International Journal of Mass Spectrometry

Published by Elsevier
Print ISSN: 1387-3806
Publications
Offline high performance liquid chromatography combined with matrix assisted laser desorption and Fourier transform ion cyclotron resonance mass spectrometry (HPLC-MALDI-FTICR/MS) provides the means to rapidly analyze complex mixtures of peptides, such as those produced by proteolytic digestion of a proteome. This method is particularly useful for making quantitative measurements of changes in protein expression by using (15)N-metabolic labeling. Proteolytic digestion of combined labeled and unlabeled proteomes produces complex mixtures that with many mass overlaps when analyzed by HPLC-MALDI-FTICR/MS. A significant challenge to data analysis is the matching of pairs of peaks which represent an unlabeled peptide and its labeled counterpart. We have developed an algorithm and incorporated it into a compute program which significantly accelerates the interpretation of (15)N metabolic labeling data by automating the process of identifying unlabeled/labeled peak pairs. The algorithm takes advantage of the high resolution and mass accuracy of FTICR mass spectrometry. The algorithm is shown to be able to successfully identify the (15)N/(14)N peptide pairs and calculate peptide relative abundance ratios in highly complex mixtures from the proteolytic digest of a whole organism protein extract.
 
The collisionally activated mass spectral fragmentations of N-(2,4-dinitrophenyl)alanine and phenylalanine [M - H](-) may be gas-phase analogs of the base-catalyzed cyclization of N-(2,4-dinitrophenyl)amino acids in aqueous dioxane. This latter reaction is one source of the 2-substituted 5-nitro-1H-benzimidazole-3-oxides, which are antibacterial agents. The fragmentation of both compounds, established by tandem mass spectrometric experiments and supported by molecular modeling using DFT methods, indicate that the [M - H](-) ions dissociate via sequential eliminations of CO(2) and H(2)O to produce deprotonated benzimidazole-N-oxide derivatives. The gas-phase cyclization reactions are analogous to the base-catalyzed cyclization in solution, except that in the latter case, the reactant must be a dianion for the reaction to occur on a reasonable time scale. The cyclization of N-(2-nitrophenyl)phenylalanine, which has one less nitro group, requires a stronger base for the cyclization than the compound with a second nitro group at the 4-position. Following losses of CO(2) and H(2)O are expulsions of both neutral molecules and free radicals, the latter being examples of violations of the even-electron ion rule.
 
Hepatocellular cancer is a serious human disease with an unfortunately low survival rate. It further poses a significant epidemic threat to our society through its viral vectors associated with cirrhosis conditions preceding the cancer. A search for biomarkers of these diseases enlists analytical glycobiology, in general, and quantitative biomolecular mass spectrometry (MS), in particular, as valuable approaches to cancer research. The recent advances in quantitative glycan permethylation prior to MALDI-MS oligosaccharide profiling has enabled us to compare the glycan quantitative proportions in the small serum samples of cancer and cirrhotic patients against control individuals. We were further able to fractionate the major serum proteins from the minor components and compare statistically their differential glycosylation, elucidating some causes of quantitatively unusual glycosylation events. Numerous glycan structures were tentatively identified and connected with the origin proteins, with a particular emphasis on sialylated and fucosylated glycans.
 
This laboratory has introduced a chemical method for residue-specific protein cleavage and has provided a preliminary assessment of the suitability of microwave accelerated acid cleavage as a proteomic tool. This report is a continuing assessment of the fate of common protein modifications in microwave-accelerated acid cleavage. We have examined the cleavage of ribonuclease A and the related N-linked glycoprotein ribonuclease B, and the O-linked glycoprotein alpha crystallin A chain, using MALDI-TOF and LC-ESI-MS to identify the peptide products. RNase A and B each contain four disulfide bonds, and the addition of a reducing reagent, such as dithiothreitol, was found to be required to achieve efficient acidic proteolysis. The linkage of the glycosidic group to the asparagine side-chain in ribonuclease B was found not to be cleaved by brief microwave treatment in 12.5 % acetic acid. The distribution of the heterogeneous carbohydrate side chain in the glycopeptide products of acid cleavage was compared to that of the glycopeptide products of tryptic digestion. Hydrolysis within the carbohydrate chain itself is minimal under the conditions used. The O-linked side-chain on alpha crystalline A was found to be cleaved during acid cleavage of the protein.
 
At sufficiently high mass accuracy, it is possible to distinguish phosphorylated from unmodified peptides by mass measurement alone. We examine the feasibility of that idea, tested against a library of all possible in silico tryptic digest peptides from the human proteome database. The overlaps between in silico tryptic digest phosphopeptides generated from known phosphorylated proteins (1-12 sites) and all possible unmodified human peptides are considered for assumed mass error ranges of ±10, ±50, ±100, ±1,000, and ±10,000 ppb. We find that for mass error ±50 ppb, 95% of all phosphorylated human tryptic peptides can be distinguished from nonmodified peptides by accurate mass alone through the entire nominal mass range. We discuss the prospect of on-line LC MS/MS to identify phosphopeptide precursor ions in MS1 for selected dissociation in MS2 to identify the peptide and site(s) of phosphorylation.
 
Complex mixtures of high molecular weight fractions of pooled neutral human milk oligosaccharides (obtained via gel permeation chromatography) have been investigated. The subfractions were each permethylated and analyzed by high-resolution mass spectrometry, using matrix-assisted laser desorption/ionization (MALDI)-Fourier transform ion cyclotron resonance (FTICR) mass spectrometry, in order to investigate their oligosaccharide compositions. The obtained spectra reveal that human milk contains more complex neutral oligosaccharides than have been described previously; the data show that these oligosaccharides can be highly fucosylated, and that their poly-N-acetyllactosamine cores are substituted with up to 10 fucose residues on a an oligosaccharide that has 7-N-acetyllactosamine units. This is the first report of the existence in human milk of this large range of highly fucosylated oligosaccharides which possess novel, potentially immunologically active structures.
 
Non-ergodic as well as ergodic activation methods are capable of maintaining the integrity of base pairs during the top-down analysis of nucleic acids. Here, we investigate the significance of this characteristic in the investigation of higher-order structures of increasing complexity. We show that cognate fragments produced by typical backbone cleavages may not be always detected as separate sequence ions, but rather as individual products that remain associated through mutual pairing contacts. This effect translates into unintended masking of cleavage events that take place in double-stranded regions, thus leading to the preferential detection of fragments originating from unpaired regions. Such effect is determined by the stability of the weak non-covalent association between complementary stretches, which is affected by base composition, length of the double-stranded structure, and charge of the precursor ion selected for analysis. Although such effect may prevent the achievement of full sequence coverage for primary structure determination, it may provide the key to correctly differentiate double- versus single-stranded regions, in what could be defined as gas-phase footprinting experiments. In light of the critical role played by base pairs in defining the higher-order structure of nucleic acids, these approaches will be expected to support an increased utilization of mass spectrometry for the investigation of nucleic acid structure and dynamics.
 
