Missing monomer
In some cases, a position can be occupied by a monomer or not. Example: A trailing Lysine might be present at the C-terminus of an antibody or not. An underscore is used to denote a potential blank position.
Single Monomer – no probability
Any single monomer of a list may be found at given position. The list elements are separated by a comma and grouped using parentheses. No probability for the occurrence of a distinct monomer is given.
Single Monomer with probability
Any single monomer of a list may be found at given position, probability of occurrence of given monomer within that list is known, but product contains exactly one monomer.
The chromatogram of a sequence doesn’t allow to define exactly which monomer is available a certain position. But it allows giving information about the probability for the potential monomers.
Monomer mixture
A mixture of monomers of a list may be found at given position.
Mixture of 4 proteins with differing monomers at positions 5 and 10.
10% PEPTIDE1{A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D.
40% PEPTIDE1{A.A.A.A.G.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D.
10% PEPTIDE1{A.A.A.A.A.A.A.A.A.G.A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D.
40% PEPTIDE1{A.A.A.A.G.A.A.A.A.G.A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D.
Resulting HELM string with ambiguity notation:
PEPTIDE1{A.A.A.A.(A+G).A.A.A.A.(A+G).A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D.D.D.
Unknown monomer
Unknown monomers (0..n monomers) may be found at given position.
Unknown monomers (1..n monomers) may be found at given position.
PEPTIDE1{A.A.A.A.(X,*).A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E}|PEPTIDE2{G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.C.S.S.S.S.S.S.S.S.S.P.P.P.P.P.P.P.P.P.K.K.K.K.K.K.K.K.K.K.K.K.K}$$$
Unknown monomers (1) may be found at given position in PEPTIDE.
PEPTIDE1{A.A.A.A.X.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E}|PEPTIDE2{G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.C.S.S.S.S.S.S.S.S.S.P.P.P.P.P.P.P.P.P.K.K.K.K.K.K.K.K.K.K.K.K.K}$$$
Unknown monomers (1) may be found at given position in RNA.
RNA1{R(A)P.R(G)P.R(N)P.R(A)P}$$$
I am not sure how to enter examples like these into the editor.
The HELM design document includes the following:
Missing monomer In some cases, a position can be occupied by a monomer or not. Example: A trailing Lysine might be present at the C-terminus of an antibody or not. An underscore is used to denote a potential blank position.
PEPTIDE1{A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.(_,K)}|PEPTIDE2{G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.C.S.S.S.S.S.S.S.S.S.P.P.P.P.P.P.P.P.P.K.K.K.K.K.K.K.K.K.K.K.K.K}$$$$
Single Monomer – no probability Any single monomer of a list may be found at given position. The list elements are separated by a comma and grouped using parentheses. No probability for the occurrence of a distinct monomer is given.
PEPTIDE1{A.A.A.A.(A,G,W,[Aha]).A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E}|PEPTIDE2{G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.C.S.S.S.S.S.S.S.S.S.P.P.P.P.P.P.P.P.P.K.K.K.K.K.K.K.K.K.K.K.K.K}$$$$
Single Monomer with probability Any single monomer of a list may be found at given position, probability of occurrence of given monomer within that list is known, but product contains exactly one monomer.
PEPTIDE1{A.A.A.A.(A:1.1,G:69.5,W:25.5,[Aha]:3.9).A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E}|PEPTIDE2{G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.C.S.S.S.S.S.S.S.S.S.P.P.P.P.P.P.P.P.P.K.K.K.K.K.K.K.K.K.K.K.K.K}$$$$
The chromatogram of a sequence doesn’t allow to define exactly which monomer is available a certain position. But it allows giving information about the probability for the potential monomers. Monomer mixture A mixture of monomers of a list may be found at given position.
PEPTIDE1{A.A.A.A.(A+G+W+[Aha]).A.(A+G).A.A.A.A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E}|PEPTIDE2{G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.C.S.S.S.S.S.S.S.S.S.P.P.P.P.P.P.P.P.P.K.K.K.K.K.K.K.K.K.K.K.K.K}$$$$
Monomer mixture with ratios A mixture of monomers of a list may be found at given position, ratio of monomers within that list is known.
PEPTIDE1{A.A.A.A.(A:1.1+G:69.5+W:25.5+[Aha]:3.9).A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E}|PEPTIDE2{G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.C.S.S.S.S.S.S.S.S.S.P.P.P.P.P.P.P.P.P.K.K.K.K.K.K.K.K.K.K.K.K.K}$$$$
Mixture of 4 proteins with differing monomers at positions 5 and 10. 10% PEPTIDE1{A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D. 40% PEPTIDE1{A.A.A.A.G.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D. 10% PEPTIDE1{A.A.A.A.A.A.A.A.A.G.A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D. 40% PEPTIDE1{A.A.A.A.G.A.A.A.A.G.A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D.
Resulting HELM string with ambiguity notation: PEPTIDE1{A.A.A.A.(A+G).A.A.A.A.(A+G).A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D.D.D.
Unknown monomer Unknown monomers (0..n monomers) may be found at given position.
PEPTIDE1{A.A.A.A.*.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E}|PEPTIDE2{G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.C.S.S.S.S.S.S.S.S.S.P.P.P.P.P.P.P.P.P.K.K.K.K.K.K.K.K.K.K.K.K.K}$$$$
Unknown monomers (1..n monomers) may be found at given position. PEPTIDE1{A.A.A.A.(X,*).A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E}|PEPTIDE2{G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.C.S.S.S.S.S.S.S.S.S.P.P.P.P.P.P.P.P.P.K.K.K.K.K.K.K.K.K.K.K.K.K}$$$
Unknown monomers (1) may be found at given position in PEPTIDE. PEPTIDE1{A.A.A.A.X.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E.E}|PEPTIDE2{G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.G.C.S.S.S.S.S.S.S.S.S.P.P.P.P.P.P.P.P.P.K.K.K.K.K.K.K.K.K.K.K.K.K}$$$
Unknown monomers (1) may be found at given position in RNA. RNA1{R(A)P.R(G)P.R(N)P.R(A)P}$$$
I am not sure how to enter examples like these into the editor.