def __init__(self,name, code, code3,composition):
#: Full name of the AA
self.name = name
#: One letter code
self.code = code
#: Three letter code
self.code3 = code3
#: Elemental composition
self.composition = {}
self.composition = composition
#: Library of elements
self.elementsLib = Elements()
self.deltaMass = Formulas.mass(self.composition, elementsLib = self.elementsLib) #self.calDeltaMass()
def __init__(self, name, code, code3, composition):
#: Full name of the AA
self.name = name
#: One letter code
self.code = code
#: Three letter code
self.code3 = code3
#: Elemental composition
self.composition = {}
self.composition = composition
#: Library of elements
self.elementsLib = Elements()
self.deltaMass = Formulas.mass(
self.composition,
elementsLib=self.elementsLib) #self.calDeltaMass()
def __init__(self, aminoacid, tpp_Mod, unimodAccession, peakViewAccession, is_labeling, composition):
#self.aminoacid = Aminoacid()
self.aminoacid = aminoacid
self.is_Nterminal = False
self.is_Cterminal = False
if self.aminoacid == 'N-term' : self.is_Nterminal = True
if self.aminoacid == 'C-term' : self.is_Cterminal = True
self.unimodAccession = unimodAccession
self.peakviewAccession = peakViewAccession
self.TPP_Mod = tpp_Mod
self.composition = composition
self.is_labeling = is_labeling
#if deltaMass : self.deltamass = deltaMass
self.deltamass = Formulas.mass(composition) #self._getMass()
self.id = aminoacid + str(int(round(self.deltamass,0)))
def __init__(self, aminoacid, tpp_Mod, unimodAccession, peakViewAccession,
is_labeling, composition):
#self.aminoacid = Aminoacid()
self.aminoacid = aminoacid
self.is_Nterminal = False
self.is_Cterminal = False
if self.aminoacid == 'N-term': self.is_Nterminal = True
if self.aminoacid == 'C-term': self.is_Cterminal = True
self.unimodAccession = unimodAccession
self.peakviewAccession = peakViewAccession
self.TPP_Mod = tpp_Mod
self.composition = composition
self.is_labeling = is_labeling
#if deltaMass : self.deltamass = deltaMass
self.deltamass = Formulas.mass(composition) #self._getMass()
self.id = aminoacid + str(int(round(self.deltamass, 0)))
def _getMassFromSequence(self):
#self.aaList = Aminoacides()
mass = 0
for aa in self.sequence[:]:
for ac in self.aaList.list:
if aa == ac.code:
mass += ac.deltaMass
#Adding an H2O to the mass, as it is calculated by using delta masses
mass += Formulas.mass(Formulas.H2O) #(1.007825032 *2 + 15.99491462)
#Adding modifications deltamass
for aaPosMod in self.modifications.iterkeys():
mass += self.modifications[aaPosMod].deltamass
return mass
def _getMassFromSequence(self):
#self.aaList = Aminoacides()
mass = 0
for aa in self.sequence[:]:
for ac in self.aaList.list:
if aa == ac.code:
mass += ac.deltaMass
#Adding an H2O to the mass, as it is calculated by using delta masses
mass += Formulas.mass(Formulas.H2O) #(1.007825032 *2 + 15.99491462)
#Adding modifications deltamass
for aaPosMod in self.modifications.iterkeys() :
mass += self.modifications[aaPosMod].deltamass
return mass
def getMZfragment(self,
ion_type,
ion_number,
ion_charge,
label='',
fragmentlossgain=0.0):
#Check label
if len(label) > 0 and label not in self.labelings:
print "Coding error: this labeling is not reported!! %s" % label
sys.exit(2)
#Check ion type
#if ion_type not in self.iontypes :
#print "This ion type can not be processed :" , ion_type
#print "This is the list of ion types considered in this library : " , self.iontypes
#sys.exit(2)
massH = 1.007825032
massO = 15.99491462
massN = 14.00307401
massC = 12.0000000
massProton = 1.0072765
massNH3 = Formulas.mass(Formulas.NH3) #massN + 3 * massH
