Setting PEPNOVO_PTMS

Adding Recognized PTMs

If a PTM is in the below list of recognized PTMs, you can add it as follows:

 PEPNOVO_PTMS=N+1:Q-57

Adding New PTMs

If you would like to add a new PTM not in the list below, you just need to add it to a text file in the SPS code base before specifying it in the PEPNOVO_PTMS parameter. If you are compiling the source code, modify sps/trunk/resources/Models_pepnovo/PepNovo_PTMs.txt and make sure to re-compile. If you are using a release package, just modify sps/bin/resources/Models_pepnovo/PepNovo_PTMs.txt. This file encodes PTMs in the exact same format as below, just add the appropriate line and you should be good to go!

List of Recognized PTMs

Below is the current list of recognized PTMs, The "symbol" indicates the string that should be used to specify the PTM in the parameter.

#AA  offset      type locations symbol PTM-name
C    57.021464   FIXED     ALL  C+57 Carbamidomethyl

H    57.021464   OPTIONAL  ALL  H+57 Carbamidomethyl
D    57.021464   OPTIONAL  ALL  D+57 Carbamidomethyl
E    57.021464   OPTIONAL  ALL  E+57 Carbamidomethyl
C    -57.021	 OPTIONAL  ALL	C-57 Loss-Carbamidomethyl

W    12.0	 OPTIONAL  ALL  W+12 Formaldehyde
W    3.994915    OPTIONAL  ALL  W+4  kynurenin-oxidation

S    37.955882   OPTIONAL  ALL  S+38 Potassium
K    37.955882   OPTIONAL  ALL  K+38 Potassium
N    37.955882   OPTIONAL  ALL  N+38 Potassium
P    37.955882   OPTIONAL  ALL  P+38 Potassium
L    37.955882   OPTIONAL  ALL  L+38 Potassium
R    37.955882   OPTIONAL  ALL  R+38 Potassium
V    37.955882   OPTIONAL  ALL  V+38 Potassium
I    37.955882   OPTIONAL  ALL  I+38 Potassium
E    37.955882   OPTIONAL  ALL  E+38 Potassium
M    37.955882   OPTIONAL  ALL  M+38 Potassium
D    37.955882   OPTIONAL  ALL  D+38 Potassium
G    37.955882   OPTIONAL  ALL  G+38 Potassium
A    37.955882   OPTIONAL  ALL  A+38 Potassium

R    55.053433   OPTIONAL  ALL  R+55 Thr->Arg_substitution

Q    21.981943   OPTIONAL  ALL  Q+22 Sodium_adduct
V    21.981943   OPTIONAL  ALL  V+22 Sodium_adduct
P    21.981943   OPTIONAL  ALL  P+22 Sodium_adduct
N    21.981943   OPTIONAL  ALL  N+22 Sodium_adduct
Y    21.981943   OPTIONAL  ALL  Y+22 Sodium_adduct
T    21.981943   OPTIONAL  ALL  T+22 Sodium_adduct
H    21.981943   OPTIONAL  ALL  H+22 Sodium_adduct
D    21.981943   OPTIONAL  ALL  D+22 Sodium_adduct
E    21.981943   OPTIONAL  ALL  E+22 Sodium_adduct
S    21.981943   OPTIONAL  ALL  S+22 Sodium_adduct
F    21.981943   OPTIONAL  ALL  F+22 Sodium_adduct
A    21.981943   OPTIONAL  ALL  A+22 Sodium_adduct
M    21.981943   OPTIONAL  ALL  M+22 Sodium_adduct
I    21.981943   OPTIONAL  ALL  I+22 Sodium_adduct
L    21.981943   OPTIONAL  ALL  L+22 Sodium_adduct
G    21.981943   OPTIONAL  ALL  G+22 Sodium_adduct

L    42.010565   OPTIONAL  ALL  L+42 Acetylation
T    42.010565   OPTIONAL  ALL  T+42 Acetylation
S    42.010565   OPTIONAL  ALL  S+42 Acetylation
Y    42.010565   OPTIONAL  ALL  Y+42 Acetylation
G    42.010565   OPTIONAL  ALL  G+42 Acetylation
V    42.010565   OPTIONAL  ALL  V+42 Acetylation
M    42.010565   OPTIONAL  ALL  M+42 Acetylation
P    42.010565   OPTIONAL  ALL  P+42 Acetylation
D    42.010565   OPTIONAL  ALL  D+42 Acetylation
A    42.010565   OPTIONAL  ALL  A+42 Acetylation
K    42.010565   OPTIONAL  ALL  K+42 Acetylation

