Feature Based Retention Time Alignment for Improved HDX MS Analysis

An algorithm for retention time alignment of mass shifted hydrogen-deuterium exchange (HDX) data based on an iterative distance minimization procedure is described. The algorithm performs pairwise comparisons in an iterative fashion between a list of features from a reference file and a file to be time aligned to calculate a retention time mapping function. Features are characterized by their charge, retention time and mass of the monoisotopic peak. The algorithm is able to align datasets with mass shifted features, which is a prerequisite for aligning hydrogen-deuterium exchange mass spectrometry datasets. Confidence assignments from the fully automated processing of a commercial HDX software package are shown to benefit significantly from retention time alignment prior to extraction of deuterium incorporation values.      

Laserspray and Matrix-Assisted Ionization Inlet Coupled to High-Field FT-ICR Mass Spectrometry for Peptide and Protein Analysis

We present the first coupling of laser spray ionization inlet (LSII) and matrix assisted ionization inlet (MAII) to high-field Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) for generation of electrospray-like ions to take advantage of increased sensitivity, mass range, and mass resolving power afforded by multiple charging. We apply the technique to top-down protein analysis and characterization of metalloproteins. We also present a novel method for generation of multiply-charged copper–peptide complexes with varying degrees of copper adduction by LSII. We show an application of the generated copper–peptide complexes for protein charge state and molecular weight determination, particularly useful for an instrument such as a linear ion trap mass analyzer.      

Traveling Wave Ion Mobility Mass Spectrometry Study of Low Generation Polyamidoamine Dendrimers

We reported the use of ion mobility (IM) combined with mass spectrometry (MS) as an analytical tool to investigate low generation polyamidoanine (PAMAM) dendrimers. This analytical approach has been employed to separate ions of defective structures with different charge state but exactly the same m/z value. Tandem mass spectrometry (MS/MS) after IM separation allowed a comprehensive structural characterization of defective dendrimers. In addition, IM was used to evaluate the collision cross-sections of ions of perfect dendrimers. They showed a good correlation with calculated collision cross-sections obtained by the trajectory method (TM) and were also consistent with dimensions reported by other established analytical methods.      

Structural Analysis of Triacylglycerols by Using a MALDI-TOF/TOF System with Monoisotopic Precursor Selection

A new MALDI-TOF/TOF system with monoisotopic precursor selection was applied to the analysis of triacylglycerols in an olive oil sample. Monoisotopic precursor selection made it possible to obtain product-ion mass spectra without interference from species that differed by a single double bond. Complete structure determination of all triacylglycerols, including structural isomers, was made possible by interpreting the charge-remote fragmentation resulting from high-energy collision-induced dissociation (CID) of the sodiated triacylglycerols.      

The Effect of Organic Modifiers on Electrospray Ionization Charge-State Distribution and Desorption Efficiency for Oligonucleotides

The chemical composition of the solution has a critical impact on the electrospray desorption efficiency of oligonucleotides. Several physiochemical properties of various organic modifiers were investigated with respect to their role in the desorption process of oligonucleotides. The Henry’s Law Constant, which reflects the volatility of alkylamines, was found to have a prominent effect on both the electrospray charge state distribution and desorption efficiency of oligonucleotides. Alkylamines with higher $ \mathrm{k}_{\mathrm{H,cc}}\left( {\mathrm{aq}/\mathrm{gas}} \right) $ values such as hexylamine, piperidine, and imidazole reduced the charge state distribution by forming complexes with the oligonucleotide and dissociating from it in the gas phase, while alkylamines with extremely low $ \mathrm{k}_{\mathrm{H,cc}}\left( {\mathrm{aq}/\mathrm{gas}} \right) $ values reduced the electrospray charge state distribution by facilitating ion emission at an earlier stage of the electrospray desorption process. Ion-pairing agents with moderate $ \mathrm{k}_{\mathrm{H,cc}}\left( {\mathrm{aq}/\mathrm{gas}} \right) $ values do not alter the electrospray charge state distribution of oligonucleotides and their ability to enhance oligonucleotide ionization followed the order of decreasing $ \mathrm{k}_{\mathrm{H,cc}}\left( {\mathrm{aq}/\mathrm{gas}} \right) $ values. The Henry’s Law Constant also correlated to the impact of the acidic modifiers on oligonucleotide ionization efficiency. Ionization enhancement effects were observed with hexafluoroisopropanol, and this effect was attributed to its low $ \mathrm{k}_{\mathrm{H,cc}}\left( {\mathrm{aq}/\mathrm{gas}} \right) $ and moderate acidity. The comprehensive effects of both alkylamine and hexafluoroisoproapnol on the electrospray ionization desorption of oligonucleotides were also evaluated, and acid-base equilibrium was found to play a critical role in determining these effects.      

