Mascot: The trusted reference standard for protein identification by mass spectrometry for 25 years

Amino acid reference data

The data in this table are for amino acid residues. To calculate the mass of a neutral peptide or protein, sum the residue masses plus the masses of the terminating groups (e.g. H at the N-terminus and OH at the C-terminus).
Residue 3-
letter
code		 1-
letter
code		 Mono-
isotopic
mass		 Average
mass		 Structure
Alanine
C3H5NO		 Ala A 71.037114 71.0779 Ala
Arginine
C6H12N4O		 Arg R 156.101111 156.1857 Arg
Asparagine
C4H6N2O2		 Asn N 114.042927 114.1026 Asn
Aspartic acid
C4H5NO3		 Asp D 115.026943 115.0874 Asp
Asn or Asp Asx B      
Cysteine
C3H5NOS		 Cys C 103.009185 103.1429 Cys
Glutamic acid
C5H7NO3		 Glu E 129.042593 129.114 Glu
Glutamine
C5H8N2O2		 Gln Q 128.058578 128.1292 Gln
Glu or Gln Glx Z      
Glycine
C2H3NO		 Gly G 57.021464 57.0513 Gly
Histidine
C6H7N3O		 His H 137.058912 137.1393 His
Isoleucine
C6H11NO		 Ile I 113.084064 113.1576 Ile
Leucine
C6H11NO		 Leu L 113.084064 113.1576 Leu
Lysine
C6H12N2O		 Lys K 128.094963 128.1723 Lys
Methionine
C5H9NOS		 Met M 131.040485 131.1961 Met
Phenylalanine
C9H9NO		 Phe F 147.068414 147.1739 Phe
Proline
C5H7NO		 Pro P 97.052764 97.1152 Pro
Serine
C3H5NO2		 Ser S 87.032028 87.0773 Ser
Threonine
C4H7NO2		 Thr T 101.047679 101.1039 Thr
Selenocysteine
C3H5NOSe		 Sec U 150.95363 150.0379 SeC
Tryptophan
C11H10N2O		 Trp W 186.079313 186.2099 Trp
Tyrosine
C9H9NO2		 Tyr Y 163.06332 163.1733 Tyr
Unknown Xaa X      
Valine
C5H9NO		 Val V 99.068414 99.1311 Val

 

When Mascot tests a peptide containing ambiguous residue codes, it expands and tests all possibilities. For example, a peptide containing a single B will be tested twice, once with N at that position and once with D. A peptide containing a single X will generate 20 peptides to be tested. To avoid excessive search times, Mascot will test all possibilities up to a maximum of 3 B or Z residues and 1 X residue per peptide. Above this limit, the weighted average mass will be used (~ 110 Da).