def convert_to_identification_item_dict(spectrum_match,
seen=None,
id_tracker=None):
if seen is None:
seen = set()
charge = spectrum_match.scan.precursor_information.charge
if spectrum_match.target.id not in seen:
return None
data = {
"charge_state":
charge,
"experimental_mass_to_charge":
mass_charge_ratio(
spectrum_match.scan.precursor_information.neutral_mass, charge),
"calculated_mass_to_charge":
mass_charge_ratio(spectrum_match.target.total_mass, charge),
"peptide_id":
id_tracker(spectrum_match.target),
"peptide_evidence_id":
spectrum_match.target.id,
"score": {
"name": "GlycReSoft:score",
"value": spectrum_match.score
},
"params": [
{
"name": "GlycReSoft:q-value",
"value": spectrum_match.q_value
},
],
"id":
spectrum_match.id
}
return data
def decharge(self,
include_envelopes=True,
charge_carrier=PROTON,
new_charge=1):
"""Transfomr multiply charged deconvoluted peaks into singly charged deconvoluted peaks.
This operation returns a copy of the peak set, the input peak set is unchanged.
Parameters
----------
include_envelopes : bool, optional
Whether or not to charge-transform the isotopic envelope fitted in :attr:`DeconvolutedPeak.envelope`
(the default is True)
charge_carrier : float, optional
The charge carrier mass to use when recalculating m/z (the default is PROTON)
new_charge : int, optional
The new charge to set all peaks to, the default being +1
Returns
-------
DeconvolutedPeakSet
"""
peaks = []
for peak in self:
mz = mass_charge_ratio(peak.neutral_mass,
new_charge,
charge_carrier=charge_carrier)
if include_envelopes:
envelope = Envelope([
EnvelopePair(
mass_charge_ratio(
calc_neutral_mass(p.mz, peak.charge, charge_carrier),
new_charge, charge_carrier), p.intensity)
for p in peak.envelope
])
else:
envelope = peak.envelope
new_peak = DeconvolutedPeak(peak.neutral_mass, peak.intensity,
new_charge, peak.signal_to_noise, None,
peak.full_width_at_half_max,
peak.a_to_a2_ratio,
peak.most_abundant_mass, peak.average_mass,
peak.score, envelope, mz, peak.fit,
peak.chosen_for_msms, peak.area)
peaks.append(new_peak)
new_peak_set = self.__class__(peaks)
new_peak_set.reindex()
return new_peak_set
def __init__(self,
neutral_mass,
intensity,
charge,
signal_to_noise,
index,
full_width_at_half_max,
a_to_a2_ratio=0,
most_abundant_mass=0,
average_mass=0,
score=0,
envelope=None,
mz=0,
fit=None,
chosen_for_msms=False,
area=0):
if index is None:
index = _Index()
if envelope is None:
envelope = ()
self.neutral_mass = neutral_mass
self.intensity = intensity
self.signal_to_noise = signal_to_noise
self.index = index
self.full_width_at_half_max = full_width_at_half_max
self.charge = charge
self.a_to_a2_ratio = a_to_a2_ratio
self.most_abundant_mass = most_abundant_mass
self.average_mass = average_mass
self.score = score
self.envelope = Envelope(envelope)
self.mz = mz or mass_charge_ratio(self.neutral_mass, self.charge)
self.fit = fit
self.chosen_for_msms = chosen_for_msms
self.area = area
def convert_to_identification_item_dict(spectrum_match, seen=None, id_tracker=None):
if seen is None:
seen = set()
charge = spectrum_match.scan.precursor_information.charge
if spectrum_match.target.id not in seen:
return None
data = {
"charge_state": charge,
"experimental_mass_to_charge": mass_charge_ratio(
spectrum_match.scan.precursor_information.neutral_mass, charge),
"calculated_mass_to_charge": mass_charge_ratio(
spectrum_match.target.total_mass, charge),
"peptide_id": id_tracker(spectrum_match.target),
"peptide_evidence_id": spectrum_match.target.id,
"score": {"name": "GlycReSoft:score", "value": spectrum_match.score},
"params": [
{"name": "GlycReSoft:q-value", "value": spectrum_match.q_value},
],
"id": spectrum_match.id
}
return data
def mass(self, charge=0, charge_carrier=Composition("Na").mass):
"""Calculate the mass of this structure from its elemental composition.
Parameters
----------
charge : int, optional
Instead of calculating neutral mass, calculate the mass to charge ratio
with charge = `charge`
charge_carrier : float, optional
The charge carrier to use when charge is non-zero. By default this is a sodium.