Laser-induced acoustic desorption (LIAD) combined with ClMn(H(2)O)(+) chemical ionization (CI) was tested for the analysis of nonpolar lipids and selected steroids in a Fourier-transform ion cyclotron resonance mass spectrometer (FT-ICR). The nonpolar lipids studied, cholesterol, 5α-cholestane, cholesta-3,5-diene, squalene, and β-carotene, were found to solely form the desired water replacement product (adduct-H(2)O) with the ClMn(H(2)O)(+) ions. The steroids, androsterone, dehydroepiandrosterone (DHEA), estrone, estradiol, and estriol, also form abundant adduct-H(2)O ions, but less abundant adduct-2H(2)O ions were also observed. Neither (+)APCI nor (+)ESI can ionize the saturated hydrocarbon lipid, cholestane. APCI successfully ionizes the unsaturated hydrocarbon lipids to form exclusively the intact protonated analytes. However, it causes extensive fragmentation for cholesterol and the steroids. The worst case is cholesterol that does not produce any stable protonated molecules. On the other hand, ESI cannot ionize any of the hydrocarbon analytes, saturated or unsaturated. However, ESI can be used to protonate the oxygen-containing analytes with substantially less fragmentation than for APCI in all cases except for cholesterol and estrone. In conclusion, LIAD/ClMn(H(2)O)(+) chemical ionization is superior over APCI and ESI for the mass spectrometric characterization of underivatized nonpolar lipids and steroids.
 
Hydrogen/deuterium exchange measurements by mass spectrometry (HX-MS) can be used to report localized conformational mobility within folded proteins, where exchange predominantly occurs through low energy fluctuations in structure, allowing transient solvent exposure. Changes in conformational mobility may impact protein function, even in cases where structural changes are unobservable. Previous studies of the MAP kinase, ERK2, revealed increases in HX upon activation occured at the hinge between conserved N- and C-terminal domains, which could be ascribed to enhanced backbone flexibility. This implied that kinase activation modulates interdomain closure, and was supported by evidence for two modes of nucleotide binding that were consistent with closed vs open conformations in active vs inactive forms of ERK2, respectively. Thus, phosphorylation of ERK2 releases constraints to interdomain closure, by modulating hinge flexibility. In this study, we examined ERK1, which shares 90% sequence identity with ERK2. HX-MS measurements of ERK1 showed similarities with ERK2 in overall deuteration, consistent with their similar tertiary structures. However, the patterns of HX that were altered upon activation of ERK1 differed from those in ERK2. In particular, alterations in HX at the hinge region upon activation of ERK2 did not occur in ERK1, suggesting that the two enzymes differ with respect to their regulation of hinge mobility and interdomain closure. In agreement, HX-MS measurements of nucleotide binding suggested revealed domain closure in both inactive and active forms of ERK1. We conclude that although ERK1 and ERK2 are closely related with respect to primary sequence and tertiary structure, they utilize distinct mechanisms for controlling enzyme function through interdomain interactions.
 
Collisional activation of selected conformations by multidimensional ion mobility spectrometry (IMS-IMS), combined with mass spectrometry (MS), is described as a method to determine semi-quantitative activation energies for interconversion of different structures of the nonapeptide bradykinin (BK, Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg). This analysis is based on a calibration involving collision-induced dissociation measurements of ions with known dissociation energies (i.e., "thermometer" ions) such as leucine enkephalin, BK, and amino acid-metal cation systems. The energetic barriers between six conformations of [BK+3H](3+) range from 0.23 ±0.01 to 0.55 ±0.03 eV. Prior results indicate that the major peaks in the IMS distributions correspond to specific combinations of cis and trans configurations of the three proline residues in the peptide sequence. The analysis allows us to directly assess pathways for specific transitions. The combination of structural assignments, experimentally determined barrier heights, onset of the quasi-equilibrium region, and dissociation threshold are used to derive a semi-quantitative potential energy surface for main features of [BK+3H](3+).
 
Sulfoquinovosyldiacylglycerol (SQDG) lipids, found in plants and photosynthetic bacteria, can substitute for phospholipids under phosphate limiting conditions. Here, various low-energy ion activation strategies have been evaluated for the identification and characterization of deprotonated SQDG lipids from a crude membrane lipid extract of Rhodobacter sphaeroides, using collision- induced dissociation - tandem mass spectrometry (CID-MS/MS) in either a triple quadrupole mass spectrometer or in a hybrid quadrupole ion trap-multipole mass spectrometer coupled with high resolution / accurate mass analysis capabilities. In the triple quadrupole instrument, using energy resolved CID-MS/MS experiments, the SQDG head group specific product ion at m/z 225 (C(6)H(9)O(7)S(-)), rather than m/z 81 (SO(3)H(-)), was determined to provide the greatest sensitivity for SQDG lipid detection, and is therefore the preferred `fingerprint' ion for the identification of this lipid class from within complex lipid mixtures when using precursor ion scan mode MS/MS experiments. A comparison of conventional ion trap CID-MS/MS and -MS(n), with `low Q' CID-MS/MS, pulsed Q dissociation (PQD)-MS/MS and higher energy collision induced dissociation (HCD)-MS/MS performed in an LTQ Orbitrap Velos mass spectrometer, revealed that HCD-MS/MS coupled with high resolution/accurate mass analysis represents the most sensitive, and perhaps most importantly the most specific strategy, for ion trap based identification and characterization of SQDG lipids, due to the ability to readily distinguish the SQDG head group specific product ion at m/z 225.0069 from other products that may be present at the same nominal m/z value. Finally, the mechanisms responsible for formation of each of the major product ions observed by low-energy CID-MS/MS of deprotonated SQDG lipids were elucidated using uniform H/D exchange, HCD-MS/MS and high resolution mass analysis. Formation of the m/z 225 `fingerprint' ion occurs via a charge-remote cis-elimination reaction, likely involving transfer of a hydrogen from the hydroxyl group located on the C2 position of the sugar ring.
 
Ions derived from nano-electrospray ionization (nano-ESI) of α-synuclein, a 14.5 kDa, 140 amino acid residue protein that is a major component of the Lewy bodies associated with Parkinson's disease, have been subjected to ion trap and beam-type collisional activation. The former samples products from fragmentation at rates generally lower than 100 s(-1) whereas the latter samples products from fragmentation at rates generally greater than 10(3) s(-1). A wide range of protein charge states spanning from as high as [M+17H](17+) to as low as [M+4H](4+) have been formed either directly from nano-ESI or via ion/ion proton transfer reactions involving the initially formed protein cations and have been subjected to both forms of collision-induced dissociation (CID). The extent of sequence information (i.e., number of distinct amide bond cleavages) available from either CID method was found to be highly sensitive to protein precursor ion charge state. Furthermore, the relative contributions of the various competing dissociation channels were also dependent upon precursor ion charge state. The qualitative trends in the changes in extent of amide bond cleavages and identities of bonds cleaved with precursor ion charge state were similar for two forms of CID. However, for every charge state examined, roughly twice the primary sequence information resulted from beam-type CID relative to ion trap CID. For example, evidence for cleavage of 86% of the protein amide bonds was observed for the [M+9H](9+) precursor ion using beam-type CID whereas 41% of the bonds were cleaved for the same precursor ion using ion trap CID. The higher energies required to drive fragmentation reactions at rates necessary to observe products in the beam experiment access more of the structurally informative fragmentation channels, which has important implications for whole protein tandem mass spectrometry.
 
