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  • 1
    Keywords: AB-INITIO ; PEPTIDE ; Germany ; PROTEIN ; PROTEINS ; PROTON ; CLEAVAGE ; MOBILITY ; SPECTROMETRY ; fragmentation ; PRODUCT ; PEPTIDES ; DISSOCIATION ; GLYCYLGLYCINE ; MAIN FRAGMENTATION PATHWAYS ; PROTONATED PEPTIDES ; RRKM ; CHANNEL ; STATES ; GAS-PHASE ; CHEMISTRY ; PRODUCTS ; PROTON-TRANSFER ; ab initio calculations ; AMIDE BOND ; peptide fragmentation pathways ; protonated arginine ; TANDEM MASS-SPECTRA
    Abstract: Arginine is often involved at the C-terminus of peptides obtained from tryptic digests of proteins. The very basic guanidine group of the side-chain of arginine has a large effect on the backbone fragmentation of protonated peptides. Furthermore, arginine exhibits specific fragmentation reactions involving its side-chain. Various tautomerization states, conformers and side-chain dissociation channels of protonated arginine were studied using theoretical methods. The guanidine loss of protonated arginine is proved to be an S(N)2 substitution on the delta-carbon of the side-chain, starting from species containing the NepsilonH-C+(NetaH2)(Neta'H2) or -Nepsilon+H2-C(NetaH)(Neta'H2) moieties and leads to formation to either protonated guanidine or protonated proline. In the corresponding transition structures the proline moiety is protonated. Under low-energy collision conditions the extra proton transfers to the guanidine moiety, leading to the formation of C+(NH2)(3). On the other hand, the lifetime of the fragmenting species under high-energy collision conditions is shorter, resulting in enhanced formation of protonated proline and its dissociation products. The first step of ammonia loss is the leaving of a preformed NH3 from tautomers containing the -NepsilonH-C(NetaH3+)(Neta'H) or -N-epsilon-C(NetaH3+)(Neta'H2) moieties. The resulting protonated carbodiimide group can be stabilized by intramolecular nucleophilic attack, leading to ring formation. Overall, reactions involved in the ammonia loss from protonated arginine can be considered as an S(N)1 substitution on the central zeta-carbon of the guanidine group. Copyright (C) 2004 John Wiley Sons, Ltd
    Type of Publication: Journal article published
    PubMed ID: 15386755
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  • 2
    Keywords: PEPTIDE ; Germany ; QUANTIFICATION ; screening ; PROTEIN ; PROTEINS ; SAMPLE ; SAMPLES ; QUANTITATION ; SIGNAL ; WATER ; ACID ; ACIDS ; NUMBER ; SPECTROMETRY ; MASS-SPECTROMETRY ; PEPTIDES ; ADDUCTS ; AMINO-ACIDS ; QUANTITATIVE-ANALYSIS ; MALDI-MS ; MASSES ; STANDARD ; CHEMISTRY ; MATRIX ; STANDARDS ; INTERNAL STANDARDS ; SODIUM ; ADDUCT FORMATION ; ENZYME-ACTIVITIES ; biocatalysis ; CATALYZED REACTIONS ; DESORPTION IONIZATION ; deuterium exchange ; gas-phase chemistry ; ion formation ; LIPASE ; MALDI ; N-HETEROCYCLIC CARBENES ; SOLVENTS ; ULTRAVIOLET
    Abstract: Ionic liquids are interesting solvents for a number of applications in chemistry and biotechnology. We characterized five different ionic liquids by laser desorption/ionization (LDI) and by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) and studied the analysis of amino acids, peptides and proteins dissolved in these solvents. Signals of both anions and cations of the ionic liquids could be observed both in LDI- and in MALDI-MS. In the latter case, adduct formation between anions and cations of the analytes was observed. Amino acids, peptides and proteins could be analyzed in ionic liquids after addition of matrix substances. Sodium and potassium adducts were not observed in any analysis involving ionic liquids. Low molecular mass compounds and peptides could be analyzed best in the presence of water-immiscible ionic liquids, whereas proteins gave the best results in water-miscible ionic liquids. Optimal analysis conditions such as molar matrix-to-analyte and ionic liquid-to-matrix ratios were determined. Homogeneity of samples in the presence of ionic liquids was reduced compared with classical MALDI preparations. Relative quantitation of amino acids was possible using isotope-labeled internal standards. MALDI-MS thus can be used for the analysis of chemical reactions and the screening of enzyme-catalyzed reactions in ionic liquids and for the analysis of the biocatalysts dissolved in these solvents. Theoretical aspects of ion formation in the presence of ionic liquids both in LDI and MALDI analysis are discussed. Copyright (C) 2004 John Wiley Sons, Ltd
    Type of Publication: Journal article published
    PubMed ID: 15578746
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  • 3
