Dissociation of multiply charged negative ions for hirudin (54–65), fibrinopeptide B, and insulin A (oxidized)

AbstractCollision-induced dissociation (CID) was performed on multiply deprotonated ions from three commercial peptides: hirudin (54–65), fibrinopeptide B, and oxidized insulin chain A. Ions were produced by electrospray ionization in a Fourier transform ion cyclotron resonance mass spectrometer. Each of these peptides contains multiple acidic residues, which makes them very difficult to ionize in the positive mode. However, the peptides deprotonate readily making negative ion studies a viable alternative. The CID spectra indicated that the likely deprotonation sites are acidic residues (aspartic, glutamic, and cysteic acids) and the C-terminus. The spectra are rife with c, y, and internal ions, although some a, b, x, and z ions form. Many of the fragment ions were formed from cleavage adjacent to acidic residues, both N- and C-terminal to the acidic site. In addition, neutral loss (e.g., NH3, CH3, H2O, and CO2) was prevalent from both the parent ions and from fragment ions. These neutral eliminations were often indicative of specific amino acid residues. The fragmentation patterns from several charge states of the parent ions, when combined, provide significant primary sequence information. These results suggest that negative mode CID of multiply deprotonated ions provides useful structural information and can be worthwhile for highly acidic peptides that do not form positive ions in abundance

Gas-phase basicities of histidine and lysine and their selected di- and tripeptides

The gas-phase basicities (GB) of histidine, lysine, and di- and triglycyl peptides containing either one histidine or one lysine residue have been determined. In all, 12 compounds were examined in a Fourier transform ion cyclotron resonance mass spectrometer. The GBs of the biomolecules were evaluated by proton transfer reactions employing a range of reference compounds with varying gas-phase basicities. In addition, the GBs were determined by using the kinetic method of collision-induced dissociation on a proton-bound dimer containing the peptide and a reference compound. The GBs of histidine and lysine were both found to be 220.8 kcal/mol via proton transfer reactions. The kinetic method experiments, including dissociation of a proton-bound dimer containing both histidine and lysine, also suggest equivalent GBs for these amino acids. However, the small peptides containing lysine are generally more basic than the corresponding histidine-containing peptides. For the peptides, the data suggest that the protonation site is on the basic side chain functional group of the histidine or lysine residues. The GBs of the di- and tripeptides are dependent upon the location of the basic residue. For example, the GBs of the tripeptides glycylglycyl-l-lysine (GlyGlyLys) and l-lysylglycylglycine (LysGlyGly) were both determined to be 230.7 kcal/mol while a GB of kcal/mol was obtained for glycyl-l-lysylglycine (GlyLysGly). A similar GB trend is seen with the histidine-containing tripeptides. Generally, the GBs obtained by using the kinetic method are slightly higher than those obtained by deprotonation reactions; however, the trends in relative GB values are essentially the same with the two techniques

MALDI MS In-Source Decay of Glycans Using a Glutathione-Capped Iron Oxide Nanoparticle Matrix

A new matrix-assisted laser desorption ionization (MALDI) mass spectrometry matrix is proposed for molecular mass and structural determination of glycans. This matrix contains an iron oxide nanoparticle (NP) core with gluthathione (GSH) molecules covalently bound to the surface. As demonstrated for the monosaccharide glucose and several larger glycans, the mass spectra exhibit good analyte ion intensities and signal-to-noise ratios, as well as an exceptionally clean background in the low mass-to-charge (<i>m</i>/<i>z</i>) region. In addition, abundant in-source decay (ISD) occurs when the laser power is increased above the ionization threshold; this indicates that the matrix provides strong energy transfer to the sample. For five model glycans, ISD produced extensive glycosidic and cross-ring cleavages in the positive ion mode from singly charged precursor ions with bound sodium ions. Linear, branched, and cyclic glycans were employed, and all were found to undergo abundant fragmentation by ISD. ¹⁸O labeling was used to clarify <i>m</i>/<i>z</i> assignment ambiguities and showed that the majority of the fragmentation originates from the nonreducing ends of the glycans. Studies with a peracetylated glycan indicated that abundant ISD fragmentation occurs even in the absence of hydroxyl groups. The ISD product ions generated using this new matrix should prove useful in the sequencing of glycans

Gas-Phase Deprotonation of the Peptide Backbone for Tripeptides and Their Methyl Esters with Hydrogen and Methyl Side Chains

