Guidelines for Naming Modifications

	RULES
1	These are names for modifications. Specificity, (residue, position, terminus), linkage, chirality, neutral loss behaviour, etc., can be indicated separately, in an application specific manner, and should not be part of the name.
2	Legal characters for modification names are the ASCII characters 0-9 A-Z a-z together with the following symbols and punctuation characters # ( ) * + , - . / : > [ ] { }
3	Names are not case-sensitive.
4	Names have a minimum length of 3 characters and a maximum length of 64 characters.
5	Modifications that correspond to deltas with different elemental formulae cannot have the same name.
6	2H not D for deuterium
7	Nucleon number comes before the element symbol, not after. That is, 18O not O18
8	There is no requirement to specify nucleon number for the most abundant natural isotope of each element. That is, N not 14N
9	Reserved keywords are delta, label, lipid, cation, and xlink.
10	The colon character is reserved for delimiting keywords from the remainder of the name
11	The plus character is reserved for delimiting combined modifications, e.g. Label:13C(9)+Phospho
12	Parentheses are reserved for counts in formulae, e.g. Delta:H(2)C(3)
13	For glycosylation, the name is constructed from the monosaccharide composition, e.g. Hex(1)HexNAc(1)dHex(1)
14	If there is no suitable name for a lipid, a name can be constructed from the keyword Lipid: plus the nominal monoisotopic mass of the delta. No instance at present
15	For isotope labels that do not change the elemental composition of the residue or terminus, the name is constructed from the keyword Label: plus a count of the labelled atoms. For example, Label:13C(6). This is an implied substitution, so that Label:13C(6) is the same as Delta:C(-6)13C(6)
16	For isotope labels that are also chemical modifications, the name is constructed from a unique keyword, and a colon delimited count of the labelled atoms. Where an isotope tag has an accepted acronym or trademark, like ICAT, this should be used as part or all of the keyword. For example ICPL and ICPL:13C(6). Heavy and light are not sufficient for isotope labels. Like Label:, this is an implied substitution
17	Where there is no obvious or unambiguous name, use the keyword Delta: followed by the complete empirical formula of the delta. For example, Delta:H(2)C(3)
18	For cations, use the keyword cation, the element symbol, and the oxidation state using Roman numerals in square brackets. If there is only a single oxidation state for the element, and this is I, it can be omitted, e.g. Cation:Na and Cation:Fe[II]

	RECOMMENDATIONS
1	Names are not intended to be IUPAC-style systematic nomenclature, ( http://www.chem.qmul.ac.uk/iupac/AminoAcid/ and http://www.acdlabs.com/iupac/nomenclature/93/r93_296.htm). The aim is a controlled list of common or trivial names.
2	Names should semi-descriptive or, at least, recognizable.
3	If there is a generally accepted name or acronym for a modification, this should be adopted.
4	As far as possible, the length of a name should be 24 characters or less.
5	Names can be unambiguously delimited from application specific prefixes and suffixes using any of the illegal characters, especially space, underscore, and @
6	As far as possible, there should be a one to one relationship between a name and a delta of a given empirical formula. Exceptions are allowed where the structures are different or where there are generally accepted names that convey additional useful information.
7	Use American English spelling (e.g. sulfate).
8	Use case to enhance readability.
9	Minimise use of hyphens. Not required for prefixes like di and tri. Do not use a hyphen to indicate "loss of" because this is too ambiguous.
10	The preference is to name the modification as a moiety, not the reaction or the reagent or the modifed residue. For example, acetyl and not acetylation or acetyl-L-lysine. This is only a preference, not a rule. It runs into difficulty when the modification is the removal of a moiety, because it is difficult to name the absence, and it may be necessary to use the reaction or process as the name.
11	Many modifications are essentially substitutions that are specific to a single residue. These can be most clearly represented using an arrow syntax, e.g. Arg->Orn, Trp->Kynurenin. This syntax must never use 1-letter codes for residues to avoid confusion with elements.
12	Try to avoid starting a name with something that might be mistaken for a specificity, e.g. N- or C-, which are often used to indicate protein terminus PTMs.
13	Related modifications should be differentiated by suffixes rather than prefixes so that they sort together in an alphabetical list.

Non-standard Amino Acid Residues

• Waters / Micromass data sheet
• DeltaMass
• Chemnetbase
• Chemical Abstracts

Aad	2-aminoadipicacid
Abu	2-Aminobutyric acid
Acm	Acetamidomethyl
Aib	2-Aminoisobutyric acid
Bum	t-butyloxymethyl
Cit	Citruline
Cmc	Carboxymethylcysteine
Cya	cysteic acid
Dha	dehydroalanine
Dhb	Dehydroamino-2-butyric acid
Gla	4-carboxyglutamic acid
Glp	pyroglutamic acid (also Pga, pGlu and
Hse	homoserine
Hsl	homoserine lactone
Hyl	Hydroxylysine
Hyp	Hydroxyproline
Iva	Isovaline
Nle	Norleucine
Orn	Ornithine
Pip	2-Piperidinecarboxylic acid
Pyr	pyruvic acid
Sar	Sarcosine
Sec	selenocysteine