def perform_peptide_match(self):
self.matched_peptides = {}
self.peptide_ms1_profiles = {}
self.retention_times = []
self.match_data = []
t0 = timer.time()
for scan_number in self.ms1_indices:
self.retention_times.append(self.scan_list[scan_number]['retentionTime'])
self.match_data.append(self.match_peptide_patterns_to_ms1profile(self.profiles[scan_number]))
for peptide in self.match_data[-1].keys():
if peptide in self.matched_peptides:
for z in self.match_data[-1][peptide].keys():
self.matched_peptides[peptide][z] = 1
if z in self.peptide_ms1_profiles[peptide]:
self.peptide_ms1_profiles[peptide][z] = mspy.combine(self.peptide_ms1_profiles[peptide][z] ,mspy.crop(
self.profiles[scan_number],
self.peptide_indexed_iso_dist[peptide][z][0][0] - 0.1,
self.peptide_indexed_iso_dist[peptide][z][-1][0] + 0.1))
else:
self.peptide_ms1_profiles[peptide][z] = mspy.crop(
self.profiles[scan_number],
self.peptide_indexed_iso_dist[peptide][z][0][0] - 0.1,
self.peptide_indexed_iso_dist[peptide][z][-1][0] + 0.1)
else:
self.matched_peptides[peptide] = {}
self.peptide_ms1_profiles[peptide] = {}
for z in self.match_data[-1][peptide].keys():
self.matched_peptides[peptide][z] = 1
self.peptide_ms1_profiles[peptide][z] = mspy.crop(
self.profiles[scan_number],
self.peptide_indexed_iso_dist[peptide][z][0][0] - 0.1,
self.peptide_indexed_iso_dist[peptide][z][-1][0] + 0.1)
t1 = timer.time() - t0
print 'Matched MS1 scans in %s ' % t1
def match_peptides_in_scans(
peptides, PatternObjects, ScanList, ms1ScanList, profiles, charge_min, charge_max, mz_min, mz_max, files
):
# Matches expected isotopic distributions of peptides in MS1 spectra
t0 = timer.time()
RetentionTimeData = {}
BasepeakData = {}
RmsdData = {}
ProfileData = {}
IntIntensity = {}
# Iterate through peptide and initiate data structures
for peptide in peptides:
RetentionTimeData[peptide] = {}
BasepeakData[peptide] = {}
RmsdData[peptide] = {}
ProfileData[peptide] = {}
IntIntensity[peptide] = defaultdict(lambda: 1)
# Iterate through charge states and initiate data structures
for z in range(charge_min, charge_max + 1):
RetentionTimeData[peptide][z] = {}
BasepeakData[peptide][z] = {}
RmsdData[peptide][z] = {}
ProfileData[peptide][z] = {}
# Iterate through files and initiate data structures
for file_iter in files:
RetentionTimeData[peptide][z][file_iter] = []
BasepeakData[peptide][z][file_iter] = []
RmsdData[peptide][z][file_iter] = []
ProfileData[peptide][z][file_iter] = None
IntIntensity[peptide][file_iter] += 0
if PatternObjects[peptide][z][0][0] < mz_min or PatternObjects[peptide][z][-1][0] > mz_max:
continue
# Iterate through scans
for scan_number in ms1ScanList[file_iter]:
RetentionTimeData[peptide][z][file_iter].append(ScanList[file_iter][scan_number]["retentionTime"])
checkPatternResult = mspy.checkpattern_fast(
signal=profiles[file_iter][scan_number], pattern=PatternObjects[peptide][z]
)
if checkPatternResult is not None:
RmsdData[peptide][z][file_iter].append(checkPatternResult.rmsd)
BasepeakData[peptide][z][file_iter].append(checkPatternResult.basepeak)
if checkPatternResult.rmsd < RmsdThreshold:
if ProfileData[peptide][z][file_iter] is None:
ProfileData[peptide][z][file_iter] = mspy.crop(
profiles[file_iter][scan_number],
PatternObjects[peptide][z][0][0] - 0.1,
PatternObjects[peptide][z][-1][0] + 0.1,
)
else:
ProfileData[peptide][z][file_iter] = mspy.combine(
ProfileData[peptide][z][file_iter],
mspy.crop(
profiles[file_iter][scan_number],
PatternObjects[peptide][z][0][0] - 0.1,
PatternObjects[peptide][z][-1][0] + 0.1,
),
)
IntIntensity[peptide][file_iter] += checkPatternResult.basepeak
else:
RmsdData[peptide][z][file_iter].append(1)
BasepeakData[peptide][z][file_iter].append(0)
if ProfileData[peptide][z][file_iter] is not None:
ProfileData[peptide][z][file_iter] = mspy.reduce(ProfileData[peptide][z][file_iter])
t1 = timer.time() - t0
print "Loaded files in %s " % t1
MatchData = {}
MatchData["RetentionTime"] = RetentionTimeData
MatchData["Basepeak"] = BasepeakData
MatchData["Rmsd"] = RmsdData
MatchData["Profile"] = ProfileData
MatchData["IntIntensity"] = IntIntensity
return MatchData