The gas-phase acidities (GAs) of six tripeptides (GlyGlyGly, GlyAlaGly, AlaGlyAla, AlaAlaAla, AibAibAib, and SarSarSar) and their methyl esters were obtained by proton transfer reactions in a Fourier transform ion cyclotron resonance mass spectrometer and G3­(MP2) molecular orbital theory calculations. All six peptides have GAs in the range 321.0–323.7 kcal/mol. Their deprotonation to produce [M – H]⁻ occurs at the C-terminal carboxylic acid group. The tripeptides are about 10 kcal/mol more acidic than the amino acids glycine (Gly) and alanine (Ala). This is consistent with the extensive hydrogen bonding that was found in the tripeptide structures. For the methyl esters, deprotonation occurs at the peptide backbone. G3­(MP2) calculations show that the most energetically favored site of deprotonation is an amide nitrogen, with the central amide being generally preferred. Nitrogen deprotonation requires 10–20 kcal/mol less energy than deprotonation at a methylene carbon. Only three of the methyl esters (GlyGlyGly-OMe, GlyAlaGly-OMe, and AlaAlaAla-OMe) deprotonate experimentally by electrospray ionization. Experimental GAs for these esters are in the range of 336.7–338.1 kcal/mol, in excellent agreement with the calculated G3­(MP2) values. Experimental GAs could not be obtained for the other three methyl esters (AlaGlyAla-OMe, AibAibAib-OMe, and SarSarSar-OMe) because they did not produce sufficient deprotonated molecular ions. Trisarcosine methyl ester, SarSarSar-OMe, cannot be deprotonated at a central amide nitrogen because methyl groups are present at these sites; consequently, it has a high G3­(MP2) GA value (less acidic) of 350.6 kcal/mol for deprotonation at the N-terminal nitrogen. For AlaGlyAla-OMe and AibAibAib-OMe, calculations of van der Waals and solvent accessible surfaces reveal that methyl groups are blocking the amide nitrogen sites. Therefore, conformational and steric hindrance effects are limiting the ability of these peptide methyl esters to deprotonate in the mass spectrometer

An Experimental and Computational Investigation into the Gas-Phase Acidities of Tyrosine and Phenylalanine: Three Structures for Deprotonated Tyrosine

Using mass spectrometry and correlated molecular orbital theory, three deprotonated structures were revealed for the amino acid tyrosine. The structures were distinguished experimentally by ion/molecule reactions involving proton transfer and trimethylsilyl azide. Gas-phase acidities from proton transfer reactions and from G3­(MP2) calculations generally agree well. The lowest energy structure, which was only observed experimentally using electrospray ionization from aprotic solvents, is deprotonated at the carboxylic acid group and is predicted to be highly folded. A second unfolded carboxylate structure is several kcal/mol higher in energy and primarily forms from protic solvents. Protic solvents also yield a structure deprotonated at the phenolic side chain, which experiments find to be intermediate in energy to the two carboxylate forms. G3­(MP2) calculations indicate that the three structures differ in energy by only 2.5 kcal/mol, yet they are readily distinguished experimentally. Structural abundance ratios are dependent upon experimental conditions, including the solvent and accumulation time of ions in a hexapole. Under some conditions, carboxylate ions may convert to phenolate ions. For phenylalanine, which lacks a phenolic group, only one deprotonated structure was observed experimentally when electrosprayed from protic solvent. This agrees with G3­(MP2) calculations that find the folded and unfolded carboxylate forms to differ by 0.3 kcal/mol

Electron transfer dissociation mass spectromerty studies of peptides

Electron transfer dissociation (ETD) is an important tandem mass spectrometry technique in peptide and protein sequencing. In the past, ETD experiments have primarily involved basic peptides. A limitation of ETD is the requirement that analytes be at least doubly cationized by electrospray ionization (ESI). In this research, a method has been developed for enhancing protonation of acidic and neutral peptides. This has allowed doubly protonated ions, [M+2H]2+, to be produced from peptides without basic residues and has enabled their study by ETD. This dissertation includes the first extensive study of non-basic peptides by ETD. The effects of a basic residue on ETD were investigated using a series of heptapeptides with one lysine, histidine, or arginine residue. The spectra contain primarily c"- and z'-ions, which result from cleavage of N-C_α bonds along the backbone. Almost all of product ions include the basic residue. Enhanced fragmentation occurs on the C-terminal side of the basic residue. Also, cn-1 formation is enhanced, where n is the number of residues in the peptide. Addition of Cr(III) nitrate to a solution of the neutral peptide heptaalanine yields abundant [M+2H]2+ formation by ESI. Eleven metal ions were tested and Cr(III) gave by far the most intense supercharging of peptides. In contrast, Cr(III) does not increase protonation of proteins. Experiments were performed to explore the supercharging mechanism. Addition of Cr(III) to the sample solution was used to produce [M+2H]2+ in the remainder of this research. Neutral peptides with alkyl side chains were studied by ETD and found to produce b- and c-ions. Two mechanisms are proposed for b-ion formation, which involves cleavage of backbone amide (O=C)-N bonds. The length of peptide chain affects ETD fragmentation, but the identity of the alkyl residue has minimal effect. Acidic peptides with one or two aspartic or glutamic acid residues produce b-, c- and zOe-ions. The mechanism of b-ion formation is probably the same as that for neutral peptides, while c- and zOe-ions result from a radical mechanism involving oxygen atoms on the acidic side chains. For highly acidic heptapeptides, c- and zOe-ions are the major products, which supports a radical mechanism. (Published By University of Alabama Libraries