The gas phase dissociation behavior of peptides containing acyl-arginine residues is investigated. These acylations are generated via a combination of ion/ion reactions between arginine-containing peptides and N-hydroxysuccinimide (NHS) esters and subsequent tandem mass spectrometry (MS/MS). Three main dissociation pathways of acylated arginine, labeled Paths 1-3, have been identified and are dependent on the acyl groups. Path 1 involves the acyl-arginine undergoing deguanidination, resulting in the loss of the acyl group and dissociation of the guanidine to generate an ornithine residue. This pathway generates selective cleavage sites based on the recently discussed "ornithine effect". Path 2 involves the coordinated losses of H2O and NH3 from the acyl-arginine side chain while maintaining the acylation. We propose that Path 2 is initiated via cyclization of the δ-nitrogen of arginine and the C-terminal carbonyl carbon, resulting in rapid rearrangement from the acyl-arginine side chain and the neutral losses. Path 3 occurs when the acyl group contains α-hydrogens and is observed as a rearrangement to regenerate unmodified arginine while the acylation is lost as a ketene.
 
Previous experiments based on charge state distributions have suggested that liquid desorption electrospray ionization (DESI) is capable of preserving solution phase protein structure during transfer to the gas phase (Journal of the American Society for Mass Spectrometry 21 (2010) 1730-1736). In order to examine this possibility more carefully, we have utilized selective non-covalent adduct protein probing (SNAPP) to evaluate protein structural evolution in both liquid DESI and standard ESI under a variety of conditions. Experiments with cytochrome c (Cytc) demonstrated that methanol induced conformational shifts previously observed with ESI are also easily observed with liquid DESI. However, undesirable acid-induced unfolding becomes apparent at very high concentrations of methanol in liquid DESI due to acetic acid in the spray solvent, suggesting that there are conditions under which liquid DESI will not preserve solution phase structure. The effects of ammonium acetate buffer on liquid DESI SNAPP experiments were examined by monitoring structural changes in myoglobin. Heme retention and SNAPP distributions were both preserved better in liquid DESI than traditional ESI, suggesting superior performance for liquid DESI in buffered conditions. Finally, liquid DESI SNAPP was used to study the natively disordered proteins α, β, and γ synuclein with SNAPP. α-Synuclein, the main component of fibrils found in patients with Parkinson's disease, yielded a significantly different SNAPP distribution compared to β and γ synuclein. This difference is indicative of highly accessible protonated basic side chains, a property known to promote fibril formation in proteins.
 
Spontaneous epithelial ovarian cancer (EOC) in the chicken presents a similar pathogenesis compared with humans including CA-125 expression and genetic mutational frequencies (e.g., p53). The high prevalence of spontaneous EOC chickens also provides a unique experimental model for biomarker discovery at the genomic, proteomic, glycomic, and metabolomic level. In an effort to exploit this unique model for biomarker discovery, longitudinal plasma samples were collected from chickens at three month intervals for one year. The study described herein involved cleaving the N-glycans from these longitudinal chicken plasma samples and analyzing them via nanoLC-FTMS/MS. Glycans identified in this study were previously found in human plasma and this work provides a promising methodology to enable longitudinal studies of the N-linked plasma glycome profile during EOC progression. The structure, abundance, and intra-variability and inter-variability for 35 N-linked glycans identified in this study are reported. The full potential of the chicken model for biomarker discovery has yet to be realized, but the initial interrogation of longitudinally-procured samples provides evidence that supports the value of this strategy in the search for glycomic biomarkers.
 
The use of tandem mass spectrometry to identify and characterize sites of protein adenosine diphosphate (ADP) ribosylation will be reviewed. Specifically, we will focus on data acquisition schemes and fragmentation techniques that provide peptide sequence and modification site information. Also discussed are uses of synthetic standards to aid characterization, and an enzymatic method that converts ADP-ribosylated peptides into ribosyl mono phosphorylated peptides making identification amenable to traditional phosphopeptide characterization methods. Finally the potential uses of these techniques to characterize poly ADP-ribosylation sites, and inherent challenges, are addressed.
 
Microwave assisted acid cleavage was applied directly to intact adenovirus type 5 to achieve denaturation and proteolysis in a single reaction. The speed of the digestion, coupled with the simplicity of MALDI analysis, allowed peptide products to be profiled in less than 5 min. Identification of peptides from a range of proteins by MALDI-TOF confirms that both denaturation and proteolysis were achieved using low concentrations of acetic acid (12.5%) and short incubations (1.5 to 2 min) at high temperatures (140° C). These conditions favor production of peptides that carry Asp on their C-termini. When this cleavage reaction is carried out in highly enriched H(2) (18)O, a single atom of (18)O is introduced site-specifically into the carboxyl terminal. The labeling reaction is applied to label reporter peptides from human adenovirus type 5 harvested from HeLa cells. Small peptide products of endogenous processing were also observed.
 
Calmodulin (CaM), a ubiquitous intracellular sensor protein, binds Ca(2+) and interacts with various targets as part of signal transduction. Using hydrogen/deuterium exchange (H/DX) and a high resolution PLIMSTEX (Protein-Ligand Interactions by Mass Spectrometry, Titration, and H/D Exchange) protocol, we examined five different states of calmodulin: calcium-free, calcium-loaded, and three states of calcium-loaded in the presence of either melittin, mastoparan, or skeletal myosin light-chain kinase (MLCK). When CaM binds Ca(2+), the extent of HDX decreased, consistent with the protein becoming stabilized upon binding. Furthermore, Ca(2+)-saturated calmodulin exhibits increased protection when bound to the peptides, forming high affinity complexes. The protocol reveals significant changes in EF hands 1, 3, and 4 with saturating levels of Ca(2+). Titration of the protein using PLIMSTEX provides the binding affinity of Ca(2+) to calmodulin within previously reported values. The affinities of calmodulin to Ca(2+) increase by factors of 300 and 1000 in the presence of melittin and mastoparan, respectively. A modified PLIMSTEX protocol whereby the protein is digested to component peptides gives a region-specific titration. The titration data taken in this way show a decrease in the root mean square fit of the residuals, indicating a better fit of the data. The global H/D exchange results and those obtained in a region-specific way provide new insight into the Ca(2+)-binding properties of this well-studied protein.
 
