print(AAs){'U', 'R', 'S', 'M', 'P', 'I', 'E', 'H', 'L', 'N', 'C', 'G', 'D', 'W', 'K', 'F', 'T', 'V', 'A', 'Q', 'Y'}Constants
Where all constats are stored
This notebook stores all constants.
Amino Acids
A set of valid amino acids.
Mass dict
A numba compatible mass dict dictionary. This is created from the modifications.tsv. Change to allow custom modifications.
get_mass_dict
get_mass_dict (modfile:str, aasfile:str, verbose:bool=True)
Function to create a mass dict based on tsv files. This is used to create the hardcoded dict in the constants notebook. The dict needs to be hardcoded because of importing restrictions when using numba. More specifically, a global needs to be typed at runtime.
Args: modfile (str): Filename of modifications file. aasfile (str): Filename of AAs file. verbose (bool, optional): Flag to print dict.
Returns: Returns a numba compatible dictionary with masses.
Raises: FileNotFoundError: If files are not found.
for _ in mass_dict:
print(f"{_+':': <12}{mass_dict[_]}")A: 71.0371138
C: 103.0091845
D: 115.0269431
E: 129.0425931
F: 147.0684139
G: 57.02146373
H: 137.0589119
I: 113.084064
K: 128.094963
L: 113.084064
M: 131.0404846
N: 114.0429275
P: 97.05276386
Q: 128.0585775
R: 156.101111
S: 87.03202843
T: 101.0476785
U: 150.9536333957
V: 99.06841392
W: 186.079313
Y: 163.0633286
cC: 160.03064823
oxM: 147.03539923000002
aA: 113.04767849000001
aC: 145.01974919
aD: 157.03750779
aE: 171.05315779
aF: 189.07897859
aG: 99.03202842
aH: 179.06947659
aI: 155.09462869
aK: 170.10552769
aL: 155.09462869
aM: 173.05104929
aN: 156.05349219000001
aP: 139.06332855
aQ: 170.06914219
aR: 198.11167569
aS: 129.04259312
aT: 143.05824319
aU: 192.9641980857
aV: 141.07897861
aW: 228.08987769
aY: 205.07389329
amA: 70.053098207
amC: 102.02516890700001
amD: 114.042927507
amE: 128.058577507
amF: 146.084398307
amG: 56.037448137
amH: 136.074896307
amI: 112.100048407
amK: 127.11094740700001
amL: 112.100048407
amM: 130.056469007
amN: 113.05891190700001
amP: 96.068748267
amQ: 127.07456190700002
amR: 155.117095407
amS: 86.048012837
amT: 100.06366290700001
amU: 149.9696178027
amV: 98.084398327
amW: 185.095297407
amY: 162.079313007
pS: 166.99835935
pT: 181.01400942
pY: 243.02965952
deamN: 115.026943093
deamQ: 129.04259309300002
cmC: 85.9826354
pgE: 111.03202841000001
pgQ: 111.03202840000002
tmt0A: 295.1895917
tmt0C: 327.1616624
tmt0D: 339.179421
tmt0E: 353.195071
tmt0F: 371.2208918
tmt0G: 281.17394163
tmt0H: 361.2113898
tmt0I: 337.2365419
tmt0K: 352.2474409
tmt0L: 337.2365419
tmt0M: 355.1929625
tmt0N: 338.1954054
tmt0P: 321.20524176000004
tmt0Q: 352.2110554
tmt0R: 380.2535889
tmt0S: 311.18450633
tmt0T: 325.2001564
tmt0U: 375.1061112957
tmt0V: 323.22089182
tmt0W: 410.2317909
tmt0Y: 387.2158065
tmt2A: 296.1929466
tmt2C: 328.16501730000004
tmt2D: 340.1827759
tmt2E: 354.1984259
tmt2F: 372.2242467
tmt2G: 282.17729653000004
tmt2H: 362.2147447
tmt2I: 338.2398968
tmt2K: 353.2507958
tmt2L: 338.2398968
tmt2M: 356.1963174
tmt2N: 339.1987603
tmt2P: 322.20859666
tmt2Q: 353.21441030000005
tmt2R: 381.25694380000004
tmt2S: 312.18786123
tmt2T: 326.2035113
tmt2U: 376.1094661957
tmt2V: 324.22424672
tmt2W: 411.23514580000005
tmt2Y: 388.2191614
tmt6A: 300.200046