Returns
-------
float
"""
if charge == 0:
return self.structure.mass()
return mass_charge_ratio(self.structure.mass(), z=charge, charge_carrier=charge_carrier)
def _poisson_approximate(mass, n_peaks, charge=1):
lmbda = mass / 1800.0
p_i = 1.0
factorial_acc = 1
total = 1.0
intensities = [1.0]
for i in range(1, n_peaks):
p_i *= lmbda
factorial_acc *= i
cur_intensity = p_i / factorial_acc
intensities.append(
cur_intensity if not math.isinf(cur_intensity) else 0.0)
total += intensities[i]
result = []
iso_shift = isotopic_shift(charge)
mz = mass_charge_ratio(mass, charge)
for i, intens in enumerate(intensities):
result.append(Peak(mz + i * iso_shift, intens / total, charge))
return TheoreticalIsotopicPattern(result, origin=mz)
def __init__(self, neutral_mass, intensity, charge, signal_to_noise, index, full_width_at_half_max,
a_to_a2_ratio=None, most_abundant_mass=None, average_mass=None, score=None,
envelope=None, mz=None, fit=None, chosen_for_msms=False, area=0):
if index is None:
index = _Index()
self.neutral_mass = neutral_mass
self.intensity = intensity
self.signal_to_noise = signal_to_noise
self.index = index
self.full_width_at_half_max = full_width_at_half_max
self.charge = charge
self.a_to_a2_ratio = a_to_a2_ratio
self.most_abundant_mass = most_abundant_mass
self.average_mass = average_mass
self.score = score
self.envelope = Envelope(envelope)
self.mz = mz or mass_charge_ratio(self.neutral_mass, self.charge)
self.fit = fit
self.chosen_for_msms = chosen_for_msms
self.area = area
def convert_to_identification_item_dict(spectrum_match, seen=None, id_tracker=None):
if seen is None:
seen = set()
charge = spectrum_match.scan.precursor_information.charge
if spectrum_match.target.id not in seen:
return None
data = {
"charge_state": charge,
"experimental_mass_to_charge": mass_charge_ratio(
spectrum_match.scan.precursor_information.neutral_mass, charge),
"calculated_mass_to_charge": mass_charge_ratio(
spectrum_match.target.total_mass, charge),
"peptide_id": id_tracker(spectrum_match.target),
"peptide_evidence_id": spectrum_match.target.id,
"score": mparam({
"name": "GlycReSoft:total score",
"value": spectrum_match.score,
"accession": "MS:XXX10A",
}),
"params": [
components.CVParam(**{
"name": "glycan dissociating, peptide preserving",
"accession": "MS:XXX111", "cvRef": "PSI-MS"}),
components.CVParam(**{
"name": "glycan eliminated, peptide dissociating",
"accession": "MS:XXX114", "cvRef": "PSI-MS"}),
{
"name": "scan start time",
"value": spectrum_match.scan.scan_time,
"unit_name": "minute"
}
],
"id": spectrum_match.id
}
if spectrum_match.is_multiscore():
score_params = [
mparam("GlycReSoft:peptide score",
spectrum_match.score_set.peptide_score, "MS:XXX10C"),
mparam("GlycReSoft:glycan score",
spectrum_match.score_set.glycan_score, "MS:XXX10B"),
mparam("GlycReSoft:glycan coverage",
spectrum_match.score_set.glycan_coverage, "MS:XXX10H"),
mparam("GlycReSoft:joint q-value",
spectrum_match.q_value, "MS:XXX10G"),
mparam("GlycReSoft:peptide q-value",
spectrum_match.q_value_set.peptide_q_value,
"MS:XXX10E"),
mparam("GlycReSoft:glycan q-value",
spectrum_match.q_value_set.glycan_q_value, "MS:XXX10F"),
mparam("GlycReSoft:glycopeptide q-value",
spectrum_match.q_value_set.glycopeptide_q_value, "MS:XXX10D"),
]
data['params'].extend(score_params)
else:
data['params'].extend([
mparam("GlycReSoft:glycopeptide q-value",
spectrum_match.q_value, "MS:XXX10D"),
])
if spectrum_match.mass_shift.name != Unmodified.name:
data['params'].append(
mparam("GlycReSoft:mass shift", "%s:%0.3f:%0.3f" % (
spectrum_match.mass_shift.name,
spectrum_match.mass_shift.mass,
spectrum_match.mass_shift.tandem_mass),
"MS:XXX10I"))
return data