This is the first comprehensive HX-MS study of a "robust" 2-Cys peroxiredoxin (Prx), namely Salmonella typhimurium AhpC (StAhpC). Prx proteins control intracellular peroxide levels and are abundant antioxidant proteins in eukaryotes, archaea and bacteria. Crystal structural analyses and structure/activity studies of several bacterial and mammalian 2-Cys Prxs have revealed that the activity of 2-Cys Prxs is regulated by redox-dependent oligmerization and a sensitivity of the active site cysteine residue to overoxidation. The propensity to overoxidation is linked to the conformational flexibility of the peroxidatic active site loop. The HX-MS results emphasize the modulation of the conformational motility of the active site loop by disulfide formation. To obtain information on the conformational impact of decamer formation on the active site loop motility, mutants with Thr77 substituted by Ile, a decamer-disrupting mutation or by Val, a decamer-stabilizing mutation, were studied. For the isoleucine mutant, enhanced mobility was observed for regions encompassing the α4 helix located in the dimer-dimer interface and regions surrounding the peroxidatic loop. In contrast, the T77V mutation resulted in an increase in conformational stability in most regions of the protein except for the active site loop and the region encompassing the resolving cysteine.
 
Through a multi-disciplinary approach, the air amplifier is being evolved as a highly engineered device to improve detection limits of biomolecules when using electrospray ionization. Several key aspects have driven the modifications to the device through experimentation and simulations. We have developed a computer simulation that accurately portrays actual conditions and the results from these simulations are corroborated by the experimental data. These computer simulations can be used to predict outcomes from future designs resulting in a design process that is efficient in terms of financial cost and time. We have fabricated a new device with annular gap control over a range of 50 to 70 μm using piezoelectric actuators. This has enabled us to obtain better aerodynamic performance when compared to the previous design (2× more vacuum) and also more reproducible results. This is allowing us to study a broader experimental space than the previous design which is critical in guiding future directions. This work also presents and explains the principles behind a fractional factorial design of experiments methodology for testing a large number of experimental parameters in an orderly and efficient manner to understand and optimize the critical parameters that lead to obtain improved detection limits while minimizing the number of experiments performed. Preliminary results showed that several folds of improvements could be obtained for certain condition of operations (up to 34 folds).
 
Rapid separation and independent analysis of isomeric species are needed for the structural characterization of carbohydrates in glycomics research. Ion mobility-mass spectrometry techniques were used to examine a series of isomeric neutral oligosaccharide-alditols derived from bovine submaxillary mucin. Several analytical techniques were employed: (1) off line separation of the oligosaccharide-alditol mixture by HPLC; (2) direct and rapid evaluation of isomeric heterogeneity of oligosaccharides by electrospray ionization-ion mobility-time of flight mass spectrometry; and (3) mobility-selected MS(2) and MS(3) to evaluate isomeric mobility peaks by dual gate ion mobility-tandem mass spectrometry. Multiple isomeric ion mobility peaks were observed for the majority of oligosaccharide-alditols, which was achieved on the millisecond time scale after LC separation. Fragmentation spectra obtained from the collision-induced dissociation of isomeric precursor ions could be essentially identical, or dramatically different for a given precursor m/z using the dual-gate ion mobility quadrupole ion trap mass spectrometer. This further confirmed the need for rapid physical resolution of isomeric precursor species prior to their tandem mass spectral analysis.
 
A method for the study of reactions of open-shell neutrals (radicals) and radical cations is described. Pyrolysis (25-1500 degrees C) of thermally labile compounds, such as, 1,5-hexadiene via a Chen nozzle yields a seeded beam of reactive species in helium. The pyrolysis products are then analyzed by electron ionization (EI) or reacted with stored ions. Electron ionization of the pyrolysis products of 1,5-hexadiene shows that both the allyl radical and allene are generated. Reactions of benzene radical cations and the pyrolysis products of 1,5-hexadiene result in carbon-carbon bond formation. Those reactions of allyl radical with the benzene radical cation yield the C(7)H(7) (+) ion of m/z 91, permitting an unusual entry into arenium ions. The reaction of allene with benzene radical cation in contrast yields C(9)H(10) (+). and C(9)H(9) (+).
 
Collision-induced dissociation of protonated AGabaAIG (where Gaba is gamma-amino butyric acid, NH(2)-(CH(2))(3)-COOH) leads to an unusually stable a(3) ion. Tandem mass spectrometry and theory are used here to probe the enhanced stability of this fragment, whose counterpart is not usually observed in CID of protonated peptides containing only alpha amino acids. Experiments are carried out on the unlabelled and (15)N-Ala labeled AGabaAIG (labeled separately at residue one or three) probing the b(3), a(3), a(3)-NH(3) (a(3) (*)), and b(2) fragments while theory is used to characterize the most stable b(3), a(3), and b(2) structures and the formation and dissociation of the a(3) ion. Our results indicate the AGabaA oxazolone b(3) isomer undergoes head-to-tail macrocyclization and subsequent ring opening to form the GabaAA sequence isomer while this chemistry is energetically disfavored for the AAA sequence. The AGabaA a(3) fragment also undergoes macrocyclization and rearrangement to form the rearranged imine-amide isomer while this reaction is energetically disfavored for the AAA sequence. The barriers to dissociation of the AGabaA a(3) ion via the a(3)→b(2) and a(3)→a(3)* channels are higher than the literature values reported for the AAA sequence. These two effects provide a clear explanation for the enhanced stability of the AGabaA a(3) ion.
 
The type I cGMP-dependent protein kinases play critical roles in regulating vascular tone, platelet activation and synaptic plasticity. PKG I α and PKG Iβ differ in their first ~100 amino acids giving each isoform unique dimerization and autoinhibitory domains with identical cGMP-binding pockets and catalytic domains. The N-terminal leucine zipper and autoinhibitory domains have been shown to mediate isoform specific affinity for cGMP. PKG Iα has a >10 fold higher affinity for cGMP than PKG Iβ, and PKG Iβ that is missing its leucine zipper has a three-fold decreased affinity for cGMP. The exact mechanism through which the N-terminus of PKG alters cGMP-affinity is unknown. In the present study, we have used deuterium exchange mass spectrometry to study how PKG Iβ's N-terminus affects the conformation and dynamics of its cGMP-binding pockets. We found that the N-terminus increases the rate of deuterium exchange throughout the cGMP-binding domain. Our results suggest that the N-terminus shifts the conformational dynamics of the binding pockets, leading to an "open" conformation that has an increased affinity for cGMP.
 
In this study, we have used glucagon as a model system for analyzing amyloid fibrillogenesis by hydrogen exchange MALDI mass spectrometry (HXMS). The hydrogen exchange mass spectrometry data correlated well with the traditional method based on Thioflavin T fluorescence and provided quantitative information by measuring the fibrillating molecules directly. The hydrogen exchange mass spectrometry data collected during fibrillogenesis revealed that glucagon fibrillation was a two component system showing an on/off type of interaction where only monomeric and fibrils were present without any substantial amount of intermediate species. This was evident by the extensive deuteration of the monomer and protection of the entire 29 residue glucagon peptide upon fibrillation.. The method complements the traditional procedures and has the potential to provide new information with respect to the nature of transient species, the structure of the growing fibrils and the mechanism of formation.
 
