def xic(self,
start_time=0,
stop_time=None,
start_mz=0,
stop_mz=None,
filter=None,
UV=False):
if filter:
assert filter.strip().lower(
) == 'full ms', 'Thermo-style XIC filters are not supported for Agilent files.'
# A full XIC can be performed with the TIC object that may have been
# retrieved regardless.
if self.ticObj and not any([start_time, stop_time, start_mz, stop_mz]):
return list(zip(self.ticObj.XArray, self.ticObj.YArray))
if stop_time == None:
stop_time = 999999
if stop_mz == None:
stop_mz = 999999
chromFilter = CreateObject(
r'Agilent.MassSpectrometry.DataAnalysis.BDAChromFilter')
chromFilter.MSLevelFilter = 0 # "All", should perhaps instead be 1 for "ms1"?
if not UV:
chromFilter.ChromatogramType = 7 # Extracted-Ion
else:
chromFilter.ChromatogramType = 4 # ExtractedWavelength
chromFilter.SingleChromatogramForAllMasses = True
mzRange = CreateObject(
r'Agilent.MassSpectrometry.DataAnalysis.MinMaxRange')
mzRange.Min = start_mz
mzRange.Max = stop_mz
mzRangeIR = mzRange.QueryInterface(bc.IRange)
chromFilter.IncludeMassRanges = (mzRange, )
# If THAT works...!
rtRange = CreateObject(
r'Agilent.MassSpectrometry.DataAnalysis.MinMaxRange')
rtRange.Min = start_time
rtRange.Max = stop_time
rtRangeIR = rtRange.QueryInterface(bc.IRange)
chromFilter.ScanRange = rtRangeIR
xic = self.source.GetChromatogram(chromFilter)[0].QueryInterface(
bda.IBDAChromData)
return list(zip(xic.XArray, xic.YArray))
