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Backbone Cleavages (backbone + cleavage)
Selected AbstractsTransition metals as electron traps.JOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 10 2009Abstract Transition metal cations Co2+, Ni2+ and Zn2+ form 1 : 1 : 1 ternary complexes with 2,2,-bipyridine (bpy) and peptides in aqueous methanol solutions that have been studied for tripeptides GGG and GGL. Electrospray ionization of these solutions produced singly charged [Metal(bpy)(peptide , H)]+ and doubly charged [Metal(bpy)(peptide)]2+ ions (Metal = metal ion) that underwent charge reduction by glancing collisions with Cs atoms at 50 and 100 keV collision energies. Electron transfer to [Metal(bpy)(peptide)]2+ ions was less than 4.2 eV exoergic and formed abundant fractions of non-dissociated charge-reduced intermediates. Charge-reduced [Metal(bpy)(peptide)]+ ions dissociated by the loss of a hydrogen atom, ammonia, water and ligands that depended on the metal ion. The Ni and Co complexes mainly dissociated by the elimination of ammonia, water, and the peptide ligand. The Zn complex dissociated by the elimination of ammonia and bpy. A sequence-specific fragment was observed only for the Co complex. Electron transfer to [Metal(bpy)(peptide , H)]+ was 0.6,1.6 eV exoergic and formed intermediate radicals that were detected as stable anions after a second electron transfer from Cs. [Metal(bpy)(peptide , H)] neutrals and their anions dissociated by the loss of bpy and peptide ligands with branching ratios that depended on the metal ion. Optimized structures for several spin states, electron transfer and dissociation energies were addressed by combined density functional theory and Mřller,Plesset perturbational calculations to aid interpretation of experimental data. The experimentally observed ligand loss and backbone cleavage in charge-reduced [Metal(bpy)(peptide)]+ complexes correlated with the dissociation energies at the present level of theory. The ligand loss in +CR, spectra showed overlap of dissociations in charge-reduced [Metal(bpy)(peptide , H)] complexes and their anionic counterparts which complicated spectra interpretation and correlation with calculated dissociation energies. Copyright © 2009 John Wiley & Sons, Ltd. [source] Fragmentations of (M,H), anions of underivatised peptides.MASS SPECTROMETRY REVIEWS, Issue 1 2009Part 2: Characteristic cleavages of Ser, of disulfides, other post-translational modifications, together with some unusual internal processes Abstract In a previous review (Bowie, Brinkworth, & Dua (2002); Mass Spectrom Rev 21:87,107) we described the characteristic backbone cleavages and side chain fragmentations which occur from (M,H), parent anions of underivatized peptides. This work is briefly summarized in the present review. Cys was not described in the previous review: here we describe the Cys characteristic side chain loss of H2S, together with its , backbone cleavage. These processes are compared with those of the related Ser. All experimental observations are backed up with theoretical studies at the HF/6-31G(d)//AM1 level of theory, a level of theory which we have shown gives good geometries and acceptable relative energies. The negative ion cleavages of a number of post-translational modifications are described. Negative ion mass spectrometry is the method of choice for identification of disulfides in both peptides and proteins. Intramolecular disulfides are identified by the presence of the fragment anion [(M,H),,H2S2], and CID MS2 of this fragment normally identifies the positions of the two Cys residues and often the full sequence of the peptide. An unsymmetrically substituted intermolecular disulfide can give up to eight characteristic fragment anions, and CID MS2 of some, or all of these often provides the full sequence of those peptides which form the initial intermolecular disulfide linkage. Negative ion cleavages of disulfides are the most energetically favored of all peptide negative cleavages studied to date. Negative ion mass spectrometry is also valuable for the identification of pyroglutamates, sulfates and phosphates. Finally, some unusual fragmentations are described which involve cyclization/elimination reactions which require the decomposing (M,H), parent anions to adopt the same helical conformation that these peptides have in solution. © 2008 Wiley Periodicals, Inc., Mass Spec Rev 28:20,34, 2009 [source] Negative ion fragmentations of deprotonated peptides.RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 13 2009The unusual case of isoAsp: a joint experimental, theoretical study. The following peptides have been examined in this study: GLDFG(OH), caeridin 1.1 [GLLDGLLGLGGL(NH2)], 11 Ala citropin 1.1 [GLFDVIKKVAAVIGGL(NH2)], Crinia angiotensin [APGDRIYVHPF(OH)] and their isoAsp isomers. It is not possible to differentiate between Asp- and isoAsp-containing peptides (used in this study) using negative ion electrospray mass spectrometry. This