A direct pathway for the fragmentation of peptide b3 fragment ions to b2 ions has, until now, not been identified. Experimental evidence for the formation of a b3 anhydride structure and isomerization to an extended macrocycle is demonstrated here by comparison of the completely different fragmentation patterns of the b3 ions generated from protonated VGEIG and its methyl ester. In particular, the absence of a b2 ion in the fragmentation spectrum of the methyl ester b3 indicates that facile fragmentation of an anhydride-type b3 is responsible for virtually all b2 ions formed. The stability of this b3 structure and the ease with which it fragments to the b2 may be responsible for the relatively high abundance of the b3 and b2 ions. IRMPD action spectroscopy measurements indicate the presence of a ring protonated oxazolone in the b2 population. VGEIG and three related analogs, VALEIG, VADEIG, and V(Aib)EIG were studied by QCID-HDX-SORI experiments in an FT-ICR instrument, and provide significant evidence for extensive alpha proton scrambling in an ion-molecule complex formed between the b2 and neutral loss fragment following formation of the b2. MS(3) and HDX of VG(2,2-d2)EIG indicate that the scrambled b2 ions have the same structure as the unscrambled b2. Based on these data and with the support of molecular modeling, we propose a new mechanism for this scrambling, in which the alpha protons are transferred in a multistep pathway during an ion-molecule complex formed between the b2 and amino-terminated anhydride ring neutral loss component.
 
Comparative analyses utilizing collision induced dissociation (CID) and vacuum ultraviolet photodissociation (VUVPD) for seven isobaric disaccharides have been performed in order to differentiate the linkage type and anomeric configuration of the isomers. Although an individual CID spectrum of a disaccharide ion provides information related to its structure, CID does not sufficiently differentiate mixture components due to the identical mass-to-charge values of most of the intense fragments. In contrast to the ambiguity of the CID analyses for the disaccharide mixture, VUVPD (157 nm) generates unique fragments for each disaccharide ion that are useful for distinguishing individual components from the mixture. When combined with a gas-phase ion mobility separation of the ions, the identification of each component from the mixture can be obtained.
 
CD34, a type I transmembrane glycoprotein, is a surface antigen which is expressed on several cell types, including hematopoietic progenitors, endothelial cells, as well as mast cells. Recently, CD34 has been described as a marker for epidermal stem cells in mouse hair follicles, and is expressed in outer root sheath cells of the human hair follicle. Although the biological function and regulation of CD34 is not well understood, it is thought to be involved in cell adhesion as well as possibly having a role in signal transduction. In addition, CD34 was shown to be critical for skin tumor development in mice, although the exact mechanism remains unknown.Many proteins' functions and biological activities are regulated through post-translational modifications. The extracellular domain of CD34 is heavily glycosylated but the role of these glycans in CD34 function is unknown. Additionally, two sites of tyrosine phosphorylation have been reported on human CD34 and it is known that CD34 is phosphorylated, at least in part, by protein kinase C; however, the precise location of the sites of phosphorylation has not been reported. In an effort to identify specific phosphorylation sites in CD34 and delineate the possible role of protein kinase C, we undertook the identification of the in vitro sites of phosphorylation on the intracellular domain of mouse CD34 (aa 309-382) following PKC treatment. For this work, we are using a combination of enzymatic proteolysis and peptide sequencing by mass spectrometry. After which the in vivo sites of phosphorylation of full-length mouse CD34 expressed from HEK293F cells were determined. The observed in vivo sites of phosphorylation, however, are not consensus PKC sites, but our data indicate that one of these sites may possibly be phosphorylated by AKT2. These results suggest that other kinases, as well as PKC, may have important signaling functions in CD34.
 
Serpin Structure and Mechanism A. The structure of α 1 -antitrypsin (1QLP). Secondary structure elements are labeled. B. The Michaelis complex between a serpin (black) and target protease (white) (1K90). C. The covalently linked serpin-protease complex after the inhibitory conformational change (1EZX). In addition to the protease, the serpin's inserted reactive center loop is also shown in white.  
Unfolding Monitored by Fluorescence  
Unfolding Monitored by HXMS Mass spectra for 8 peptides from diverse regions of HPα 1 -AT pulse labeled for 10 s in D 2 O/ GuDCl after equilibration at increasing concentrations of GuHCl.
Effects of glycosylation on native H/D exchange Normalized deuterium uptake vs time curves for 20 peptides from HPα 1 -AT (squares) and RCα 1 -AT (diamonds).  
Protein glycosylation commonly stabilizes proteins thereby increasing protein half-lives and protecting against denaturation or proteolytic degradation. While generally beneficial, such stabilization is potentially disadvantageous in the case of inhibitory serpins. These protease inhibitors are metastable and a conformational transition to a more stable form is key to their function. Instability is therefore essential for these inhibitory serpins and mutagenesis has demonstrated that substantial stabilization results in compromised function. We have used optical spectroscopy and hydrogen/deuterium exchange and mass spectrometry to investigate the effects of glycosylation on the human serpin alpha-1 antitrypsin (α(1)-AT). Previous studies found that unglycosylated recombinant α(1)-AT populates a molten globule at low denaturant and that the ability to populate this state is correlated with efficient protease inhibition. Further, a high degree of conformational flexibility was found in several important regions. Guanidine hydrochloride denaturation monitored by circular dichroism indicates that plasma α(1)-AT, which is glycosylated at 3 sites, is substantially stabilized relative to the unglycosylated form. However, hydrogen exchange reveals complete loss of protection in plasma α(1)-AT above 1 M GuHCl, similar to what is seen for the recombinant form. Sugars therefore appear to stabilize the compact denatured state of α(1)-AT without significant stabilization of the folded state. Native state hydrogen exchange reveals minor perturbations to native flexibility, but high flexibility in key regions such as the f helix is conserved. β-strand 1c is stabilized in plasma α(1)-AT, which may confer increased resistance to forming pathogenic polymers. Overall, our results indicate that glycosylation of inhibitory serpins does not interfere with either native state flexibility or the native instability that is required for efficient function, though it may confer resistance to degradation by proteases and thus extend the half-life of circulating serpins.
 
Forming hydrated clusters containing triply charged metal ions is challenging due to the competing process of dissociation by forming the metal hydroxide with one less net charge and a protonated water molecule. It is demonstrated for the first time that it is possible to form such clusters using a method we call "nanodrop mass spectrometry". Clusters of the form [M(H(2)O)(n)](3+), where M = Ce, Eu, and La, are generated using electrospray ionization and are mass analyzed in a Fourier-transform ion cyclotron resonance mass spectrometer with an ion cell cooled to -140 °C. Clusters containing trivalent La with n ranging from 16 to over 160 can be readily produced. These clusters are stable at this temperature for many seconds, enabling all standard methods to probe structure and reactivity of these unusual species. Photodissociation experiments on extensively hydrated clusters of trivalent lanthanum using resonant infrared radiation indicate that a minimum of 17 water molecules is necessary to stabilize these trivalent clusters under the low-energy ion excitation conditions and long time frame of these experiments. These results indicate that a minimum droplet size of approximately a nanometer is necessary for these trivalent species to survive intact. This suggests that elemental speciation of trivalent metal ions from aqueous solutions should be possible using nanodrop mass spectrometry.
 
