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Benjamin J. Bythell Árpád Somogyi Béla Paizs 《Journal of the American Society for Mass Spectrometry》2009,20(4):618-624
A recent statistical study (Savitski, M. M.; Falth, M.; Eva Fung, Y. M.; Adams, C. M.; Zubarev, R. A. J. Am. Soc. for Mass Spectrom. doi: 10.1016/j.jasms.2008.08.003) of a large spectral database indicated that the product ion spectra of doubly protonated
tryptic peptides fall into two distinct classes. The main factor distinguishing the two classes is the relative abundance
of the y
N-2 fragment: for Class I spectra y
N-2 is the most abundant y fragment while for Class II other y ions dominate the corresponding spectra. To explain the dominance of y
N-2 for Class I spectra formation of a nontraditional b
2 ion with a diketopiperazine (6-membered cyclic peptide) rather than an oxazolone structure was proposed. Here we present
evidence from tandem mass spectrometry, hydrogen/deuterium exchange, and density functional calculations that do not support
this proposal. Namely, that CID of doubly protonated YIGSR, YGGFLR, and YIYGSFK produce Class I product ion spectra, yet the
b
2 fragment is shown to have the traditional oxazolone structure. 相似文献
6.
Isoperimetric inequalities are applied to a moving-boundaryproblem for doubly-connected domains. This problem occurs forexample in electrochemistry, in which case the domains in questionare the electrolyte of an electrolytic cell. The two electrodessurrounding the electrolyte are assumed to grow or dissolve,at different rates in general, by electrochemical reaction.We obtain optimal estimates showing, for example, that the leastchange in volume of each electrode always occurs in sphericalsymmetry. 相似文献
7.
a(n) ions are frequently formed in collision-induced dissociation (CID) of protonated peptides in tandem mass spectrometry (MS/MS) based sequencing experiments. These ions have generally been assumed to exist as immonium derivatives (-HN(+)═CHR). Using a quadrupole ion trap mass spectrometer, MS/MS experiments have been performed and the structure of a(n) ions formed from oligoglycines was probed by infrared spectroscopy. The structure and isomerization reactions of the same ions were studied using density functional theory. Overall, theory and infrared spectroscopy provide compelling evidence that a(n) ions undergo cyclization and/or rearrangement reactions, and the resulting structure(s) observed under our experimental conditions depends on the size (n). The a(2) ion (GG sequence) undergoes cyclization to form a 5-membered ring isomer. The a(3) ion (GGG sequence) undergoes cyclization initiated by nucleophilic attack of the carbonyl oxygen of the N-terminal glycine residue on the carbon center of the C-terminal immonium group forming a 7-membered ring isomer. The barrier to this reaction is comparatively low at 10.5 kcal mol(-1), and the resulting cyclic isomer (-5.4 kcal mol(-1)) is more energetically favorable than the linear form. The a(4) ion with the GGGG sequence undergoes head-to-tail cyclization via nucleophilic attack of the N-terminal amino group on the carbon center of the C-terminal immonium ion, forming an 11-membered macroring which contains a secondary amine and three trans amide bonds. Then an intermolecular proton transfer isomerizes the initially formed secondary amine moiety (-CH(2)-NH(2)(+)-CH(2)-NH-CO-) to form a new -CH(2)-NH-CH(2)-NH(2)(+)-CO- form. This structure is readily cleaved at the -CH(2)-NH(2)(+)- bond, leading to opening of the macrocycle and formation of a rearranged linear isomer with the H(2)C═NH(+)-CH(2)- moiety at the N terminus and the -CO-NH(2) amide bond at the C terminus. This rearranged linear structure is much more energetically favorable (-14.0 kcal mol(-1)) than the initially formed imine-protonated linear a(4) ion structure. Furthermore, the barriers to these cyclization and ring-opening reactions are low (8-11 kcal mol(-1)), allowing facile formation of the rearranged linear species in the mass spectrometer. This finding is not limited to 'simple' glycine-containing systems, as evidenced by the IRMPD spectrum of the a(4) ion generated from protonated AAAAA, which shows a stronger tendency toward formation of the energetically favorable (-12.3 kcal mol(-1)) rearranged linear structure with the MeHC═NH(+)-CHMe- moiety at the N terminus and the -CO-NH(2) amide bond at the C terminus. Our results indicate that one needs to consider a complex variety of cyclization and rearrangement reactions in order to decipher the structure and fragmentation pathways of peptide a(n) ions. The implications this potentially has for peptide sequencing are also discussed. 相似文献
8.