    Keywords: PEPTIDE ; SPECTRA ; Germany ; PATHWAY ; INFORMATION ; MOLECULES ; IONS ; PHOSPHORYLATION ; SEQUENCE ; SEQUENCES ; RECOGNITION ; ACID ; ACIDS ; IDENTIFICATION ; DIFFERENCE ; REQUIRES ; COLLISION-INDUCED DISSOCIATION ; ELECTROSPRAY ; mass spectrometry ; SPECTROMETRY ; tandem mass spectrometry ; TANDEM MASS-SPECTROMETRY ; fragmentation ; MASS-SPECTROMETRY ; PEPTIDES ; FRAGMENTS ; SERIES ; AMINO-ACIDS ; DISSOCIATION ; PROTONATED PEPTIDES ; NOMENCLATURE ; accurate mass measurement ; GAS-PHASE ; METHIONINE ; neutral loss ; peptide sequencing
    Abstract: The widespread occurrence of the neutral loss of one to six amino acid residues as neutral fragments from doubly protonated tryptic peptides is documented for 23 peptides with individual sequences. Neutral loss of amino acids from the N-terminus of doubly charged tryptic peptides results in doubly charged y-ions, forming a ladder-like series with the ions [M + 2H](2+) = y(max)(2+), y(max-1)(2+), y(max-2)(2+), etc. An internal residue such as histidine, proline, lysine or arginine appears to favor this type of fragmentation, although it was sometimes also observed for peptides without this structure. For doubly protonated non-tryptic peptides with one of these residues at or near the N-terminus, we observed neutral loss from the C-terminus, resulting in a doubly charged b-type ion ladder. The analyses were performed by Q-TOF tandem mass spectrometry, facilitating the recognition of neutral loss ladders by their 2+ charge state and the conversion of the observed mass differences into reliable sequence information. It is shown that the neutral loss of amino acid residues requires low collision offset values, a simple mechanistic explanation based on established fragmentation rules is proposed and the utility of this neutral loss fragmentation pathway as an additional source for dependable peptide sequence information is documented. Copyright (C) 2003 John Wiley Sons, Ltd
    Type of Publication: Journal article published
    PubMed ID: 14648821
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  • 4
    Keywords: PEPTIDE ; SPECTRA ; COMBINATION ; Germany ; PROTEIN ; DOMAIN ; IDENTIFICATION ; mass spectrometry ; tandem mass spectrometry ; TANDEM MASS-SPECTROMETRY ; fragmentation ; DATABASE ; acetylation ; PEPTIDES ; CHROMATOGRAPHY ; domain structure ; dynamin A ; ELASTASE DIGESTION ; limited proteolysis ; PROTEIN-PHOSPHORYLATION ; QUADRUPOLE-TIME ; TOP-DOWN
    Abstract: The post-translational modifications of the 96 kDa protein dynamin A from Dictyostelium discoideum were analyzed using Q- TOF mass spectrometry. The accurate molecular mass of the intact protein revealed a covalent modification causing an additional mass of 42 Da. The modification could be identified as N-terminal acetylation by tandem mass, spectrometry. Extracted ion chromatograms for the a(1) and b(1) ion of the tryptic T1 peptide were used to detect the acetylated peptide within 54 nanoelectrospray ionization tandem mass spectra. Owing to the accurate molecular mass of the intact protein, additional covalent modifications could be excluded. In addition to the covalent modification, the domain structure of dynamin A was determined by applying a combination of limited proteolysis, sodium dodecylsulfate polyacrylamide gel electrophoresis, automated tandem mass spectrometry and protein database searching. Copyright (C) 2003 John Wiley Sons, Ltd
    Type of Publication: Journal article published
    PubMed ID: 12644989
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  • 5
    Keywords: AB-INITIO ; PATHWAY ; PATHWAYS ; TOOL ; MOLECULES ; RELEASE ; MOLECULE ; SPECTROMETRY ; MASS-SPECTROMETRY ; AMINO-ACIDS ; RECONSTRUCTION ; PROTONATED PEPTIDES ; ELIMINATION ; HIGH-LEVEL ; MASSES ; AMIDE BOND ; peptide fragmentation pathways ; Beauveria ; BEAUVERIA-BASSIANA ; beauverolide ; cyclodepsipeptide ; ENTOMOPATHOGENIC FUNGI ; FAST-ATOM-BOMBARDMENT ; fungus ; LIPID DROPLET FORMATION ; MOUSE MACROPHAGES ; Paecilomyces ; SCAN MASS-SPECTROMETRY ; spore
    Abstract: Profiling of cyclic tetradepsipeptides beauverolides was tested as a chemotaxonomic tool for fungal strain identification/discrimination. Two new tetradepsipeptides, beauverolides Q and R, were characterized by tandem mass spectrometry. Specific elimination of 113 atomic mass units from both protonated and sodiated molecules of beauverolides is ubiquitous for all 12 most dominant congeners evaluated in this profiling study. Reconstruction of the total ion chromatogram, according to this neutral fragment release, was used for data filtering and selectivity enhancement. Selective ring opening and fragment ion formation of beauverolide I are discussed in detail utilizing high-level theoretical modeling of the fragmentation pathways. Copyright (C) 2004 John Wiley Sons, Ltd
    Type of Publication: Journal article published
    PubMed ID: 15329847
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