Aromatic sulfides bearing a nitro group undergo sulfur oxidation upon electrospray ionization in the positive-ion mode. For example, 2-nitrophenyl phenyl sulfide, its para nitro isomer, and its chloro and methyl substituted analogs pick up an oxygen atom to afford [M + H + O](+) and [M + Na + O](+) ions upon ESI. Elemental-composition determination and tandem mass spectrometry confirm the reactions. Another oxidation of the sulfur, by the ortho nitro group of the [M + H](+) ions, occurs as intramolecular oxygen-transfer processes, evidenced by characteristic losses of SO, SO(2) and SO(2)H(*), the latter yielding the carbazole radical cation, and the generation of the aryl-SO(+) product ion. The intramolecular oxidation via oxygen transfer from the nitro group to the sulfur was corroborated by molecular modeling. The results substantiate both inter- and intramolecular oxidation and provide more evidence that care must be taken when analyzing not only methionine-containing peptides but also small sulfides.
 
Three complementary experimental approaches for elucidating human milk oligosaccharide (HMOs) isomers by Fourier Transform Ion Cyclotron Resonance mass spectrometry (FT-ICR) are described: tandem-MS disruption by double resonance to distinguish different fragmentation pathways, examination of fragment intensity ratios arising from differential alkali metal ion affinities and monitoring competitive fragmentation rates. The interpretation of the fragmentation pattern from a mechanistic and thermochemical point of view permits the assignment of not only pure isomers but, in some cases, mixtures of them. Methodologically the procedures are simple, reliable and rapid making unnecessary both the use of previous separation techniques and tedious chemical modifications of the HMOs. In principle, the rationale can be expanded to resolve other isomeric mixtures of biological nature.
 
Transthyretin (TTR) amyloidosis and hemoglobinopathies are the archetypes of molecular diseases where point mutation characterization is diagnostically critical. We have developed a Top-down analytical platform for variant and/or modified protein sequencing and are examining the feasibility of using this platform for the analysis of hemoglobin/TTR patient samples and evaluating the potential clinical applications. The platform is based on a commercial high resolution hybrid orbitrap mass spectrometer (LTQ-Orbitrap(™)) with automated sample introduction; automated data analysis is performed by our own software algorithm (BUPID topdown).The analytical strategy consists of iterative data capture, first recording a mass profile of the protein(s). The presence of a variant is revealed by a mass shift consistent with the amino acid substitution. Nozzle-skimmer dissociation (NSD) of the protein(s) yields a wide variety of sequence-defining fragment ions. The fragment ion containing the amino acid substitution or modification can be identified by searching for a peak exhibiting the mass shift observed in the protein mass profile. This fragment ion can then be selected for MS/MS analysis in the ion trap to yield sequence information permitting the identification of the variant. Substantial sequence coverage has been obtained in this manner. This strategy allows for a stepwise MS/MS analysis of the protein structure. The sequence information obtained can be supplemented with whole protein NSD fragmentation and MS/MS analysis of specific protein charge states. The analyses of variant forms of TTR and hemoglobin are presented to illustrate the potential of the method.
 
Gangliosides are anionic glycosphingolipids widely distributed in vertebrate tissues and fluids. Their structural and quantitative expression patterns depend on phylogeny and are distinct down to the species level. In milk, gangliosides are exclusively associated with the milk fat globule membrane. They may participate in diverse biological processes but more specifically to host-pathogen interactions. However, due to the molecular complexities, the analysis needs extensive sample preparation, chromatographic separation, and even chemical reaction, which makes the process very complex and time-consuming. Here, we describe a rapid profiling method for bovine and human milk gangliosides employing matrix-assisted desorption/ionization (MALDI) Fourier transform ion cyclotron resonance (FTICR) mass spectrometry (MS). Prior to the analyses of biological samples, milk ganglioside standards GM3 and GD3 fractions were first analyzed in order to validate this method. High mass accuracy and high resolution obtained from MALDI FTICR MS allow for the confident assignment of chain length and degree of unsaturation of the ceramide. For the structural elucidation, tandem mass spectrometry (MS/MS), specifically as collision-induced dissociation (CID) and infrared multiphoton dissociation (IRMPD) were employed. Complex ganglioside mixtures from bovine and human milk were further analyzed with this method. The samples were prepared by two consecutive chloroform/methanol extraction and solid phase extraction. We observed a number of differences between bovine milk and human milk. The common gangliosides in bovine and human milk are NeuAc-NeuAc-Hex-Hex-Cer (GD3) and NeuAc-Hex-Hex-Cer (GM3); whereas, the ion intensities of ganglioside species are different between two milk samples. Kendrick mass defect plot yields grouping of ganglioside peaks according to their structural similarities. Gangliosides were further probed by tandem MS to confirm the compositional and structural assignments. We found that only in human milk gangliosides was the ceramide carbon always even numbered, which is consistent with the notion that differences in the oligosaccharide and the ceramide moieties confer to their physiological distinctions.
 
The levels of post-source metastable ion decay (PSD) observed in several peptides and proteins ionized by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI TOF-MS) are measured utilizing both infrared (IR) and ultraviolet (UV) desorption wavelengths. A gridless deceleration ion optic is employed to temporally separate stable analyte ions from analyte metastable neutral and ion fragments. Comparisons of the extent of PSD that is observed in UV-MALDI at 337 nm and IR-MALDI at multiple wavelengths between 2.8 and 3.0 mum are made using the same matrices and analytes. The amount of PSD observed using IR-MALDI was found to be highly dependent on the specific IR wavelength (2.8-3.0 mum) employed for desorption. IR wavelengths shorter than 2.86 mum tended to produce higher levels of PSD, while longer IR wavelengths typically produced significantly less PSD when using a number of common MALDI matrices. Relative PSD levels are quantified by determining the percentage of the neutral fragment signal intensity to the intensity of the stable singly protonated molecular species observed in decelerated MALDI spectra. These studies suggest that an analyte ion activation pathway leading to significant PSD in IR-MALDI may proceed by way of vibrational excitation of the analyte molecules during the desorption event.
 
Protonated poly(ethylene glycol), produced by electrospray ionization (ESI), with molecular weights ranging from 0.3 to 5 kDa and charge states from 1+ to 7+ were characterized using high-field asymmetric waveform ion mobility spectrometry (FAIMS). Results for all but some of the 3+ and 4+ charge states are consistent with a single gas-phase conformer or family of unresolved conformers for each of these charge states. The FAIMS compensation voltage scans resulted in peaks that could be accurately fit with a single Gaussian for each peak. The peak widths increase linearly with compensation voltage for maximum ion transmission but do not depend on m/z or molecular weight. Fitting parameters obtained from the poly(ethylene glycol) data were used to analyze conformations of oxidized and reduced lysozyme formed from different solutions. For oxidized lysozyme formed from a buffered aqueous solution, a single conformer (or group of unresolved conformers) was observed for the 7+ and 8+ charge states. Two conformers were observed for the 9+ and 10+ charge states formed from more denaturing solutions. Data for the fully reduced form indicate the existence of up to three different conformers for each charge state produced directly by ESI and a general progression from a more extended to a more folded structure with decreasing charge state. These results are consistent with those obtained previously by proton-transfer reactivity and drift tube ion mobility experiments, although more conformers were identified for the fully reduced form of lysozyme using FAIMS.
 