massH2O = Formulas.mass(Formulas.H2O) #(massH *2 + massO)
massCO2 = Formulas.mass(Formulas.CO2) #(massC + 2 * massO)
protonMass = 1.007825032
massN15 = 15.0001089
massShiftN15 = massN15 - massN
massC13 = 13.003355
massShiftC13 = massC13 - massC
frg_number = int(ion_number)
frg_charge = int(ion_charge)
mzfragment = 0
frg_seq = ''
#precursors
if ion_type == 'p':
mzfragment = self.getMZ(frg_charge, label)
return mzfragment
#a series
if ion_type == 'a':
frg_seq = self.sequence[:frg_number]
mzfragment = self.getDeltaMassFromSequence(frg_seq)
mzfragment -= (massC + massO)
#Adding modifications deltamass
for aaPosMod in self.modifications.iterkeys():
if aaPosMod <= frg_number:
mzfragment += self.modifications[aaPosMod].deltamass
#b series
if ion_type == 'b':
frg_seq = self.sequence[:frg_number]
mzfragment = self.getDeltaMassFromSequence(frg_seq)
#Adding modifications deltamass
for aaPosMod in self.modifications.iterkeys():
if aaPosMod <= frg_number:
mzfragment += self.modifications[aaPosMod].deltamass
#c series
if ion_type == 'c':
frg_seq = self.sequence[:frg_number]
mzfragment = self.getDeltaMassFromSequence(frg_seq)
mzfragment += massNH3
#Adding modifications deltamass
for aaPosMod in self.modifications.iterkeys():
if aaPosMod <= frg_number:
mzfragment += self.modifications[aaPosMod].deltamass
#x series
if ion_type == 'x':
frg_seq = self.sequence[-frg_number:]
mzfragment = self.getDeltaMassFromSequence(frg_seq)
mzfragment += massCO2
#Adding modifications deltamass
for aaPosMod in self.modifications.iterkeys():
if (len(self.sequence) - frg_number) < aaPosMod:
mzfragment += self.modifications[aaPosMod].deltamass
#y series
if ion_type == 'y':
frg_seq = self.sequence[-frg_number:]
mzfragment = self.getDeltaMassFromSequence(frg_seq)
mzfragment += massH2O
#Adding modifications deltamass
for aaPosMod in self.modifications.iterkeys():
if (len(self.sequence) - frg_number) < aaPosMod:
mzfragment += self.modifications[aaPosMod].deltamass
#z series
if ion_type == 'z':
frg_seq = self.sequence[-frg_number:]
mzfragment = self.getDeltaMassFromSequence(frg_seq)
mzfragment += massH2O
mzfragment -= massNH3
#Adding modifications deltamass
for aaPosMod in self.modifications.iterkeys():
if (len(self.sequence) - frg_number) < aaPosMod:
mzfragment += self.modifications[aaPosMod].deltamass
# 15N labeling: adds up the shift mass
if label == '15N' or label == 'N15':
frg_composition = self._getCompositionSeq(frg_seq)
if 'N' in frg_composition:
shift = (float(frg_composition['N']) * massShiftN15)
mzfragment += shift
#AQUA_KR labeling: adds up the shift mass
if label == 'AQUA_KR':
#Update (23.nov.2010): AQUA_KR only modifies Lys and Arg in the C-terminal position.
#Update (1.dec.2010) : I am a jerk. I should have taken it only for y ions , and not for the b ones
if 'K' in self.sequence[-1:] and ion_type == 'y':
mzfragment += 6 * massShiftC13 + 2 * massShiftN15
if 'R' in self.sequence[-1:] and ion_type == 'y':
mzfragment += 6 * massShiftC13 + 4 * massShiftN15
if label == 'SILAC_K6R10':
#All K and R amino acides are shifted 6 Da and 10 Da.
numK = 0
numR = 0
for aa in frg_seq[:]:
if aa == 'K': numK += 1
if aa == 'R': numR += 1
mzfragment += numK * (6 * massShiftC13)
mzfragment += numR * (6 * massShiftC13 + 4 * massShiftN15)
if label == 'SILAC_K8R10':
#All K and R amino acides are shifted 8 Da and 10 Da.
numK = 0
numR = 0
for aa in frg_seq[:]:
if aa == 'K': numK += 1
if aa == 'R': numR += 1
mzfragment += numK * (6 * massShiftC13 + 2 * massShiftN15)
mzfragment += numR * (6 * massShiftC13 + 4 * massShiftN15)
if label == 'SILAC_K8R6':
#All K and R amino acides are shifted 8 Da and 6 Da.