tmt6C: 332.1721167
tmt6D: 344.1898753
tmt6E: 358.2055253
tmt6F: 376.2313461
tmt6G: 286.18439593
tmt6H: 366.2218441
tmt6I: 342.2469962
tmt6K: 357.2578952
tmt6L: 342.2469962
tmt6M: 360.2034168
tmt6N: 343.2058597
tmt6P: 326.21569606
tmt6Q: 357.2215097
tmt6R: 385.2640432
tmt6S: 316.19496062999997
tmt6T: 330.2106107
tmt6U: 380.11656559569997
tmt6V: 328.23134612
tmt6W: 415.2422452
tmt6Y: 392.2262608
itraq4KA: 215.13952419999998
itraq4KC: 247.1115949
itraq4KD: 259.1293535
itraq4KE: 273.14500350000003
itraq4KF: 291.1708243
itraq4KG: 201.12387413
itraq4KH: 281.1613223
itraq4KI: 257.1864744
itraq4KK: 272.1973734
itraq4KL: 257.1864744
itraq4KM: 275.142895
itraq4KN: 258.1453379
itraq4KP: 241.15517426
itraq4KQ: 272.1609879
itraq4KR: 300.2035214
itraq4KS: 231.13443883
itraq4KT: 245.15008890000001
itraq4KU: 295.0560437957
itraq4KV: 243.17082432
itraq4KW: 330.1817234
itraq4KY: 307.16573900000003
itraq4K: 272.1973734
itraq4Y: 307.16573900000003
itraq8KA: 375.2393133
itraq8KC: 407.211384
itraq8KD: 419.2291426
itraq8KE: 433.2447926
itraq8KF: 451.2706134
itraq8KG: 361.22366323
itraq8KH: 441.2611114
itraq8KI: 417.2862635
itraq8KK: 432.2971625
itraq8KL: 417.2862635
itraq8KM: 435.2426841
itraq8KN: 418.245127
itraq8KP: 401.25496336000003
itraq8KQ: 432.260777
itraq8KR: 460.3033105
itraq8KS: 391.23422793
itraq8KT: 405.249878
itraq8KU: 455.1558328957
itraq8KV: 403.27061342
itraq8KW: 490.2815125
itraq8KY: 467.2655281
itraq8K: 432.2971625
itraq8Y: 467.2655281
eA: 337.1209813
eC: 369.093052
eD: 381.1108106
eE: 395.1264606
eF: 413.1522814
eG: 323.10533123
eH: 403.1427794
eI: 379.1679315
eK: 394.1788305
eL: 379.1679315
eM: 397.1243521
eN: 380.126795
eP: 363.13663136
eQ: 394.142445
eR: 422.1849785
eS: 353.11589592999997
eT: 367.131546
eU: 417.03750089569996
eV: 365.15228142
eW: 452.1631805
eY: 429.1471961
arg10R: 166.10938057776002
arg6R: 162.121241
lys8K: 136.10916278888
Electron: 0.00054857990907
Proton: 1.00727646687
Hydrogen: 1.00782503223
C13: 13.003354835
Oxygen: 15.994914619
OH: 17.002739651229998
H2O: 18.01056468346
NH3: 17.02654910112
delta_M: 1.00286864
delta_S: 0.0109135# Test that there is an entry for each AA
for _ in AAs:
assert _ in mass_dict.keys()
print(mass_dict['A'])
print(mass_dict['K'])71.0371138
128.094963Isotopes
We define a jitclass that stores the base mass, the number of isotopes, and their abundances. We create the typed dictionary isotopes that stores different default isotopes.
Isotope
Isotope (*args, **kwargs)
Jit-compatible class to store isotopes
Attributes: m0 (int): Mass of pattern dm0 (int): dm of pattern (number of isotopes) int0 (np.float32[:]): Intensities of pattern
for _ in isotopes:
print(f'Element {_}: base mass {isotopes[_].m0:<20} intensities {isotopes[_].intensities}')Element C: base mass 12.0 intensities [0.9893 0.0107 0. ]
Element H: base mass 1.0079400539398193 intensities [9.99885e-01 1.15000e-04 0.00000e+00]
Element O: base mass 15.994915008544922 intensities [9.9757e-01 3.8000e-04 2.0500e-03]
Element N: base mass 14.003073692321777 intensities [0.99636 0.00364]
Element S: base mass 31.972070693969727 intensities [9.499e-01 7.500e-03 4.250e-02 1.000e-04]
Element I: base mass 126.90447235107422 intensities [1.]
