Peptide Spectrum Interpretation: Tables of useful Data

 

ElementMonoisotopic
atomic mass
H 1.007 825 032
C12.000 000 000
N14.003 074 005
O15.994 914 622
P30.973 761 51
S31.972 070 69
Table 0. Monoisotopic atomic masses.

 

EnxymeCleaves at:except if:
arg Cafter Rbefore P
asp Nbefore D 
chymotrypsinafter F, (L, M,) W or Ybefore P; after PY
cyanogen bromideafter M 
Glu C (basic)after Ebefore P or E
Glu C (acidic)after D or Ebefore D or E
Lys Cafter K 
pepsin (high acidity)after F or L 
pepsin (low acidity)after A, E, F, L, Q, W or Y 
proteinase Kafter A, C, F, G, M, S, W or Y 
trypsinafter K or Rbefore P
Table M1. Cleavage sites of endopeptidases.

 

elementbaryon
number
abundancebaryon
number
abundancebaryon
number
abundancebaryon
number
abundance
H199.988%20.012%    
C1298.93%131.07%    
N1499.63%150.37%    
O1699.76%170.04%180.20%  
S3294.93%330.76%344.29%360.02%
Table M2. Relative abundances of isotopes of H, C, N, O, S.

 

peptidemassnotes
IQVR515.330555F
SRIQVR758.463693i
VATVSLPR842.509975F
NKPGVYTK906.504889 
FPTDDDDK952.389979 
LSSPATLNSR1045.564195F
APVLSDSSCK1063.509383 
SSGSSYPSLLQCLK1526.752466 
VCNYVNWIQQTIAAN1793.864475 
LSSPATLNSRVATVSLPR1869.055780i
SCAAAGTECLISGWGNTK1882.842754 
LGEHNIDVLEGNEQFINAAK2211.104580F
SSYPGQITGNMICVGFLEGGK2215.052746 
SSYPGQITGNM*ICVGFLEGGK2231.047661m
IITHPNENGNTLDNDIMLIK2265.154902 
IITHPNENGNTLDNDIM*LIK2281.149816m
SSGSSYPSLLQCLKAPVLSDSSCK2571.243459i
NKPGVYTKVCNYVNWIQQTIAAN2681.350975i
VATVSLPRSCAAAGTECLISGWGNTK2706.334339i
IQVRLGEHNIDVLEGNEQFINAAK2707.416745 
SRIQVRLGEHNIDVLEGNEQFINAAK2950.549884i
Table M3. Trypsin autolytic peptides and their masses.
Notes:
FVery strong peak
iPeptide with a missed internal cleavage point.
Peptide with an oxidized methionine.

 

1-letter code3-letter codenamestructure (side-chain only is shown, except for proline)relative frequencymonoisotopic mass, Da
GGlyglycineH7%57.021464
AAlaalanineCH37%71.037114
SSerserineCH2OH8%87.032028
PProproline6%97.052764
VValvalineCH(CH3)CH36%99.068414
TThrthreonineCH(OH)CH36%101.047678
CCyscysteineCH2S5%103.009184
IIleisoleucineCH(CH3)CH2CH310%113.084064
LLeuleucineCH2CH2CH2CH34%113.084064
NAsNaspagineCH2CONH25%114.042927
DAspaspartic acidCH2COOH5%115.026943
QGlNglutamineCH2CH2CONH26%128.058578
KLyslysineCH2CH2CH2CH2NH27%128.094963
EGluglutamic acidCH2CH2COOH2%129.042593
MMetmethionineCH2CH2SCH32%131.040485
HHishistidine4%137.058912
FPhephenylalanineCH2C6H52%147.068414
RArgarginineCH2CH2CH2NHC(NH2)=NH5%156.101111
YTyrtyrosine3%163.063329
WTrptryptophan1%186.079313
  carboxymethylated cysteine  161.051049
  carbamidated cysteine  160.030648
  oxidised methionine  147.035399
Table M4. Amino acids and their masses.

 

modificationamino acid involvedcontextmass difference, Da
water lossS, Tmass spec-18.010565
ammonia lossQ, K, R, N; esp. n-terminal Qmass spec-17.026549
urea lossc-terminal Rmass spec-60.032363
hydrationH, Rmass spec, esp. B ions+18.010565
methylation various+14.015650
hydroxylationK, Ppost-translational, in collagen+15.994915
hydroxylationPpost-translational, in plant cell walls+15.994915
oxidationMlab preparation. partial+15.994915
acetylationS +42.010565
carbamidationClab preparation. complete+57.021464
carboxylationClab preparation. complete +58.005479
phosphorylationT,S,Ypost-translational+79.966330
amidationc-terminal -0.984016
formylation  +27.994915
sulfation  +79.956815
N-linked glycosylationNpost-translational. sugar usually lost before MSlarge, depends on the sugar
O-linked glycosylationT, S, hydroxy-Kpost-translational. sugar usually lost before MSlarge, depends on the sugar
fucosylationS +146.057908
contamination by Na+  +21.981944
contamination by K+  +37.955588
contamination by Cu+  +61.921776
Table M8. Modifications to ion masses.

 

Ion typeCompositionM/z ratioFrequency
AΣ +H COS-27quite common
BΣ +HS+1common
CΣ +H +NH +H +HS+18rare
XΣ +OH +COS+45rare
YΣ +OH +H +HS+19very common
ZΣ +OH NHS+21very rare
doubly-charged parentparent ion +H+(parent M/z + 1) / 2very common
trebly-charged parentparent ion +H+ +H+(parent M/z + 2) / 3rare
internal ionΣ +OH +H +HS+19rare
immonium ionΣ +H -COS-27rare
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.


Main peptide MS page. Copyright N.S.Wedd 2003, 2004.
Last updated 2007-07-11.