Carotenoid chemical structures.  
Positive ion APCI tandem mass spectra of carotenes. A) β-carotene; B) [ 13 C 6 ]-β-carotene; C) α-carotene; and D) lycopene.  
Positive ion APCI tandem mass specta of selected xanthophylls. A) astaxanthin; B) βcryptoxanthin ; C) lutein; and D) zeaxanthin.  
Negative ion APCI tandem mass specta of carotenes. A) β-carotene; B) α-carotene; C) lycopene; and D) γ-carotene.  
Negative ion APCI tandem mass spectra of selected xanthophylls. A) astaxanthin; B) βcryptoxanthin ; C) lutein; and D) zeaxanthin.  
Carotenoids are natural pigments synthesized by plants and photosynthetic microorganisms, some of which, like β-carotene, are precursors of vitamin A, and others such as lutein and lycopene might function in the prevention of age-related macular degeneration and prostate cancer, respectively. Mass spectrometry provides high sensitivity and selectivity for the identification and quantitative analysis of carotenoids in biological samples, and previous studies have described how atmospheric pressure chemical ionization (APCI) offers distinct advantages over electrospray and fast atom bombardment for the analysis of specific carotenoids. Since APCI product ion tandem mass spectra have been reported for only a few carotenoids, a detailed investigation of twelve carotenes and xanthophylls was carried out using both positive ion and negative ion APCI tandem mass spectrometry with collision-induced dissociation. Using protonated molecules as precursor ions in positive ion mode and radical anions in negative ion mode, characteristic fragment ions were identified that may be used to distinguish between carotenoids.
 
Fragmentation of multiply-charged peptide ions via interaction with products of gas discharge at atmospheric pressure conditions was studied using ion mobility separation - fragmentation cell - linear ion trap mass spectrometer. The observed fragmentation spectra mainly consisted of c- type ions that are specific to electron capture dissociation. Experiments with different gases flowing through the discharge and different discharge polarities suggested that fragmentation proceeds via capture of free electrons. Fragmentation of a model phosphorylated peptide using this technique produced c- type fragments with an intact phosphorylation group. High field asymmetric waveform ion mobility separation of a peptide mixture prior to the fragmentation cell demonstrated the feasibility of conducting MS/MS-like experiments at atmospheric pressure conditions.
 
Negative ion formation in the three perfluoroethers (PFEs) diglyme (C(6)F(14)O(3)), triglyme (C(8)F(18)O(4)) and crownether (C(10)F(20)O(5)) is studied following electron attachment in the range from ∼0 to 15 eV. All three compounds show intense low energy resonances at subexcitation energies (<3 eV) decomposing into a variety of negatively charged fragments. These fragment ions are generated via dissociative electron attachment (DEA), partly originating from sequential decompositions on the metastable (μs) time scale as observed from the MIKE (metastable induced kinetic energy) scans. Only in perfluorocrownether a signal due to the non-decomposed parent anion is observed. Additional and comparatively weaker resonances are located in the energy range between ∼10 and 17 eV which preferentially decompose into lighter ions. It is suggested that specific features of perfluoropolyethers (PFPEs) relevant in applications, e.g., the strong bonding to surfaces induced by UV radiation of the substrate or degradation of PFPE films in computer hard disc drives can be explained by their pronounced sensitivity towards low energy electrons.
 
Lipids in Escherichia coli and Bacillus subtilis were analyzed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry and TOF/TOF tandem mass spectrometry. Lipids were extracted from bacterial cells using an equal volume mixture of dichloromethane, ethanol, and water, which formed a biphasic system with the lipids in the organic layer. The resulting mass spectra of the extracts from both bacteria showed a series of peaks corresponding to sodiated phospholipids - primarily phosphatidylethanolamines (PE) and phosphatidylglycerols (PG). The relative amounts of the phospholipids and the fatty acid compositions inferred from the spectra were in good agreement with previously reported values from GC/MS and thin-layer chromatography studies. E. coli and B. subtilis were easily differentiated by dissimilarities in the composition and relative amounts of the phospholipids present as well as by the presence of lysyl-phosphatidylglycerol and diglucosyl diglycerides solely in the B. subtilis mass spectra. Changes in lipid content in the bacteria during their growth phases were also monitored. In E. coli, the spectra indicated an increase in the amount of the unique C(cy-17) fatty acid (in which the fatty acid chain contains a cyclopropane ring) formed during exponential growth. During stationary growth, the spectra indicated an increase in the amount of saturated fatty acids. In B. subtilis, the phospholipid composition remained relatively unchanged during exponential growth, but the amount of PG slightly decreased while the amount of PE slightly increased during stationary growth. No significant changes were observed for the lysyl-phosphatidylglycerols or glycolipids during the exponential or stationary growth phases.
 
A mixture of glycosaminoglycan (GAG) chains from a plasma proteoglycan bikunin was fractionated using native, continuous-elution polyacrylamide gel electrophoresis, and the resulting fractions were analyzed by electrospray ionization Fourier transform mass spectrometry (ESI FTMS). Molecular mass analysis of the intact GAG afforded information about the length and composition of GAG chains in the mixture. Ambiguity in the interpretation of the intact GAG mass spectra was eliminated by conducting an additional experiment in which the GAG chains of known molecular mass were treated with a GAG-degrading enzyme, chondroitinase ABC, and the digestion products were analyzed by ESI FTMS. The plasma bikunin GAG chains consisted predominantly of odd number of saccharides, although few chains consisting of even number of saccharides were also detected. Majority of the analyzed chains were tetrasulfated or pentasulfated and comprised by 29 to 41 monosaccharides.
 
Heparin interacts with many proteins and is involved in biological processes such as anticoagulation, angiogenesis, and antitumorigenic activities. These heparin-protein interactions can be influenced by the binding of various metal ions to these complexes. In particular, physiologically relevant metal cations influence heparin-protein conformations through electronic interactions inherent to this polyanion. In this study, we employed ion mobility mass spectrometry (IMMS) to observe conformational changes that occur in fully-sulfated heparin octasaccharides after the successive addition of metal ions. Our results indicate that binding of positive counter ions causes a decrease in collision cross section (CCS) measurements, thus promoting a more compact octasaccharide structure.
 
Xeroderma pigmentosum (XP) is a genetic disease affecting 1 in 10,000-100,000 and predisposes people to early-age skin cancer, a disease that is increasing. Those with XP have decreased ability to repair UV-induced DNA damage, leading to increased susceptibility of cancerous non-melanomas and melanomas. A vital, heterotrimeric protein complex is linked to the nucleotide excision repair pathway for the damaged DNA. The complex consists of XPC protein, human centrin 2, and RAD23B. One of the members, human centrin 2, is a ubiquitous, acidic, Ca(2+)-binding protein belonging to the calmodulin superfamily. The XPC protein contains a sequence motif specific for binding to human centrin 2. We report here the Ca(2+)-binding properties of human centrin 2 and its interaction with the XPC peptide motif. We utilized a region-specific H/D exchange protocol to localize the interaction of the XPC peptide with the C-terminal domain of centrin, the binding of which is different than that of calmodulin complexes. The binding dynamics of human centrin 2 to the XPC peptide in the absence and presence of Ca(2+) are revealed by the observation of EX1 H/D exchange regime, indicating that a locally unfolded population exists in solution and undergoes fast H/D exchange.
 