Element K: base mass 38.963706970214844 intensities [9.32581e-01 1.17000e-04 6.73020e-02]Averagine Model
#Masses of the averagine model
for _ in averagine_aa:
print(f"{_} {averagine_aa[_]}")C 4.9384
H 7.7583
N 1.3577
O 1.4773
S 0.0417Protease dict
A numba compatible dictionary that stores different regular expressions needed for digestion. The dictionary was largely taken from the Pyteomics website which in turn derived the rules are from expasy. Some entries (Lys-C/ Lys-N) were updated according to OpenMS. A useful resource for testing Regex can be found here.
#Entries in the protease_dict:
for _ in protease_dict:
print(f"{_:<35} {protease_dict[_]}")arg-c R
asp-n \w(?=D)
bnps-skatole W
caspase 1 (?<=[FWYL]\w[HAT])D(?=[^PEDQKR])
caspase 2 (?<=DVA)D(?=[^PEDQKR])
caspase 3 (?<=DMQ)D(?=[^PEDQKR])
caspase 4 (?<=LEV)D(?=[^PEDQKR])
caspase 5 (?<=[LW]EH)D
caspase 6 (?<=VE[HI])D(?=[^PEDQKR])
caspase 7 (?<=DEV)D(?=[^PEDQKR])
caspase 8 (?<=[IL]ET)D(?=[^PEDQKR])
caspase 9 (?<=LEH)D
caspase 10 (?<=IEA)D
chymotrypsin high specificity ([FY](?=[^P]))|(W(?=[^MP]))
chymotrypsin low specificity ([FLY](?=[^P]))|(W(?=[^MP]))|(M(?=[^PY]))|(H(?=[^DMPW]))
clostripain R
cnbr M
enterokinase (?<=[DE]{3})K
factor xa (?<=[AFGILTVM][DE]G)R
formic acid D
glutamyl endopeptidase E
granzyme b (?<=IEP)D
hydroxylamine N(?=G)
iodosobenzoic acid W
lys_c K(?!P)
lys_c/p K
lys_n .K
ntcb \w(?=C)
pepsin ph1.3 ((?<=[^HKR][^P])[^R](?=[FL][^P]))|((?<=[^HKR][^P])[FL](?=\w[^P]))
pepsin ph2.0 ((?<=[^HKR][^P])[^R](?=[FLWY][^P]))|((?<=[^HKR][^P])[FLWY](?=\w[^P]))
proline endopeptidase (?<=[HKR])P(?=[^P])
proteinase k [AEFILTVWY]
staphylococcal peptidase i (?<=[^E])E
thermolysin [^DE](?=[AFILMV])
thrombin ((?<=G)R(?=G))|((?<=[AFGILTVM][AFGILTVWA]P)R(?=[^DE][^DE]))
trypsin_full ([KR](?=[^P]))|((?<=W)K(?=P))|((?<=M)R(?=P))
trypsin_exception ((?<=[CD])K(?=D))|((?<=C)K(?=[HY]))|((?<=C)R(?=K))|((?<=R)R(?=[HR]))
non-specific ()
trypsin ([KR](?=[^P]))Losses
#Entries in the loss_dict:
for _ in loss_dict:
print(f"{_:<5} {loss_dict[_]}") 0.0
-H2O 18.01056468346
-NH3 17.03052Labels
for label in label_dict:
print(label_dict[label])label(mod_name='tmt6', channels=['tmt10-126', 'tmt10-127N', 'tmt10-127C', 'tmt10-128N', 'tmt10-128C', 'tmt10-129N', 'tmt10-129C', 'tmt10-130N', 'tmt10-130C', 'tmt10-131', 'tmt10-131C'], masses=array([126.127726, 127.124761, 127.131081, 128.128116, 128.134436,
129.131471, 129.13779 , 130.134825, 130.141145, 131.13818 ,
131.144499]), reference_channel='tmt10-126', mods_fixed_terminal=['tmt6<^'], mods_variable=['tmt6Y', 'tmt6K'])