P    43.005814   OPTIONAL  ALL  P+43 Carbamylation
A    43.005814   OPTIONAL  ALL  A+43 Carbamylation
N    43.005814   OPTIONAL  ALL  N+43 Carbamylation
M    43.005814   OPTIONAL  ALL  M+43 Carbamylation
E    43.005814   OPTIONAL  ALL  E+43 Carbamylation
T    43.005814   OPTIONAL  ALL  T+43 Carbamylation
G    43.005814   OPTIONAL  ALL  G+43 Carbamylation
D    43.005814   OPTIONAL  ALL  D+43 Carbamylation
L    43.005814   OPTIONAL  ALL  L+43 Carbamylation
F    43.005814   OPTIONAL  ALL  F+43 Carbamylation
I    43.005814   OPTIONAL  ALL  I+43 Carbamylation
Q    43.005814   OPTIONAL  ALL  Q+43 Carbamylation
S    43.005814   OPTIONAL  ALL  S+43 Carbamylation
V    43.005814   OPTIONAL  ALL  V+43 Carbamylation
K    43.005814   OPTIONAL  ALL  K+43 Carbamylation

E    -18.010565  OPTIONAL  ALL  E-18 Dehydration
D    -18.010565  OPTIONAL  ALL  D-18 Dehydration
S    -18.010565  OPTIONAL  ALL  S-18 Dehydration
T    -18.010565  OPTIONAL  ALL  T-18 Dehydration

M    -29.992806  OPTIONAL  ALL  M-30 Homoserine
V    -29.992806  OPTIONAL  ALL  V-30 Homoserine

M    -48.003371  OPTIONAL  ALL  M-48 HomoserineLactone
K    -48.003371  OPTIONAL  ALL  K-48 HomoserineLactone

K    28.031300   OPTIONAL  ALL  K+28 Di-Methylation

M    31.989829   OPTIONAL  ALL  M+32 Dioxidation
W    31.989829   OPTIONAL  ALL  W+32 Dioxidation

S    27.994915   OPTIONAL  ALL  S+28 Formylation
T    27.994915   OPTIONAL  ALL  T+28 Formylation


M    15.994915   OPTIONAL  ALL  M+16 Oxidation
H    15.994915   OPTIONAL  ALL  H+16 Oxidation
W    15.994915   OPTIONAL  ALL  W+16 Oxidation

D    15.994915   OPTIONAL  ALL  D+16 Hydroxylation
K    15.994915   OPTIONAL  ALL  K+16 Hydroxylation
N    15.994915   OPTIONAL  ALL  N+16 Hydroxylation
P    15.994915   OPTIONAL  ALL  P+16 Hydroxylation

N    0.984016    OPTIONAL  ALL  N+1  Deamidation
D    0.984016    OPTIONAL  ALL  D+1  Deamidation
Q    0.984016    OPTIONAL  ALL  Q+1  Deamidation
R    0.984016    OPTIONAL  ALL  R+1  Deamidation
F    0.984016    OPTIONAL  ALL  F+1  Deamidation

C    14.015650   OPTIONAL  ALL  C+14 Methylation
H    14.015650   OPTIONAL  ALL  H+14 Methylation
K    14.015650   OPTIONAL  ALL  K+14 Methylation
N    14.015650   OPTIONAL  ALL  N+14 Methylation
Q    14.015650   OPTIONAL  ALL  Q+14 Methylation
R    14.015650   OPTIONAL  ALL  R+14 Methylation

S    79.966331   OPTIONAL  ALL  S+80 Phosphorylation
T    79.966331   OPTIONAL  ALL  T+80 Phosphorylation
Y    79.966331   OPTIONAL  ALL  Y+80 Phosphorylation

R    10.008269   OPTIONAL  ALL  R+10 SILAC_R
K    8.014199    OPTIONAL  ALL  K+8  SILAC_K

Q    -17.026549  OPTIONAL  +1   Q-17 Pyro-glu
N    -17.002740  OPTIONAL  ALL  N-17 N-Succinimide
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