Carbonation and Other Super Saturated Gases as Solution Modifiers for Improved Sensitivity in Solvent Assisted Ionization Inlet (SAII) and ESI

Solvent Assisted Ionization Inlet (SAII) produces ions in a heated inlet to a mass spectrometer from aqueous and aqueous/organic solutions with high sensitivity. However, the use of acid modifiers, which typically aids electrospray ionization, generally results in ion suppression in SAII. Here we demonstrate that the use of carbonation and other super-saturated gases as solution modifiers increases analyte ion abundance and reduces metal cation adduction in SAII. Carbonation is also found to enhance electrospray ionization. The mechanistic and practical utility of carbonation in mass spectrometry is addressed.      

Biomimetic Antireflective Silicon Nanocones Array for Small Molecules Analysis

Biomimetic antireflective silicon nanocones array is used for analysis of small molecules by mass spectrometry. The role of the absorbed laser energy and its distribution in the laser desorption/ionization process has been investigated by varying the antireflective features precisely. By optimizing the antireflective silicon array, the absorbed laser energy can be channeled completely into the desorption/ionization of analytes. The optimized silicon array exhibits excellent performance to detect peptide, amino acid, drug molecule, and carbohydrate without any interference in the low-mass region.      

OmniSpect: An Open MATLAB-Based Tool for Visualization and Analysis of Matrix-Assisted Laser Desorption/Ionization and Desorption Electrospray Ionization Mass Spectrometry Images

We present omniSpect, an open source web- and MATLAB-based software tool for both desorption electrospray ionization (DESI) and matrix-assisted laser desorption ionization (MALDI) mass spectrometry imaging (MSI) that performs computationally intensive functions on a remote server. These functions include converting data from a variety of file formats into a common format easily manipulated in MATLAB, transforming time-series mass spectra into mass spectrometry images based on a probe spatial raster path, and multivariate analysis. OmniSpect provides an extensible suite of tools to meet the computational requirements needed for visualizing open and proprietary format MSI data.      

Generation and Characterization of a Distonic Biradical Anion Formed from an Enediynone Prodrug in the Gas Phase

A negatively charged biradical intermediate was successfully generated in the gas phase via cyclization of the deprotonated bicyclo[8.3.0]trideca-12-ene-2,7-diyn-1-one precursor. The inherent negative charge of this biradical allows its characterization via collision-activated dissociation and reactions with a variety of neutral substrates in an FT-ICR mass spectrometer. Although the biradical is unreactive toward reagents that usually react rapidly with positively charged biradicals, such as dimethyl disulfide, it reacts with the halogen-containing substrates carbon tetrachloride, carbon tetrabromide, and bromotrichloromethane via bromine or chlorine atom abstraction, which supports its biradical structure. The results presented in this study indicate that cyclizations commonly used in solution to form biradical intermediates from enediyne compounds may also occur in the gas phase.      

