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Fragmentation Channels (fragmentation + channel)
Selected AbstractsZwitterionic States in Gas-Phase Polypeptide Ions Revealed by 157-nm Ultra-Violet PhotodissociationCHEMISTRY - A EUROPEAN JOURNAL, Issue 30 2006Frank Kjeldsen Dr. Abstract A new method of detecting the presence of deprotonation and determining its position in gas-phase polypeptide cations is described. The method involves 157-nm ultra-violet photodissociation (UVPD) and is based on monitoring the losses of CO2 (44 Da) from electronically excited deprotonated carboxylic groups relative to competing COOH losses (45 Da) from neutral carboxylic groups. Loss of CO2 is a strong indication of the presence of a zwitterionic [(+),,,(,),,,(+)] salt bridge in the gas-phase polypeptide cation. This method provides a tool for studying, for example, the nature of binding within polypeptide clusters. Collision-activated dissociation (CAD) of decarboxylated cations localizes the position of deprotonation. Fragment abundances can be used for the semiquantitative assessment of the branching ratio of deprotonation among different acidic sites, however, the mechanism of the fragment formation should be taken into account. Cations of Trp-cage proteins exist preferentially as zwitterions, with the deprotonation position divided between the Asp9 residue and the C terminus in the ratio 3:2. The majority of dications of the same molecule are not zwitterions. Furthermore, 157-nm UVPD produces abundant radical cations M.+ from protonated molecules through the loss of a hydrogen atom. This method of producing M.+ ions is general and can be applied to any gas-phase peptide cation. The abundance of the molecular radical cations M.+ produced is sufficient for further tandem mass spectrometry (MS/MS), which, in the cases studied, yielded side-chain loss of a basic amino acid as the most abundant fragmentation channel together with some backbone cleavages. [source] Influence of differently ionized species on fragmentation pathways and energetics of a potential adenosine receptor antagonist using a triple quadrupole and a multistage LTQ-OrbitrapÔ FTMS instrumentJOURNAL OF HETEROCYCLIC CHEMISTRY, Issue 4 2009Wendy Zhong A systematic study was conducted to investigate the influence of differently ionized species on the fragmentation pathways and energetics of a piperazine-containing adenosine by using different cations or anions. Very different fragmentation mechanisms were observed in protonated- versus sodiated-molecules, which indicated that the proton is mobilized to promote the charge-direct fragmentation, whereas Na+ cation was fixed at the heterotricyclic ring structure provoking charge-remote fragment ions. This finding was also supported by the results observed in the fragmentation behaviors in the deprotonated-molecule. The energetics of these fragment ions were also explored by using the breakdown curves obtained from the triple quadrupole and LTQ-OrbitrapÔ instrument. The data indicated that the lowest energy pathways in the protonated-molecule [M+H]+ involve breaking a CN bond connecting an ethylene bridge and heterotricyclic ring structure. The lowest energy pathway is the cleavage of a CO bond connecting the methoxy ethyl group and phenolic oxygen to form a distonic radical ion for a sodiated-molecule [M+Na+]and a deprotonated-molecule [M-H],. The data suggest that by choosing the differently ionized species, one can probe different fragmentation channels that can provide additional structure information for an unknown impurity and possibly degradation product identification. In addition, by comparing the data obtained from triple quadrupole and LTQ-Orbitrap instruments, one can develop further understanding of the differences in the fragmentation behaviors due to the variations in the collision activation-dissociation process. From the side-by-side comparison with the breakdown curves obtained for both instruments, the difference in fragmentation behaviors caused by the difference in dissociation processes that occur in these two types of instruments can be probed. J. Heterocyclic Chem., (2009). [source] Do collisions inside the collision cell play a relevant role in CID-LIFT experiments?,JOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 1 2007Gloriano Moneti Abstract Collision experiments are a valid approach to characterize the ionic species generated by matrix assisted laser desorption ionization (MALDI). When a time-of-flight analyzer is employed, three different approaches are available for these experiments: the postsource decay (PSD), the LIFT and the MALDI-TOF/TOF. The last two are of particular interest because of the overcoming of the PSD problems related to mass calibration of the product ion spectra. Experiments performed by LIFT on linear or cyclic peptides, in presence or in absence of collision gas in the collision cell, gave evidence of an unexpected behavior: the two spectra were practically superimposable, and in the former case only a few new fragmentation channels were activated with low yield. These results mean that the selected ion exhibits a large amount of internal energy, capable of promoting fragmentation processes in the time window corresponding to the flight time between ion source and the acceleration electrode placed after the collision cell. Experiments performed by varying the plume density show that this internal energy uptake occurs in the expanding plume, through multiple collisions. The LIFT data have been compared with those achieved by collisions of ESI-generated [MH]+ ions of angotensin II performed under ,in-source' conditions and by triple-quadrupole experiments. The obtained results show a strong similarity among the spectra, indicating that the internal energy uptake in a MALDI source is comparable with that of 40-eV ions colliding with Ar in a triple-quadrupole instrument. Copyright © 2006 John Wiley & Sons, Ltd. [source] Fragmentation pathways of protonated peptidesMASS SPECTROMETRY REVIEWS, Issue 4 2005Béla Paizs Abstract The fragmentation pathways of protonated peptides are reviewed in the present paper paying special attention to classification of the known fragmentation channels into a simple hierarchy defined according to the chemistry involved. It is shown that the ,mobile proton' model of peptide fragmentation can be used to understand the MS/MS spectra of protonated peptides only in a qualitative manner rationalizing differences observed for low-energy collision induced dissociation of peptide ions having or lacking a mobile proton. To overcome this limitation, a deeper understanding of the dissociation chemistry of protonated peptides is needed. To this end use of the ,pathways in competition' (PIC) model that involves a detailed energetic and kinetic characterization of the major peptide fragmentation pathways (PFPs) is proposed. The known PFPs are described in detail including all the pre-dissociation, dissociation, and post-dissociation events. It is our hope that studies to further extend PIC will lead to semi-quantative understanding of the MS/MS spectra of protonated peptides which could be used to develop refined bioinformatics algorithms for MS/MS based proteomics. Experimental and computational data on the fragmentation of protonated peptides are reevaluated from the point of view of the PIC model considering the mechanism, energetics, and kinetics of the major PFPs. Evidence proving semi-quantitative predictability of some of the ion intensity relationships (IIRs) of the MS/MS spectra of protonated peptides is presented. © 2004 Wiley Periodicals, Inc., Mass Spec Rev 24:508,548, 2005 [source] | ||||||||||