib import pyplot
import matplotlib
from pathlib import Path
#matplotlib.use('Agg')
#file_name = "20190911_Kew_APPI_Elliot_DRY_IAT100ms_50ulmin_000001.d"
#file_name = "20190912_Kew_LDI_Elliot_DRY_C4_0_C4_000001.d"
#file_name= "20190912_kew_ldi_elliot_spe_f4_anchorchip_0_f4_000001.d"
#file_name = "20190912_Kew_LDI_Elliot_DRY_C4_AnchorChip_0_C4_000001.d"
#file_name = "20190911_Kew_ESI_Elliot_DRY_IAT100ms_000001.d"
#file_name = "20190911_Kew_ESI_Elliot_SPE_IAT100ms_000002.d"
#file_name = "20190912_Kew_LDI_Elliot_Whole_B15_1500um_0_B15_000001.d"
file_location = Path.cwd() / "tests/tests_data/ESI_NEG_SRFA.d"
bruker_reader = ReadBrukerSolarix(file_location)
bruker_transient = bruker_reader.get_transient()
T = bruker_transient.transient_time
print(T, "T")
B = 15
mass_spectrum_obj = bruker_transient.get_mass_spectrum(plot_result=False, auto_process=True)
#mass_spectrum_obj.plot_profile_and_noise_threshold()
MolecularFormulaSearchSettings = MolecularFormulaSearchSettings()
