def precursor_information(self) -> List[PrecursorInformation]:
out = []
for _, info in self.extended_index.msn_ids.items():
mz = info['mz']
prec_neutral_mass = info['neutral_mass']
charge = info['charge']
if charge == 'ChargeNotProvided':
charge = ChargeNotProvided
intensity = info['intensity']
precursor_scan_id = info['precursor_scan_id']
product_scan_id = info['product_scan_id']
orphan = info.get('orphan', False)
coisolation = info.get('coisolation', [])[:]
defaulted = info.get('defaulted', False)
pinfo = PrecursorInformation(mz,
intensity,
charge,
precursor_scan_id,
self,
prec_neutral_mass,
charge,
intensity,
product_scan_id=product_scan_id,
orphan=orphan,
coisolation=coisolation,
defaulted=defaulted)
if prec_neutral_mass is None or charge is None:
continue
out.append(pinfo)
return out
def precursor_information(self):
out = []
for key, info in self.extended_index.msn_ids.items():
mz = info['mz']
neutral_mass = info['neutral_mass']
charge = info['charge']
if charge == 'ChargeNotProvided':
charge = ChargeNotProvided
intensity = info['intensity']
precursor_scan_id = info['precursor_scan_id']
product_scan_id = info['product_scan_id']
orphan = info.get('orphan', False)
defaulted = info.get('defaulted', False)
pinfo = PrecursorInformation(mz,
intensity,
charge,
precursor_scan_id,
self,
neutral_mass,
charge,
intensity,
product_scan_id=product_scan_id,
orphan=orphan,
defaulted=defaulted)
out.append(pinfo)
return out
def get_precursor_information(self, bind=None):
'''Create a list of :class:`~.PrecursorInformation` objects
from :attr:`msn_ids`'s records.
Returns
-------
list
'''
out = []
for _, info in self.msn_ids.items():
mz = info['mz']
neutral_mass = info['neutral_mass']
if neutral_mass is None:
continue
charge = info['charge']
if charge == "ChargeNotProvided":
charge = ChargeNotProvided
intensity = info['intensity']
precursor_scan_id = info['precursor_scan_id']
product_scan_id = info['product_scan_id']
pinfo = PrecursorInformation(
mz, intensity, charge, precursor_scan_id,
bind, neutral_mass, charge, intensity,
product_scan_id=product_scan_id,
coisolation=info.get('coisolation'))
out.append(pinfo)
return out
def _precursor_information(self, scan):
scan_number = scan.scan_number
filt = self._source.GetFilterForScanNumber(scan_number + 1)
precursor_mz = filt.GetMass(filt.MSOrder - 2)
trailers = self._trailer_values(scan)
charge = int(trailers.get("Charge State", 0))
if charge == 0:
charge = ChargeNotProvided
inten = 0
precursor_scan_number = None
if precursor_scan_number is None:
last_index = self._scan_index(scan) - 1
current_level = self._ms_level(scan)
i = 0
while last_index >= 0 and i < 100:
prev_scan = self.get_scan_by_index(last_index)
if prev_scan.ms_level >= current_level:
last_index -= 1
else:
precursor_scan_number = prev_scan._data.scan_number
break
i += 1
if precursor_scan_number is not None:
precursor_scan_id = self.get_scan_by_index(
precursor_scan_number).id
return PrecursorInformation(precursor_mz,
inten,
charge,
precursor_scan_id,
source=self,
product_scan_id=self._scan_id(scan))
def _precursor_information(self, scan):
if self._ms_level(scan) == 1:
return None
scan_number = scan.scan_number
pinfo_struct = self._source.GetPrecursorInfoFromScanNum(scan_number)
precursor_scan_number = None
labels, flags, _ = self._source.GetAllMSOrderData(scan_number)
if pinfo_struct:
mz = pinfo_struct.monoIsoMass
charge = pinfo_struct.chargeState
intensity = float(labels.intensity[0])
precursor_scan_number = pinfo_struct.scanNumber
else:
mz = labels.mass[0]
intensity = float(labels.intensity[0])
charge = labels.charge[0]
if not charge:
charge = ChargeNotProvided
trailer = self._source.GetTrailerExtraForScanNum(scan_number)
_mz = trailer.get('Monoisotopic M/Z', 0.0)