numK = 0
numR = 0
for aa in frg_seq[:]:
if aa == 'K': numK += 1
if aa == 'R': numR += 1
mzfragment += numK * (6 * massShiftC13 + 2 * massShiftN15)
mzfragment += numR * (6 * massShiftC13)
mzfragment += frg_charge * massProton
mzfragment += fragmentlossgain
mzfragment /= frg_charge
return mzfragment
elementsLib=self.elementsLib) #self.calDeltaMass()
if __name__ == "__main__":
myAAs = Aminoacides()
# for aa in myAAs.list:
# for elem,num in aa.composition.iteritems():
# print("%s: %s" % (elem,num))
print("1-letter code 3-letter code Chemical formula Monoisotopic")
print("-" * 65)
for aa in myAAs.list:
print("%-10s %-15s %-20s %s" %
(aa.code, aa.code3, Formulas.compositionString(
aa.composition), aa.deltaMass))
##1-letter code 3-letter code Chemical formula Monoisotopic
##-----------------------------------------------------------------
##A Ala H5C3ON 71.03711379
##R Arg H12C6ON4 156.101111044
##N Asn H6C4O2N2 114.042927452
##D Asp H5C4O3N 115.02694303
##C Cys H5C3SON 103.00918448
##E Glu H7C5O3N 129.042593094
##Q Gln H8C5O2N2 128.058577516
##G Gly H3C2ON 57.021463726
##H His H7C6ON3 137.058911874
##I Ile H11C6ON 113.084063982
##L Leu H11C6ON 113.084063982
##K Lys H12C6ON2 128.094963024
from peptide import Peptide
from modifications import Modifications
from elements import Formulas
mods = Modifications()
phospho = mods.mods_unimods[21]
oxi = mods.mods_TPPcode['M[147]'];
cys = mods.mods_TPPcode['C[160]'];
nTMT = mods.mods_TPPcode['n[230]'];
TMT = mods.mods_TPPcode['K[357]'];
massNH3 = Formulas.mass(Formulas.NH3) #massN + 3 * massH
massH2O = Formulas.mass(Formulas.H2O) #(massH *2 + massO)
p1 = Peptide('CKDALA',modifications={1: cys})
p2 = Peptide('CKDALA',modifications={1: cys, 0: nTMT, 2:TMT})
for pep in [ p1, p2 ]:
# annot , ion_masses = pep.all_ions(ionseries = ['y','b'],
# frg_z_list = [1,2],
# fragmentlossgains = [0, ],
# mass_limits = [100,3000],
# label = '')
# for a in annot:
# print a
print "PEPTIDE:", pep.getSequenceWithMods("TPP"), "\tpreMz:", pep.getMZ(2) #CHARGE=2
for v in range(1, len(pep.sequence)):
self.elementsLib = Elements()
self.deltaMass = Formulas.mass(self.composition, elementsLib = self.elementsLib) #self.calDeltaMass()
if __name__ == "__main__":
myAAs = Aminoacides()
# for aa in myAAs.list:
# for elem,num in aa.composition.iteritems():
# print("%s: %s" % (elem,num))
print("1-letter code 3-letter code Chemical formula Monoisotopic")
print("-"*65)
for aa in myAAs.list:
print("%-10s %-15s %-20s %s" % (aa.code, aa.code3, Formulas.compositionString(aa.composition), aa.deltaMass))
##1-letter code 3-letter code Chemical formula Monoisotopic
##-----------------------------------------------------------------
##A Ala H5C3ON 71.03711379
##R Arg H12C6ON4 156.101111044
##N Asn H6C4O2N2 114.042927452
##D Asp H5C4O3N 115.02694303
##C Cys H5C3SON 103.00918448
##E Glu H7C5O3N 129.042593094
##Q Gln H8C5O2N2 128.058577516
##G Gly H3C2ON 57.021463726
##H His H7C6ON3 137.058911874
##I Ile H11C6ON 113.084063982
##L Leu H11C6ON 113.084063982
##K Lys H12C6ON2 128.094963024
def getMZfragment(self, ion_type, ion_number, ion_charge, label='', fragmentlossgain=0.0):
#Check label
if len(label) > 0 and label not in self.labelings :
print "Coding error: this labeling is not reported!! %s" % label
sys.exit(2)
#Check ion type
#if ion_type not in self.iontypes :
#print "This ion type can not be processed :" , ion_type
#print "This is the list of ion types considered in this library : " , self.iontypes
#sys.exit(2)
massH = 1.007825032
massO = 15.99491462
massN = 14.00307401
massC = 12.0000000
massProton = 1.0072765
massNH3 = Formulas.mass(Formulas.NH3) #massN + 3 * massH
massH2O = Formulas.mass(Formulas.H2O) #(massH *2 + massO)
massCO2 = Formulas.mass(Formulas.CO2) #(massC + 2 * massO)
protonMass = 1.007825032
massN15 = 15.0001089
