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Symbols and Mass Values

Symbols

The following symbols are recognised in Unimod composition and neutral loss fields. Some represent elements while others represent molecular sub-units. Note that C, F, H, etc. are symbols for elements, not one letter codes for amino acids.
Symbol Description
13CCarbon 13
15NNitrogen 15
18OOxygen 18
2HDeuterium
AcAcetate
AgSilver
AuGold
BrBromine
CCarbon
CaCalcium
ClChlorine
CuCopper
dHexDeoxy-hexose
FFluorine
FeIron
HHydrogen
HepHeptose
HexHexose
HexAHexosamine
HexNAcN-Acetyl Hexosamine
HgMercury
IIodine
KPotassium
Kdn3-deoxy-d-glycero-D-galacto-nonulosonic acid
Kdo2-keto-3-deoxyoctulosonic acid
LiLithium
MeMethyl
MoMolybdenum
NNitrogen
NaSodium
NeuAcN-acetyl neuraminic acid
NeuGcN-glycoyl neuraminic acid
NiNickel
OOxygen
PPhosphorous
PentPentose
PhosPhosphate
SSulphur
SeSelenium
SulfSulphate
WaterWater
ZnZinc

Mass values

All mass values in Unimod are calculated from the IUPAC atomic weights and isotopic abundances tabulated by WebElements:
Element Name Monoisotopic Average
HHydrogen1.0078250351.00794
2HDeuterium2.0141017792.014101779
LiLithium7.0160036.941
CCarbon1212.0107
13CCarbon1313.0033548313.00335483
NNitrogen14.00307414.0067
15NNitrogen1515.0001089715.00010897
OOxygen15.9949146315.9994
18OOxygen1817.999160317.9991603
FFluorine18.9984032218.9984032
NaSodium22.989767722.98977
PPhosphorous30.97376230.973761
SSulfur31.972070732.065
ClChlorine34.9688527235.453
KPotassium38.963707439.0983
CaCalcium39.962590640.078
FeIron55.934939355.845
NiNickel57.935346258.6934
CuCopper62.929598963.546
ZnZinc63.929144865.409
BrBromine78.918336179.904
SeSelenium79.916519678.96
MoMolybdenum97.905407395.94
AgSilver106.905092107.8682
IIodine126.904473126.90447
AuGold196.966543196.96655
HgMercury201.970617200.59

Monoisotopic mass is calculated using the mass of the most abundant natural isotope of each constituent element. An average mass is calculated using the "atomic weight" of each constituent element, which is the weighted average of all its natural isotopes. This definition of monoisotopic mass conforms to that given in Standard Definitions of Terms Relating to Mass Spectrometry, Phil. Price, J. Am. Soc. Mass Spectrom. (1991) 2 336-348. Some sources suggest that monoisotopic mass is calculated from the lightest natural isotope of each element, but this is wrong.

The compositions and mass values in Unimod define the differences (or "deltas") between the modified and unmodified residues. Although monoisotopic values are displayed with 6 decimal places, actual accuracies will usually be 7 to 8 significant figures. In the case of average masses, accuracies will usually be 5 to 6 significant figures.