if _mz > 0:
mz = _mz
_charge = trailer.get('Charge State', 0)
if _charge != 0:
charge = _charge
# Guess which previous scan was the precursor by iterating
# backwards until a scan is found with a lower MS level
if precursor_scan_number is None:
last_index = self._scan_index(scan) - 1
current_level = self._ms_level(scan)
i = 0
while last_index > 0 and i < 100:
prev_scan = self.get_scan_by_index(last_index)
if prev_scan.ms_level >= current_level:
last_index -= 1
else:
precursor_scan_number = prev_scan._data.scan_number
break
i += 1
if intensity is None:
intensity = 0.0
if mz is None:
mz = 0.0
if charge is None or charge == 0:
charge = ChargeNotProvided
pinfo = PrecursorInformation(mz,
intensity,
charge,
_make_id(precursor_scan_number),
0,
0,
0,
product_scan_id=_make_id(
scan.scan_number))
return pinfo
def _precursor_information(self, scan):
if self._ms_level(scan) < 2:
return None
spectrum_obj = self._get_spectrum_obj(scan)
precursor_scan_id = make_scan_id_string(spectrum_obj.ParentScanId)
n, ions = spectrum_obj.GetPrecursorIon()
if n < 1:
return None
mz = ions[0]
charge, _ = spectrum_obj.GetPrecursorCharge()
intensity, _ = spectrum_obj.GetPrecursorIntensity()
return PrecursorInformation(mz, intensity, charge, precursor_scan_id, self)
def _precursor_information(self, scan):
scan_number = scan.scan_number
filt = self._source.GetFilterForScanNumber(scan_number + 1)
precursor_mz = filt.GetMass(filt.MSOrder - 2)
trailers = self._trailer_values(scan)
_precursor_mz = float(trailers.get("Monoisotopic M/Z", 0))
if _precursor_mz > 0:
precursor_mz = _precursor_mz
# imitate proteowizard's firmware bug correction
isolation_window = self._isolation_window(scan)
if (isolation_window.upper + isolation_window.lower) / 2 <= 2.0:
if (isolation_window.target - 3.0 > precursor_mz) or (
isolation_window.target + 2.5 < precursor_mz):
precursor_mz = isolation_window.target
elif precursor_mz not in isolation_window:
precursor_mz = isolation_window.target
charge = int(trailers.get("Charge State", 0))
if charge == 0:
charge = ChargeNotProvided
inten = 0
precursor_scan_number = None
if precursor_scan_number is None:
last_index = self._scan_index(scan) - 1
current_level = self._ms_level(scan)
i = 0
while last_index >= 0 and i < 100:
prev_scan = self.get_scan_by_index(last_index)
if prev_scan.ms_level >= current_level:
last_index -= 1
else:
precursor_scan_number = prev_scan._data.scan_number
break
i += 1
if precursor_scan_number is not None:
precursor_scan_id = self.get_scan_by_index(
precursor_scan_number).id
else:
import warnings
warnings.warn("Could not resolve precursor scan for %s" %
(self._scan_id(scan), ))
precursor_scan_id = None
return PrecursorInformation(precursor_mz,
inten,
charge,
precursor_scan_id,
source=self,
product_scan_id=self._scan_id(scan))
def precursor_information(self):
out = []
for key, info in self.extended_index.msn_ids.items():
mz = info['mz']
neutral_mass = info['neutral_mass']
charge = info['charge']
intensity = info['intensity']
precursor_scan_id = info['precursor_scan_id']
product_scan_id = info['product_scan_id']
pinfo = PrecursorInformation(mz,
intensity,
charge,
precursor_scan_id,
self,
neutral_mass,
charge,
intensity,
product_scan_id=product_scan_id)
out.append(pinfo)
return out
def _precursor_information(self, scan):
if self._ms_level(scan) == 1:
return None
set_mass_str = self.info_reader.GetScanItem(
scan.function, scan.block if scan.block >= 0 else scan.scan,
MassLynxRawDefs.MassLynxScanItem.SET_MASS.value)
if set_mass_str:
set_mass = float(set_mass_str)
else:
set_mass = 0.0
if set_mass == 0:
lower_bound, upper_bound = self.info_reader.GetAcquisitionMassRange(
scan.function)
set_mass = (lower_bound + upper_bound) / 2.
