Peptide Spectrum Interpretation: Tables of useful Data

Monoisotopic atomic masses.
Amino acids and their masses.
Modifications to peptide ion masses.
Masses of ions found in tandem spectra.
Relative abundances of isotopes of H, C, N, O, S.
Cleavage sites of endopeptidases.
Trypsin autolytic peptides and their masses.

Element	Monoisotopic atomic mass
H	1.007 825 032
C	12.000 000 000
N	14.003 074 005
O	15.994 914 622
P	30.973 761 51
S	31.972 070 69

Table 0. Monoisotopic atomic masses.

Enxyme	Cleaves at:	except if:
arg C	after R	before P
asp N	before D
chymotrypsin	after F, (L, M,) W or Y	before P; after PY
cyanogen bromide	after M
Glu C (basic)	after E	before P or E
Glu C (acidic)	after D or E	before D or E
Lys C	after K
pepsin (high acidity)	after F or L
pepsin (low acidity)	after A, E, F, L, Q, W or Y
proteinase K	after A, C, F, G, M, S, W or Y
trypsin	after K or R	before P

Table M1. Cleavage sites of endopeptidases.

element	baryon number	abundance	baryon number	abundance	baryon number	abundance	baryon number	abundance
H	1	99.988%	2	0.012%
C	12	98.93%	13	1.07%
N	14	99.63%	15	0.37%
O	16	99.76%	17	0.04%	18	0.20%
S	32	94.93%	33	0.76%	34	4.29%	36	0.02%

Table M2. Relative abundances of isotopes of H, C, N, O, S.

peptide	mass	notes
IQVR	515.330555	F
SRIQVR	758.463693	i
VATVSLPR	842.509975	F
NKPGVYTK	906.504889
FPTDDDDK	952.389979
LSSPATLNSR	1045.564195	F
APVLSDSSCK	1063.509383
SSGSSYPSLLQCLK	1526.752466
VCNYVNWIQQTIAAN	1793.864475
LSSPATLNSRVATVSLPR	1869.055780	i
SCAAAGTECLISGWGNTK	1882.842754
LGEHNIDVLEGNEQFINAAK	2211.104580	F
SSYPGQITGNMICVGFLEGGK	2215.052746
SSYPGQITGNM*ICVGFLEGGK	2231.047661	m
IITHPNENGNTLDNDIMLIK	2265.154902
IITHPNENGNTLDNDIM*LIK	2281.149816	m
SSGSSYPSLLQCLKAPVLSDSSCK	2571.243459	i
NKPGVYTKVCNYVNWIQQTIAAN	2681.350975	i
VATVSLPRSCAAAGTECLISGWGNTK	2706.334339	i
IQVRLGEHNIDVLEGNEQFINAAK	2707.416745
SRIQVRLGEHNIDVLEGNEQFINAAK	2950.549884	i

Table M3. Trypsin autolytic peptides and their masses.

Notes:
F	Very strong peak
i	Peptide with a missed internal cleavage point.
m	Peptide with an oxidized methionine.

1-letter code	3-letter code	name	structure (side-chain only is shown, except for proline)	relative frequency	monoisotopic mass, Da
G	Gly	glycine	–H	7%	57.021464
A	Ala	alanine	–CH3	7%	71.037114
S	Ser	serine	–CH2–OH	8%	87.032028
P	Pro	proline		6%	97.052764
V	Val	valine	–CH(–CH3)–CH3	6%	99.068414
T	Thr	threonine	–CH(–OH)–CH3	6%	101.047678
C	Cys	cysteine	–CH2–S	5%	103.009184
I	Ile	isoleucine	–CH(–CH3)–CH2–CH3	10%	113.084064
L	Leu	leucine	–CH2–CH2–CH2–CH3	4%	113.084064
N	AsN	aspagine	–CH2–CO–NH2	5%	114.042927
D	Asp	aspartic acid	–CH2–COOH	5%	115.026943
Q	GlN	glutamine	–CH2–CH2–CO–NH2	6%	128.058578
K	Lys	lysine	–CH2–CH2–CH2–CH2–NH2	7%	128.094963
E	Glu	glutamic acid	–CH2–CH2–COOH	2%	129.042593
M	Met	methionine	–CH2–CH2–S–CH3	2%	131.040485
H	His	histidine		4%	137.058912
F	Phe	phenylalanine	–CH2–C6H5	2%	147.068414
R	Arg	arginine	–CH2–CH2–CH2–NH–C(–NH2)=NH	5%	156.101111
Y	Tyr	tyrosine		3%	163.063329
W	Trp	tryptophan		1%	186.079313
		carboxymethylated cysteine			161.051049
		carbamidated cysteine			160.030648
		oxidised methionine			147.035399

Table M4. Amino acids and their masses.

modification	amino acid involved	context	mass difference, Da
water loss	S, T	mass spec	-18.010565
ammonia loss	Q, K, R, N; esp. n-terminal Q	mass spec	-17.026549
urea loss	c-terminal R	mass spec	-60.032363
hydration	H, R	mass spec, esp. B ions	+18.010565
methylation		various	+14.015650
hydroxylation	K, P	post-translational, in collagen	+15.994915
hydroxylation	P	post-translational, in plant cell walls	+15.994915
oxidation	M	lab preparation. partial	+15.994915
acetylation	S		+42.010565
carbamidation	C	lab preparation. complete	+57.021464
carboxylation	C	lab preparation. complete	+58.005479
phosphorylation	T,S,Y	post-translational	+79.966330
amidation	c-terminal		-0.984016
formylation			+27.994915
sulfation			+79.956815
N-linked glycosylation	N	post-translational. sugar usually lost before MS	large, depends on the sugar
O-linked glycosylation	T, S, hydroxy-K	post-translational. sugar usually lost before MS	large, depends on the sugar
fucosylation	S		+146.057908
contamination by Na+			+21.981944
contamination by K+			+37.955588
contamination by Cu+			+61.921776

Table M8. Modifications to ion masses.

Ion type	Composition	M/z ratio	Frequency
A	Σ +H –CO	S-27	quite common
B	Σ +H	S+1	common
C	Σ +H +NH +H +H	S+18	rare
X	Σ +OH +CO	S+45	rare
Y	Σ +OH +H +H	S+19	very common
Z	Σ +OH –NH	S+21	very rare
doubly-charged parent	parent ion +H+	(parent M/z + 1) / 2	very common
trebly-charged parent	parent ion +H+ +H+	(parent M/z + 2) / 3	rare
internal ion	Σ +OH +H +H	S+19	rare
immonium ion	Σ +H -CO	S-27	rare

Table T1. Masses of ions found in tandem spectra.

'Σ' here denotes the total mass of the constituent amino acids, as given in table 2.

The Frequency column applies to low-energy collisions in a modern QTOF
spectrometer, higher-energy collisions in older spectrometers gave rise to a
greater variety of ions.