9780521516358book.pdf

9.5.3 Comparison of MS and Edman sequencing

Edman degradation (Section 8.4.3) to obtain the complete sequence of a protein is

uncommon nowadays since genomes are available to search with fragmentary

sequences. Most intact proteins, if they are not processed from a secretory or pro-

peptide form, are blocked at the N-terminus, most commonly with an acetyl group.

Other amino terminal blocking includes fatty acylation, most commonly with a

myristoyl, C 12 fatty acid, attached through a glycine residue but the presence of many

shorter-chain fatty acids is known to occur. Cyclisation of glutamine to a pyroglutamyl

Table 9.2Symbols and residue masses of the protein amino acids

Name Symbol Residue massa Side chain

Alanine A, Ala 71.079 CH 3 -

Arginine R, Arg 156.188 HN¼C(NH 2 )—NH—(CH 2 ) 3 -

Asparagine N, Asn 114.104 H 2 N—CO—CH 2 -

Aspartic acid D, Asp 115.089 HOOC—CH 2 -

Cysteine C, Cys 103.145 HS—CH 2 -

Glutamine Q, Gln 128.131 H 2 N—CO—(CH 2 ) 2 -

Glutamic acid E, Glu 129.116 HOOC—(CH 2 ) 2 -

Glycine G, Gly 57.052 H-

Histidine H, His 137.141 Imidazole-CH 2 -

Isoleucine I, Ile 113.160 CH 3 —CH 2 —CH(CH 3 )-

Leucine L, Leu 113.160 (CH 3 ) 2 —CH—CH 2 -

Lysine K, Lys 128.17 H 2 N—(CH 2 ) 4 -

Methionine M, Met 131.199 CH 3 —S—(CH 2 ) 2 -

Metsulphoxide Met.SO 147.199 CH 3 —S(O)—(CD 2 ) 2 -

Phenylalanine F, Phe 147.177 Phenyl-CH 2 -

Proline P, Pro 97.117 Pyrrolidone-CH-

Serine S, Ser 87.078 HO—CH 2 -

Threonine T, Thr 101.105 CH 3 —CH(OH)-

Tryptophan W, Trp 186.213 Indole-NH—CH¼C—CH 2 -

Tyrosine Y, Tyr 163.176 4-OH-Phenyl-CH 2 -

Valine V, Val 99.133 CH 3 —CH(CH 2 )-

Note:aResidue mass is the mass in a peptide bond, i.e. after loss of H 2 O when the peptide bond is

formed. The numbers in bold in the residue mass column indicate amino acids that may be ambiguous

in a sequence determined by tandem MS due to close similarity or identity in mass.

382 Mass spectrometric techniques