pinfo = PrecursorInformation(set_mass,
0,
ChargeNotProvided,
source=self,
product_scan_id=scan.id)
return pinfo
def get_precursor_information(self, bind=None):
out = []
for key, info in self.msn_ids.items():
mz = info['mz']
neutral_mass = info['neutral_mass']
charge = info['charge']
if charge == "ChargeNotProvided":
charge = ChargeNotProvided
intensity = info['intensity']
precursor_scan_id = info['precursor_scan_id']
product_scan_id = info['product_scan_id']
pinfo = PrecursorInformation(mz,
intensity,
charge,
precursor_scan_id,
bind,
neutral_mass,
charge,
intensity,
product_scan_id=product_scan_id,
coisolation=info.get('coisolation'))
out.append(pinfo)
return out
def _precursor_information(self, scan):
if self._ms_level(scan) == 1:
return None
scan_number = scan.scan_number
pinfo_struct = self._source.GetPrecursorInfoFromScanNum(scan_number)
precursor_scan_number = None
labels, flags, _ = self._source.GetAllMSOrderData(scan_number)
if pinfo_struct:
# this struct field is unreliable and may fall outside the
# isolation window
mz = pinfo_struct.monoIsoMass
charge = pinfo_struct.chargeState
intensity = float(labels.intensity[0])
# this struct field is unreliable, and simple to infer
# precursor_scan_number = pinfo_struct.scanNumber + 1
else:
mz = labels.mass[0]
intensity = float(labels.intensity[0])
charge = labels.charge[0]
if not charge:
charge = ChargeNotProvided
trailer = self._source.GetTrailerExtraForScanNum(scan_number)
_mz = trailer.get('Monoisotopic M/Z', 0.0)
# prefer the trailer m/z if available?
if _mz > 0:
mz = _mz
# imitate proteowizard's firmware bug correction
isolation_window = self._isolation_window(scan)
if (isolation_window.upper + isolation_window.lower) / 2 <= 2.0:
if (isolation_window.target - 3.0 > mz) or (isolation_window.target + 2.5 < mz):
mz = isolation_window.target
elif mz not in isolation_window:
mz = isolation_window.target
_charge = trailer.get('Charge State', 0)
if _charge != 0:
charge = _charge
# Guess which previous scan was the precursor by iterating
# backwards until a scan is found with a lower MS level
if precursor_scan_number is None:
last_index = self._scan_index(scan) - 1
current_level = self._ms_level(scan)
i = 0
while last_index >= 0 and i < 100:
prev_scan = self.get_scan_by_index(last_index)
if prev_scan.ms_level >= current_level:
last_index -= 1
else:
precursor_scan_number = prev_scan._data.scan_number
break
i += 1
if intensity is None:
intensity = 0.0
if mz is None:
mz = 0.0
if charge is None or charge == 0:
charge = ChargeNotProvided
pinfo = PrecursorInformation(
mz, intensity, charge, _make_id(precursor_scan_number),
source=self,
product_scan_id=_make_id(scan.scan_number))
return pinfo
def _precursor_information(self, scan):
scan_number = scan.scan_number
filt = self._source.GetFilterForScanNumber(scan_number + 1)
precursor_mz = filt.GetMass(filt.MSOrder - 2)
trailers = self._trailer_values(scan)
_precursor_mz = float(trailers.get("Monoisotopic M/Z", 0))
if _precursor_mz > 0:
precursor_mz = _precursor_mz
# imitate proteowizard's firmware bug correction
isolation_window = self._isolation_window(scan)
if (isolation_window.upper + isolation_window.lower) / 2 <= 2.0:
if (isolation_window.target - 3.0 > precursor_mz) or (
isolation_window.target + 2.5 < precursor_mz):
precursor_mz = isolation_window.target
elif precursor_mz not in isolation_window:
precursor_mz = isolation_window.target
charge = int(trailers.get("Charge State", 0))
if charge == 0:
charge = ChargeNotProvided
inten = 0
precursor_scan_number = None
precursor_scan_number = trailers.get('Master Scan Number')
if precursor_scan_number == 0:
precursor_scan_number = None
if precursor_scan_number is not None:
precursor_scan_number = int(precursor_scan_number) - 1
if self.get_scan_by_index(
precursor_scan_number).ms_level >= self._ms_level(scan):
precursor_scan_number = None
if precursor_scan_number is None:
current_level = self._ms_level(scan)
# We want to start looking for the most recent spectrum with the next lowest MS
# level. The expecteation is that we couldn't determine the precursor scan accurately,
# so we'll probe backwards until the next best candidate.
current_index = self._scan_index(scan)
# Use the index of the current scan to check the index of the previous scans at a lower
# MS level. This may be None, in which case there is no earlier scan recorded.
lookup = self._get_previous_scan_index_for_ms_level(
current_index, current_level - 1)
if lookup is not None:
last_index = lookup
else:
last_index = current_index - 1
i = 0
while last_index >= 0 and i < 100:
prev_scan = self.get_scan_by_index(last_index)
if prev_scan.ms_level >= current_level:
last_index -= 1
else:
precursor_scan_number = prev_scan._data.scan_number
break
i += 1
if precursor_scan_number is not None:
precursor_scan_id = self.get_scan_by_index(
precursor_scan_number).id
else:
import warnings
warnings.warn("Could not resolve precursor scan for %s" %
(self._scan_id(scan), ))
precursor_scan_id = None
return PrecursorInformation(precursor_mz,
inten,
charge,
precursor_scan_id,
source=self,
product_scan_id=self._scan_id(scan))