Complete and accurate profiling of cellular organelle proteomes, while challenging, is important for the understanding of detailed cellular processes at the organelle level. Mass spectrometry technologies coupled with bioinformatics analysis provide an effective approach for protein identification and functional interpretation of organelle proteomes. In this study, we have compiled human organelle reference datasets from large-scale proteomic studies and protein databases for 7 lysosome-related organelles (LROs), as well as the endoplasmic reticulum and mitochondria, for comparative organelle proteome analysis. Heterogeneous sources of human organelle proteins and rodent homologs are mapped to human UniProtKB protein entries based on ID and/or peptide mappings, followed by functional annotation and categorization using the iProXpress proteomic expression analysis system. Cataloging organelle proteomes allows close examination of both shared and unique proteins among various LROs and reveals their functional relevance. The proteomic comparisons show that LROs are a closely related family of organelles. The shared proteins indicate the dynamic and hybrid nature of LROs, while the unique transmembrane proteins may represent additional candidate marker proteins for LROs. This comparative analysis, therefore, provides a basis for hypothesis formulation and experimental validation of organelle proteins and their functional roles.
 
Technology to enable rapid screening for radiation exposure has been identified as an important need, and, as a part of a NIH / NIAD effort in this direction, metabolomic biomarkers for radiation exposure have been identified in a recent series of papers. To reduce the time necessary to detect and measure these biomarkers, differential mobility spectrometry - mass spectrometry (DMS-MS) systems have been developed and tested. Differential mobility ion filters preselect specific ions and also suppress chemical noise created in typical atmospheric-pressure ionization sources (ESI, MALDI, and others). Differential-mobility-based ion selection is based on the field dependence of ion mobility, which, in turn, depends on ion characteristics that include conformation, charge distribution, molecular polarizability, and other properties, and on the transport gas composition which can be modified to enhance resolution. DMS-MS is able to resolve small-molecule biomarkers from nearly-isobaric interferences, and suppresses chemical noise generated in the ion source and in the mass spectrometer, improving selectivity and quantitative accuracy. Our planar DMS design is rapid, operating in a few milliseconds, and analyzes ions before fragmentation. Depending on MS inlet conditions, DMS-selected ions can be dissociated in the MS inlet expansion, before mass analysis, providing a capability similar to MS/MS with simpler instrumentation. This report presents selected DMS-MS experimental results, including resolution of complex test mixtures of isobaric compounds, separation of charge states, separation of isobaric biomarkers (citrate and isocitrate), and separation of nearly-isobaric biomarker anions in direct analysis of a bio-fluid sample from the radiation-treated group of a mouse-model study. These uses of DMS combined with moderate resolution MS instrumentation indicate the feasibility of field-deployable instrumentation for biomarker evaluation.
 
Paper spray ionization has been developed as a direct, fast and low-cost sampling and ionization method for qualitative and quantitative mass spectrometric (MS) analysis of complex mixtures. Analyte ions are generated by applying a high voltage and a small volume (~10 μL) of spray solvent onto a porous substrate. The sample can be preloaded onto the paper or mixed into the spray solution. The geometry of the paper and the method of supplying the necessary internal standard are important factors that affect the ionization efficiency and subsequently the sensitivity and quantitation accuracy of the analytical data. As the cut angle of the paper tip is changed, the spray plume, the total spray current and the electric field intensity at the tip all vary correspondingly, with resulting differences in signal intensity. Sample load is another important factor for obtaining a stable MS signal and accurate quantitative results. The optimal sample load was found to be dependent on the paper size. The dissolution and spray process was also investigated and analyte transfer on paper was shown to be largely associated with bulk solution flow towards the spray tip. The information gathered from these systematic studies provides guidance for the design and optimization of a disposable sample cartridge for paper spray MS, a device which potentially is suitable for fast clinical analysis, especially for point-of-care diagnostics.
 
Intact bovine insulin, with its two chains linked via two disulfide linkages, has been used as a model system to study the incorporation of one or more gold cations as means for facilitating the cleavage of multiple disulfide bonds in a tandem mass spectrometry experiment. Gas-phase ion/ion reactions involving Au(I)Cl(2) (-) or Au(III)Cl(4) (-) were used to incorporate either one or two gold cations into multiply-protonated insulin cations, followed by ion trap collision-induced dissociation (CID) of the products. The incorporation of a single gold cation followed by CID showed little evidence for disulfide bond cleavage. Rather, the CID spectra were similar to those acquired for the same charge state with only excess protons present. However, the incorporation of two gold cations, regardless of oxidation state, resulted in efficient cleavage of the disulfide bonds connecting the two chains of insulin. Furthermore, ion trap CID of the insulin complexes containing two gold cations showed more sequence information compared to the complexes containing only one gold cation or no gold cations. The partitioning of the gold cations between the two chains upon CID proved to be largely asymmetric, as both gold cations tended to stay together. There appeared to be a slight preference for both gold cations to partition into the B-chain. However, the relatively low contribution from single chain ions with only one gold ion suggests a degree of cooperativity in the overall mechanism for separation of the two chains.
 
Matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS) is a powerful tool that has allowed researchers to directly probe tissue molecular structure and drug content with minimal manipulations, while maintaining anatomical integrity. In the present work glycerophospholipids and sphingolipids images were acquired from 16 µm thick coronal rat brain sections using MALDI-MS. Images of phosphatidylinositol 38:4 (PI 38:4), suifatide 24:1 (ST 24:1), and hydroxyl sulfatide 24:1 (ST 24:1 (OH)) were acquired in negative ion mode, while the images of phosphatidylcholine 34:1 (PC 34:1), potassiated phosphatidylcholines 32:0 (PC32:0 + K(+)) and 36:1 (PC 36:1 +K(+)) were acquired in positive ion mode. The images of PI 38:4 and PC 36:1+K(+) show the preferential distribution of these two lipids in gray matter; and the images of two sulfatides and PC 32:0+K(+) show their preferential distribution in white matter. In addition, the gray cortical band and its adjacent anatomical structures were also identified by contrasting their lipid makeup. The resulting images were compared to lipid images acquired by secondary ion mass spectrometry (SIMS). The suitability of TLC sprayers, Collison Nebulizer, and artistic airbrush were also evaluated as means for matrix deposition.
 
Top-cited authors
Tilmann D Märk
  • University of Innsbruck
P. B. Armentrout
  • University of Utah
Patrik Spanel
  • The Czech Academy of Sciences
Kurt Becker
  • NYU Tandon School of Engineering
Jim Scrivens
  • Teesside University