def deisotope_scan(self,
scan,
tolerance_da=0.0025,
tolerance_ppm=7,
max_charge=None,
require_peptide_profile=False):
"""
The Agilent MassHunter DAC has the neat feature of including its own
deisotoping algorithm! This function uses that to return the specified
scan in deisotoped form.
tolerance_da (Daltons) and tolerance_ppm (Parts-per-million) are
ADDED TOGETHER to obtain the total tolerance value for each peak.
max_charge can be set to an integer to only consider isotopic envelopes of
charge equal to or less; 'None' performs no charge filtering.
require_peptide_profile filters based on isotopic sequences having
the relative intensity profile caused by standard relative isotopic
abundances.
"""
scanObj = self.source.GetSpectrum_6(scan)
deisoFilter = CreateObject(
r'Agilent.MassSpectrometry.DataAnalysis.MsdrChargeStateAssignmentFilter'
)
if not (tolerance_da == 0.0025 and tolerance_ppm == 7
and not (max_charge or require_peptide_profile)):
deisoFilter.AbsoluteTolerance = tolerance_da
if max_charge:
deisoFilter.LimitMaxChargeState = max_charge
deisoFilter.RelativeTolerance = tolerance_ppm
deisoFilter.RequirePeptideLikeAbundanceProfile = require_peptide_profile
self.source.Deisotope(
scanObj,
deisoFilter) # Void type, not even a success return value.
return list(zip(scanObj.XArray, scanObj.YArray))
