Complete and Exact Peptide Sequence Analysis Based on Propositional Logic - Mathematical Approaches to Polymer Sequence Analysis and Related Problems - page 7

Tabl e 1. 1 Commonly considered amino acids

Name Abbreviations Molecular weight Limitations

Glycine Gly (or G) 75.07 -

Alanine Ala (or A) 89.34 -

Serine Ser (or S) 105.10 -

Proline Pro (or P) 115.14 -

Valine Val (or V) 117.15 -

Threonine Thr (or T) 119.12 -

Cysteine Cys (or C) 121.16 -

Taurine Tau 125.15 Only C-terminal

Piroglutamic acid pGlu 129.10 Only N-terminal

Leucine Leu (or L) 131.18 -

Asparagine Asn (or N) 132.12 -

Aspartic acid Asp (or D) 133.11 -

Glutamine Gln (or Q) 146.15 -

Lysine Lys (or K) 146.19 -

Glutamic acid Glu (or E) 147.13 -

Methionine Met (or M) 149.22 -

Histidine His (or H) 155.16 -

Phenylalanine Phe (or F) 165.16 -

Arginine Arg (or R) 174.21 -

Tyrosine Tyr (or Y) 181.19 -

There is a large number of possible amino acids, differing in the internal chemi-
cal structure of the radical R, and, therefore, for their functional characteristics and
their molecular weights. Many of them cannot be specified in the genetic code;
hence, the most commonly considered ones generally include the 20 reported in
Tab le 1.1 . Moreover, each amino acid may present one of the many possible modifi-
cations, such as phosphorylation, acetylation and methylation. This would produce
alterations to its standard molecular weight. Note also that the equivalent mass in-
volved in the molecular bindings leads to non-integer values for the amino acid
weights and that the very weight of each amino acid type is not a single fixed value,
but may assume different values depending on the presence of different isotopes of
the various atoms constituting the amino acid. Values reported in Table 1.1 are just
the average masses of the molecules.
An accurate and general sequencing procedure should be able to deal with the
above uncertainties, by taking as part of the problem data the information about:

Which are the components that should be considered as possible for the current
analysis;

Their weight values (in unified atomic mass units u, or daltons);

Possible limitations on the position they can assume within a peptide chain;

The desired numerical precision of the sequencing procedure, set on the basis of
the accuracy of the adopted mass spectrometry device;

And any other incidentally known information.