Benjamin J. Bythell Michaela Knapp-Mohammady Béla Paizs Alex G. Harrison 《Journal of the American Society for Mass Spectrometry》2010,21(8):1352-1363
The MSn spectra of the [M + H]+ and b 5 peaks derived from the peptides HAAAAA, AHAAAA, AAHAAA, AAAHAA, and AAAAHA have been measured, as have the spectra of the b 4 ions derived from the first four peptides. The MS2 spectra of the [M + H]+ ions show a substantial series of bn ions with enhanced cleavage at the amide bond C-terminal to His and substantial cleavage at the amide bond N-terminal to His (when there are at least two residues N-terminal to the His residue). There is compelling experimental and theoretical evidence for formation of nondirect sequence ions via cyclization/reopening chemistry in the CID spectra of the b tons when the His residue is near the C-terminus. The experimental evidence is less clear for ions when the His residue is near the N-terminus, although this may be due to the use of multiple alanine residues in the peptide making identifying scrambled peaks more difficult. The product ion mass spectra of the b 4 and b 5 ions from these isomeric peptides with cyclically permuted amino acid sequences are similar, but also show clear differences. This indicates less active cyclization/reopening followed by fragmentation of common structures for b n ions containing His than for sequences of solely aliphatic residues. Despite more energetically favorable cyclization barriers for the b 5 structures, the b 4 ions experimental data show more clear evidence of cyclization and sequence scrambling before fragmentation. For both b 4 and b 5 the energetically most favored structure is a macrocyclic isomer protonated at the His side chain. 相似文献
9.
Sinha RK Erlekam U Bythell BJ Paizs B Maître P 《Journal of the American Society for Mass Spectrometry》2011,22(9):1645-1650
Charge-directed fragmentation has been shown to be the prevalent dissociation step for protonated peptides under the low-energy
activation (eV) regime. Thus, the determination of the ion structure and, in particular, the characterization of the protonation
site(s) of peptides and their fragments is a key approach to substantiate and refine peptide fragmentation mechanisms. Here
we report on the characterization of the protonation site of oxazolone b
2
ions formed in collision-induced dissociation (CID) of the doubly protonated tryptic model-peptide YIGSR. In support of earlier
work, here we provide complementary IR spectra in the 2800–3800 cm–1 range acquired on a table-top laser system. Combining this tunable laser with a high power CO2 laser to improve spectroscopic sensitivity, well resolved bands are observed, with an excellent correspondence to the IR
absorption bands of the ring-protonated oxazolone isomer as predicted by quantum chemical calculations. In particular, it
is shown that a band at 3445 cm–1, corresponding to the asymmetric N–H stretch of the (nonprotonated) N-terminal NH2 group, is a distinct vibrational signature of the ring-protonated oxazolone structure. 相似文献
10.
Bythell BJ Hendrickson CL Marshall AG 《Journal of the American Society for Mass Spectrometry》2012,23(4):644-654
We report the use of unimolecular dissociation by infrared radiation for gaseous multiphoton energy transfer to determine
relative activation energy (Ea,laser) for dissociation of peptide sequence ions. The sequence ions of interest are mass-isolated; the entire ion cloud is then
irradiated with a continuous wave CO2 laser, and the first order rate constant, kd, is determined for each of a series of laser powers. Provided these conditions are met, a plot of the natural logarithm of
kd versus the natural logarithm of laser power yields a straight line, whose slope provides a measure of Ea,laser. This method reproduces the Ea values from blackbody radiative dissociation (BIRD) for the comparatively large, singly and doubly protonated bradykinin
ions (nominally y
9
and y
9
2+
). The comparatively small sequence ion systems produce Ea,laser values that are systematic underestimates of theoretical barriers calculated with density functional theory (DFT). However,
the relative Ea,laser values are in qualitative agreement with the mobile proton model and available theory. Additionally, novel protonated cyclic-dipeptide
(diketopiperazine) fragmentation reactions are analyzed with DFT. FT-ICR MS provides access to sequence ions generated by
electron capture dissociation, infrared multiphoton dissociation, and collisional activation methods (i.e., b
n
, y
m
, c
n
, z
m
•
ions). 相似文献