massShiftN15 = massN15 - massN
massC13 = 13.003355
massShiftC13 = massC13 - massC
frg_number = int(ion_number)
frg_charge = int(ion_charge)
mzfragment = 0
frg_seq = ''
#precursors
if ion_type == 'p' :
mzfragment = self.getMZ(frg_charge, label)
return mzfragment
#a series
if ion_type == 'a' :
frg_seq = self.sequence[:frg_number]
mzfragment = self.getDeltaMassFromSequence(frg_seq)
mzfragment -= (massC + massO)
#Adding modifications deltamass
for aaPosMod in self.modifications.iterkeys() :
if aaPosMod <= frg_number: mzfragment += self.modifications[aaPosMod].deltamass
#b series
if ion_type == 'b' :
frg_seq = self.sequence[:frg_number]
mzfragment = self.getDeltaMassFromSequence(frg_seq)
#Adding modifications deltamass
for aaPosMod in self.modifications.iterkeys() :
if aaPosMod <= frg_number: mzfragment += self.modifications[aaPosMod].deltamass
#c series
if ion_type == 'c' :
frg_seq = self.sequence[:frg_number]
mzfragment = self.getDeltaMassFromSequence(frg_seq)
mzfragment += massNH3
#Adding modifications deltamass
for aaPosMod in self.modifications.iterkeys() :
if aaPosMod <= frg_number: mzfragment += self.modifications[aaPosMod].deltamass
#x series
if ion_type == 'x' :
frg_seq = self.sequence[-frg_number:]
mzfragment = self.getDeltaMassFromSequence(frg_seq)
mzfragment += massCO2
#Adding modifications deltamass
for aaPosMod in self.modifications.iterkeys() :
if (len(self.sequence) - frg_number) < aaPosMod : mzfragment += self.modifications[aaPosMod].deltamass
#y series
if ion_type == 'y' :
frg_seq = self.sequence[-frg_number:]
mzfragment = self.getDeltaMassFromSequence(frg_seq)
mzfragment += massH2O
#Adding modifications deltamass
for aaPosMod in self.modifications.iterkeys() :
if (len(self.sequence) - frg_number) < aaPosMod : mzfragment += self.modifications[aaPosMod].deltamass
#z series
if ion_type == 'z' :
frg_seq = self.sequence[-frg_number:]
mzfragment = self.getDeltaMassFromSequence(frg_seq)
mzfragment += massH2O
mzfragment -= massNH3
#Adding modifications deltamass
for aaPosMod in self.modifications.iterkeys() :
if (len(self.sequence) - frg_number) < aaPosMod : mzfragment += self.modifications[aaPosMod].deltamass
# 15N labeling: adds up the shift mass
if label == '15N' or label == 'N15':
frg_composition = self._getCompositionSeq(frg_seq)
if 'N' in frg_composition:
shift = (float(frg_composition['N']) * massShiftN15)
mzfragment += shift
#AQUA_KR labeling: adds up the shift mass
if label == 'AQUA_KR':
#Update (23.nov.2010): AQUA_KR only modifies Lys and Arg in the C-terminal position.
#Update (1.dec.2010) : I am a jerk. I should have taken it only for y ions , and not for the b ones
if 'K' in self.sequence[-1:] and ion_type == 'y' : mzfragment += 6 * massShiftC13 + 2 * massShiftN15
if 'R' in self.sequence[-1:] and ion_type == 'y' : mzfragment += 6 * massShiftC13 + 4 * massShiftN15
if label == 'SILAC_K6R10' :
#All K and R amino acides are shifted 6 Da and 10 Da.
numK = 0
numR = 0
for aa in frg_seq[:] :
if aa == 'K' : numK += 1
if aa == 'R' : numR += 1
mzfragment += numK * (6 * massShiftC13)
mzfragment += numR * (6 * massShiftC13 + 4 * massShiftN15)
if label == 'SILAC_K8R10' :
#All K and R amino acides are shifted 8 Da and 10 Da.
numK = 0
numR = 0
for aa in frg_seq[:] :
if aa == 'K' : numK += 1
if aa == 'R' : numR += 1
mzfragment += numK * (6 * massShiftC13 + 2 * massShiftN15)
mzfragment += numR * (6 * massShiftC13 + 4 * massShiftN15)
if label == 'SILAC_K8R6' :
#All K and R amino acides are shifted 8 Da and 6 Da.
numK = 0
numR = 0
for aa in frg_seq[:] :
if aa == 'K' : numK += 1
if aa == 'R' : numR += 1
mzfragment += numK * (6 * massShiftC13 + 2 * massShiftN15)
mzfragment += numR * (6 * massShiftC13)
mzfragment += frg_charge * massProton
mzfragment += fragmentlossgain
mzfragment /= frg_charge
return mzfragment
