Chemistry Reference
In-Depth Information
TABLE 1.4. Number of Oxidations Detected by LC/FT-MS and Reactive Amino
Acid Residues Identified by LC/MS/MS for Ubiquitin
Solvent-
Accessible
Surface Area
by NMR (A 2 )
Measure Mass
(Da) by LC/
FT-MS a
Oxidation
Detected by LC/
FT-MS a
Sites of
Oxidation by
LC/MS/MS a
Peptide
Residues
1-6
780.4201
M + O
M1
23.57
Q2
69.87
12-27
1802.9145
M + O
T12
39.63
P19
65.70
S20
70.83
N25
61.76
34-42
1070.5102
M + 2O
I36
32.28
P37
67.15
P38
36.52
43-47
699.3591
M + O
48-63
1794.8742
M + O
64-72
1082.6081
M + O
a Six oxidized peptides were found in LC/FT-MS analysis, whereas three oxidized peptides were
detected in LC/MS/MS analysis. The solvent-accessible surface areas were calculated using
GETAREA 1.1 [337] using NMR structure of bovine ubiquitin [338].
Adapted from Aye et al. [141] with the permission of the American Chemical Society.
(CNBr) probes the C-terminal side of Met if it is not oxidized (MetO); however,
CNBr is highly toxic [90].
There have been several reviews on the role of MS in the field of proteomics
[89-91, 149-154]. Analysis of MS is based on the mass-to-charge ratio ( m / z )
of gaseous ions or their fragments and corresponding signal intensities. The
m / z of the resulting gas phase ions can be correlated to structural properties
of proteins in solution. Electrospray ionization (ESI)-MS and matrix-assisted
laser desorption/ionization (MALDI)-MS techniques have been applied to
determine the structure of peptides and proteins [155-167]. ESI produces
multiple charged peptides, while MALDI generates singly charged peptides,
and their fragmentation has been carried out by postsource decay (PSD) [168,
169]. High-quality MS/MS spectra of peptides are produced by high- and
low-energy collision-induced dissociation (CID) on time-of-flight (TOF)/TOF
instruments [170]. MALDI-MS analysis has also been enhanced by combining
it with the ion trap, Fourier transform mass spectrometer, and triple quadru-
pole (Q q Q LIT ).
Figure 1.6 shows the fragmented ions that may result from high- and low-
energy CID. Generally, high-energy CID results in all types of fragmented ions,
while only b , y a , and z fragments are observed in low-energy CID spectra
 
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