# No notation as of yet!!!
# Devised these myself!
# ************************************************
# The following characters are illegal characters for the short names!:
# Hyphen charater : '-'
# Hash charater : '#'
# ************************************************

Carbamidomethyl (C)=Cmm
N-Formyl (Protein)=For
Myristoylation (term)=Myr
Amide (C-term)=Ami

# These need some work for the N-term!!
Acetyl (K)=Ace
Acetyl (ST)=Ace
Acetyl (N-term)=Ace
Acetyl_heavy (N-term)=AcD3
Acetyl_heavy (K)=AcD3K

# Check these.
Methyl ester (DE)=Met
Methyl ester (C-term)=Met
Phospho (STY)=P
Phospho (ST)=P
Phospho (Y)=P
Sulphone (M)=Sul

# Not in Mascot?
NONE1=DiS
NONE2=HOx
#NONE3=For
NONE4=COx
NONE5=Cys


# These are OK.
Pyro-cmC (N-term camC)=Pyc
Pyro-glu (N-term Q)=Pyr
Pyro-glu (N-term E)=Pyr
Oxidation (M)=Mox
Deamidation (NQ)=Dam
HSe=Hse
Propionamide (C)=Prp
Carbamyl (N-term)=Car
thioprop (N-term)=Tpr
thiopropcar (N-term)=Tpc
ThiopropLys (K)=Tpl
ThiopropCarbLys (K)=Tcl
Homoarg (K)=Har
Biotin-S-S-Lysin (K)=BSL
Oxidation - 32 (W)=Wox
Oxidation - 48 (W)=Wo2
Tyrosinamine (Y)=Yam
Tyrosineaminesulfon (Y) =YAS
Tyrosinsulfon (Y) = YS
N-Formyl (Protein) = For
Nitro (Y) = NO
Cysteic_acid (C)=CyA
4H_reagent (K)=4H
Carbamyl (K)=Cak
Phospho-NL (S)=Pnl
Phospho-NL (T)=Pnl
hydroxykynurenin (W)=Hkn
kynurenin (W)=Kyn
Oxidation (HW)=Ox
Gly-Gly epsilonNH2(K) = GGe
Methyl (N-term)=Met
Tyrosinamine1 (Y)=Yam1
Lys-DSP (K)=Dsp
# Bart GH
Carbamidomethylox (C)=Cmox1
Carbamidomethyloxox (C)=Cmox2
6Da/0Da loss 5xC13 1xN15 (M) =Mloss
6Da/0Da gain (M) =Mgain
TyrosinamineAcet (Y) =Yamac
6Da/0Da loss 5xC13 1xN15 (Mox) =Moxloss
6Da/0Da gain (Mox) =Moxgain
MoxC13 (Mox) = MoxC13
# Evy T
NBS (W)=NBS
# Christian K
Hse_lact (C-term M)=HSL
HSe (C-term M)=HSe


# FSBA mods.
Tyr-SBA (Y)=Ysba
Lys-SBA (K)=Ksba
His-SBA (H)=Hsba
Cys-SBA (C)=Csba
Ser-SBA (S)=Ssba
His-SB (H)=Hsb
Cys-SB (C)=Csb
Ser-SB (S)=Ssb
Lys-SB (K)=Ksb
Tyr-SB (Y)=Ysb
O18Ser (S)=S18O
O18Thr (T)=T18O
Lys-SBO18 (K)=KsbH
Tyr-SBO18 (Y)=YsbH
Arg 6xC(13) (R)=C13
Pro 5xC(13) (P)=C13
N-Acetyl (Protein)=AcPr

# Carbonylation modifications:
# Lysine can be converted in Aminoadipic-semialdehyde
# Arginine and Proline can be converted in Glutamic-semialdehyde
# Hydrazone formed between Aminoadipic-semialdehyde and 6-Hydrazinonicotinic-Acid-Y(NO2)R
Lys-CO1 (K)=CO1
# Hydrazone formed between Glutamic-semialdehyde and 6-Hydrazinonicotinic-Acid-Y(NO2)R
RP-CO1 (RP)=CO1
# Hydrazone formed between 2-amino-3-ketobutyric-Acid and 6-Hydrazinonicotinic-Acid-Y(NO2)R
threo-CO1 (T)=CO1
# Hydrazone formed between Lysine-4-keto-Benaldehyde and 6-Hydrazinonicotinic-Acid-Y(NO2)R (for in vitro tests)
Lys-BCO1 (K)=BCO1