is because the isoAsp residue cleaves to give the same fragment anions as those formed by , and , backbone cleavage of Asp. The isoAsp fragmentations are as follows: RNHCH(CO2H),CHCONHR,,,,[RNH,(HO2CCHCHCONHR,)],,,RNH,+HO2CCHCHCONHR, and RNHCH(CO2H),CHCONHR,,,,[RNH,(HO2CCHCHCONHR,],,,,O2CCHCHCONHR,+RNH2. Calculations at the HF/6-31+G(d)//AM1 level of theory indicate that the first of these isoAsp cleavage processes is endothermic (by +115,kJ mol,1), while the second is exothermic (,85,kJ mol,1). The barrier to the highest transition state is 42,kJ mol,1. No diagnostic cleavage cations were observed in the electrospray mass spectra of the MH+ ion of the Asp- and isoAsp-containing peptides (used in this study) to allow differentiation between these two amino acid residues. Copyright © 2009 John Wiley & Sons, Ltd. [source] Factors determining the performance of triple quadrupole, quadrupole ion trap and sector field mass spectrometer in electrospray ionization mass spectrometry.RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 13 2001The sequence coverage by fragment ions resulting from collision-induced dissociation in a triple stage quadrupole (TSQ) and a quadrupole ion trap (QIT) mass spectrometer of 10,20-mer oligonucleotides was investigated. While (a-B) and w ion series were the most abundant on both instruments, additional ion series of sequence relevance were preferably formed in the TSQ. Thus, a total number of 83 fragment ions were used to deduce the complete sequence of a 10-mer oligonucleotide of mixed sequence from a tandem mass spectrum recorded on the TSQ. The complete sequence was also encoded in the 28 fragments that were obtained from the QIT under comparable fragmentation conditions. Spectrum complexity increased considerably at the cost of signal-to-noise ratio upon fragmentation of a 20-mer oligonucleotide in the TSQ, whereas spectrum interpretation with longer oligonucleotides was significantly more straightforward in spectra recorded on the QIT. The extent of fragmentation had to be optimized by appropriate setting of collision energy and choice of precursor ion charge state in order to obtain full sequence coverage by fragments for de novo sequencing. Moreover, full sequence information was also dependent on base sequence because of the low tendency of backbone cleavage at thymidines. Tandem mass spectrometry on the QIT yielded redundant information that was successfully utilized to deduce the complete sequence of 20-mer oligonucleotides with high confidence. Copyright © 2001 John Wiley & Sons, Ltd. [source] Protein glycosylation analysis by HILIC-LC-MS of Proteinase K-generated N - and O -glycopeptidesJOURNAL OF SEPARATION SCIENCE, JSS, Issue 6-7 2010Gerhild Zauner Abstract Analysis of protein glycosylation is essential in order to correlate certain disease types with oligosaccharide structures on proteins. Here, a method for the MS characterization of site-specific protein glycosylation is presented. Using asialofetuin and fetuin as model substances, a protocol for glycopeptide dissection was developed based on unspecific proteolysis by Proteinase K. The resulting glycopeptides were then resolved by nanoscale hydrophilic interaction liquid chromatography-electrospray multistage MS. The early elution range of O -glycopeptides was clearly separated from the late elution range of N -glycopeptides. Glycopeptides were analyzed by ion trap-MS/MS, which revealed fragmentations of glycosidic linkages and some peptide backbone cleavages; MS3 spectra predominantly exhibited cleavages of the peptide backbone and provided essential information on the peptide sequence. The previously reported N - and O -glycan attachment sites of fetuin could be confirmed; moreover using our method, the occupation of a new, additional O -glycosylation site serine 296 was found. In conclusion, this approach appears to be a valuable technique for in-depth analysis of the site-specific N -glycosylation and O -glycosylation of individual glycoproteins. [source] Fragmentations of (M,H), anions of underivatised peptides.MASS SPECTROMETRY REVIEWS, Issue 1 2009Part 2: Characteristic cleavages of Ser, of disulfides, other post-translational modifications, together with some unusual internal processes Abstract In a previous review (Bowie, Brinkworth, & Dua (2002); Mass Spectrom Rev 21:87,107) we described the characteristic backbone cleavages and side chain fragmentations which occur from (M,H), parent anions of underivatized peptides. This work is briefly summarized in the present review. Cys was not described in the previous review: here we describe the Cys characteristic side chain loss of H2S, together with its , backbone cleavage. These processes are compared with those of the related Ser. All experimental observations are backed up with theoretical studies at the HF/6-31G(d)//AM1 level of theory, a level of theory which we have shown gives good geometries and acceptable relative energies. The negative ion cleavages