dbmaker_defaults.txt

#atomMass
atom	mass
C	12.0
H	1.0078250
N	14.0030740
O	15.9949146
P	30.9737634
S	31.9720718
D	2.0141018
Na	22.989768

#monosaccharides
>symbols are not case-sensitive and are alphabetic characters
>Me is the number of methyl groups added in a permethylation reaction
sugar symbol number_of_each_atom
Hex	h	C=6	H=10	O=5	Me=3
dHex	d	C=6	H=10	O=4	Me=2
HexNAc	n	C=8	H=13	N=1	O=5	Me=3
HexA	a	C=6	H=8	O=6	Me=3
Pc	p	C=5	H=12	N=1	O=3	P=1	Me=0
NeuAc	s	C=11	H=17	N=1	O=8	Me=5
NeuGc	g	C=11	H=17	N=1	O=9	Me=6

#modifications
>Frequency is always or sometimes
>Where is label location. Use start(for reducing end) or sugar symbols or Me
>Me is for OH groups sensitive to permethylation
>The first letter of sugar-specific labels will be used to abbreviate - name accordingly.
name where frequency number_of_each_atom
None	start	always	H=0
AEAB	start	always	C=9	H=13	N=3
Permethylation	Me	always	C=1	H=2
Esterification	S	sometimes	C=2	H=4
pT	S	sometimes	C=7	H=6	N=7	O=-1
amidation	S	sometimes	H=1	N=1	O=-1
dimethylamidation	S	sometimes	C=2	H=5	N=1	O=-1
2AA	start	always	C=7	H=7	N=1	O=1

#preparation
>Me is the number of methyl groups added in a permethylation reaction
name symbol number_of_each_atom
Bound	bound	H=0
Enzyme-Released	enz	H=2	O=1	Me=2
Beta-Eliminated	beta	H=4	O=1	Me=3
Free-floating	frfl	H=2	O=1	Me=2
Base-hydrolyzed	bh	H=2	O=1	Me=2

#adductIons
ion	mass
None	0.00
Na	22.989769
K	38.963708
H	1.0078250

#outputOrder
sugar
NeuGc
NeuAc
Pc
HexA
dHex
Hex
HexNAc