Gas-Phase Acidities of Phosphorylated Amino Acids

Gas-phase acidities and heats of formation have been predicted at the G3­(MP2)/SCRF-COSMO level of theory for 10 phosphorylated amino acids and their corresponding amides, including phospho-serine (pSer), -threonine (pThr), and -tyrosine (pTyr), providing the first reliable set of these values. The gas-phase acidities (GAs) of the three named phosphorylated amino acids and their amides have been determined using proton transfer reactions in a Fourier transform ion cyclotron mass spectrometer. Excellent agreement was found between the experimental and predicted GAs. The phosphate group is the deprotonation site for pSer and pThr and deprotonation from the carboxylic acid generated the lowest energy anion for pTyr. The infrared spectra were calculated for six low energy anions of pSer, pThr, and pTyr. For deprotonated pSer and pThr, good agreement is found between the experimental IRMPD spectra and the calculated spectra for our lowest energy anion structure. For pTyr, the IR spectra for a higher energy phosphate deprotonated structure is in good agreement with experiment. Additional experiments tested electrospray ionization (ESI) conditions for pTyr and determined that variations in solvent, temperature, and voltage can result in a different experimental GA value, indicating that ESI conditions affect the conformation of the pTyr anion

Inhibition of an E. coli DNA glycosylase, MutM, by non-native metals

Non-native metals are well recognized carcinogens; however, most exhibit low mutagenicity. One route by which metals could contribute to carcinogenesis is by inhibition of crucial DNA repair processes. The protein targets and mechanism of inhibition, however, are not fully understood. DNA repair proteins that contain zinc finger motifs are potential targets because of their high affinity for metal ions. Insight into the ability of non-native metals to displace the native metal, zinc, and the mechanism they use to inhibit protein function is needed to fully understand this pathway¡¦s contribution to metal-induced cancer. In this dissertation, we probe MutM, an Escherichia coli zinc finger–——containing DNA glycosylase/AP lyase that excises oxidized guanine bases, 8-oxoguanine, from double stranded DNA. We identify that Zn(II)–——, Cd(II)–—— and Co(II)–——MutM complexes coordinate metal ions in the zinc finger motif in a 1:1 stoichiometric ratio. We demonstrate, for the first time, that Cd(II)binding to the MutM zinc finger affects the recognition of 8-oxoguanine containing DNA and inhibits the glycosylase activity, the first step in the mechanism. However, Co(II)–——MutM retains most of the native enzymatic activity, demonstrating the specificity for certain non-native metals. Furthermore, we characterize the conformational and dynamic changes of MutM caused by Cd(II) binding that contribute to the loss of glycosylase activity. This is the first study to relate non-native metal induced changes in structure of zinc finger DNA repair proteins to the mechanism of metal inhibition. (Published By University of Alabama Libraries

Effects of transition metal cationization on peptide dissociation by mass spectrometry

Peptide sequencing is fundamental to understanding a protein's structure and function. The field of proteomics is dedicated to how these aspects relate to human health and disease. Unfortunately, the majority of peptides and proteins are not fully sequenced. In mass spectrometry, this is often due to spectral complications and incomplete fragmentation. There is a need to develop new sample preparation techniques or dissociation methods to increase sequence information. The dissociation of transition metal-cationized peptides by collision-induced dissociation (CID), electron-transfer dissociation (ETD), and electron-transfer collisionally activated dissociation (ETcaD) has been investigated in a quadrupole ion trap (QIT). The resulting mass spectra provide a wealth of information about the primary structures of the peptides. Using transition metal ions as cationizing reagents proves beneficial to peptide sequencing by CID and, in some cases, is better than the analysis of protonated species. For instance, spectra obtained from CID of singly and doubly charged Cu(II)-heptaalanine ions, [M + Cu - H]^+ and [M + Cu]^2, are complementary and together provide cleavage at every residue and no neutral losses. This contrasts with protonated heptaalanine, [M + H]^+, which results in fewer backbone cleavages by CID and does not allow sequencing of the first three residues. Multiply charged precursor ions are required in order to carry out ETD and ETcaD. This can be problematic for acidic or neutral peptides. This work demonstrates that addition of transition metals as a cationizing reagent allows peptides to be submitted to ETD and ETcaD that do not otherwise form multiply charged precursors. ETD spectra were less complex than those produced by CID. ETcaD increases backbone cleavages for all samples studied relative to ETD. In addition, complexes that result in very few cleavages by CID are cleaved at every residue when submitted to ETcaD. Evidence for macrocyclic metallated a- and b-ions is found in ETD and ETcaD spectra in the form of nonsequential product ions. The sequence (pEEEEGDD) of the peptide component of biologically derived low-molecular-weight chromium binding substance (LMWCr) is obtained as a result of extensive mass spectrometric studies. LMWCr is proposed to be involved in carbohydrate metabolism. The sequencing of the peptide component of LMWCr by MS represents a potentially significant milestone towards understanding the pharmacological role of chromium at a molecular level. (Published By University of Alabama Libraries