of a number of post-translational modifications are described. Negative ion mass spectrometry is the method of choice for identification of disulfides in both peptides and proteins. Intramolecular disulfides are identified by the presence of the fragment anion [(M,H),,H2S2], and CID MS2 of this fragment normally identifies the positions of the two Cys residues and often the full sequence of the peptide. An unsymmetrically substituted intermolecular disulfide can give up to eight characteristic fragment anions, and CID MS2 of some, or all of these often provides the full sequence of those peptides which form the initial intermolecular disulfide linkage. Negative ion cleavages of disulfides are the most energetically favored of all peptide negative cleavages studied to date. Negative ion mass spectrometry is also valuable for the identification of pyroglutamates, sulfates and phosphates. Finally, some unusual fragmentations are described which involve cyclization/elimination reactions which require the decomposing (M,H), parent anions to adopt the same helical conformation that these peptides have in solution. © 2008 Wiley Periodicals, Inc., Mass Spec Rev 28:20,34, 2009 [source] Methylation of acidic moieties in poly(methyl methacrylate-co-methacrylic acid) copolymers for end-group characterization by tandem mass spectrometryRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 14 2010Rémi Giordanengo The complete structural characterization of a copolymer composed of methacrylic acid (MAA) and methyl methacrylate (MMA) units was achieved using tandem mass spectrometry. In a first step, collision-induced dissociation (CID) of sodiated MAA-MMA co-oligomers allowed us to determine the co-monomeric composition, the random nature of the copolymer and the sum of the end-group masses. However, dissociation reactions of MAA-based molecules mainly involve the acidic pendant groups, precluding individual characterization of the end groups. Therefore, methylation of all the acrylic acid moieties was performed to transform the MAA-MMA copolymer into a PMMA homopolymer, for which CID mainly proceeds via backbone cleavages. Using trimethylsilyldiazomethane as a derivatization agent, this methylation reaction was shown to be complete without affecting the end groups. Using fragmentation rules established for PMMA polymers together with accurate mass measurements of the product ions and knowledge of reagents used for the studied copolymer synthesis, a structure could be proposed for both end groups and it was found to be consistent with signals obtained in nuclear magnetic resonance spectra. Copyright © 2010 John Wiley & Sons, Ltd. [source] Complementary structural information of positive- and negative-ion MSn spectra of glycopeptides with neutral and sialylated N-glycansRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 5 2006Kisaburo Deguchi Positive- and negative-ion MSn spectra of chicken egg yolk glycopeptides binding a neutral and a sialylated N-glycan were acquired by using electrospray ionization linear ion trap time-of-flight mass spectrometry (ESI-LIT-TOFMS) and collision-induced dissociation (CID) with helium as collision gas. Several characteristic differences were observed between the positive- and negative-ion CID MSn (n,=,2, 3) spectra. In the positive-ion MS2 spectra, the peptide moiety was presumably stable, but the neutral N-glycan moiety caused several B-type fragmentations and the sialylated N-glycan almost lost sialic acid(s). In contrast, in the negative-ion MS2 spectra, the peptide moiety caused several side-chain and N-glycan residue (e.g., N -acetylglucosamine (GlcNAc) residue) fragmentations in addition to backbone cleavages, but the N-glycan moieties were relatively stable. The positive-ion MS3 spectra derived from the protonated peptide ion containing a GlcNAc residue (203.1,Da) provided enough information to determine the peptide amino-acid sequence including the glycosylation site, while the negative-ion MS3 spectra derived from the deprotonated peptide containing a 0,2X1 -type cross-ring cleavage (83.1,Da) complicated the peptide sequence analysis due to side-chain and 0,2X1 residue related fragmentations. However, for the structural information of the N-glycan moiety of the glycopeptides, the negative-ion CID MS3 spectra derived from the deprotonated 2,4A6 -type cross-ring cleavage ion (neutral N-glycan) or the doubly deprotonated B6 -type fragment ion (sialylated N-glycan) are more informative than are those of the corresponding positive-ion CID MS3 spectra. Thus, the positive-ion mode of CID is useful for the analyses of peptide amino-acid sequences including the glycosylation site. The negative-ion mode of CID is especially useful for sialylated N-glycan structural analysis. Therefore, in the structural analysis of N-glycopeptides, their roles are complementary. Copyright © 2006 John Wiley & Sons, Ltd. [source] Zwitterionic 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] | ||||||||||