Dual-Channel Electrospray Microchip

A dual-channel electrospray microchip has been developed for electrospray ionization mass spectrometry (ESI-MS) where aqueous samples are mixed at the Taylor cone with an organic buffer. Due to the fast and effective mixing in the Taylor cone, the aqueous sample can be well ionized with a high ion intensity. The influence of geometric parameters such as the distance between the two microchannels at their junction at the tip of the emitter has been investigated together with chemical parameters such as the organic buffer composition.      

Characterization of Aggregation Propensity of a Human Fc-Fusion Protein Therapeutic by Hydrogen/Deuterium Exchange Mass Spectrometry

Aggregation of protein therapeutics has long been a concern across different stages of manufacturing processes in the biopharmaceutical industry. It is often indicative of aberrant protein therapeutic higher-order structure. In this study, the aggregation propensity of a human Fc-fusion protein therapeutic was characterized. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) was applied to examine the conformational dynamics of dimers collected from a bioreactor. HDX-MS data combined with spatial aggregation propensity calculations revealed a potential aggregation interface in the Fc domain. This study provides a general strategy for the characterization of the aggregation propensity of Fc-fusion proteins at the molecular level.

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Ion Mobility Spectrometry-Hydrogen Deuterium Exchange Mass Spectrometry of Anions: Part 2. Assessing Charge Site Location and Isotope Scrambling

Ion mobility spectrometry (IMS) coupled with gas-phase hydrogen deuterium exchange (HDX)-mass spectrometry (MS) and molecular dynamic simulations (MDS) has been used for structural investigation of anions produced by electrospraying a sample containing a synthetic peptide having the sequence KKDDDDDIIKIIK. In these experiments the potential of the analytical method for locating charge sites on ions as well as for utilizing collision-induced dissociation (CID) to reveal the degree of deuterium uptake within specific amino acid residues has been assessed. For diffuse (i.e., more elongated) [M – 2H]^2– ions, decreased deuterium content along with MDS data suggest that the D4 and D6 residues are charge sites, whereas for the more diffuse [M – 3H]^3– ions, the data suggest that the D4, D7, and the C-terminus are deprotonated. Fragmentation of mobility-selected, diffuse [M – 2H]^2– ions to determine deuterium uptake at individual amino acid residues reveals a degree of deuterium retention at incorporation sites. Although the diffuse [M – 3H]^3– ions may show more HD scrambling, it is not possible to clearly distinguish HD scrambling from the expected deuterium uptake based on a hydrogen accessibility model. The capability of the IMS-HDX-MS/MS approach to provide relevant details about ion structure is discussed. Additionally, the ability to extend the approach for locating protonation sites on positively-charged ions is presented.

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Disambiguation of Isomeric Procyanidins with Cyclic B-Type and Non-cyclic A-Type Structures from Wine and Peanut Skin with HPLC-HDX-HRMS/MS

Hydrogen/deuterium exchange coupled with high-resolution mass spectrometry was successfully applied for the identification of A-type tetrameric, pentameric, and hexameric procyanidins in peanut skin. This extended a previous study on isomeric cyclic B-type unconventional tetramer, pentamer, and hexamer procyanidins found in wine and cranberries. Not only had the method successfully identified the procyanidins with a single A-linkage (e.g., tetrameric m/z 1153.2608) by means of distinguishing them from their isomeric cyclic B-type analogues, but this method also worked for procyanidins with two or more A-linkages (such as the tetrameric m/z 1151.2452). As a further consequence, B-type cyclic pentamers and hexamers in wine have been elucidated with hydrogen/deuterium exchange (HDX) for the first time.

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Comparison of Peptide Ion Conformers Arising from Non-Helical and Helical Peptides Using Ion Mobility Spectrometry and Gas-Phase Hydrogen/Deuterium Exchange

The dominant gas-phase conformer of [M+3H]³⁺ ions of the model peptide acetyl-PSSSSKSSSSKSSSSKSSSSK has been examined with ion mobility spectrometry (IMS), gas-phase hydrogen deuterium exchange (HDX), and mass spectrometry (MS) techniques. The [M+3H]³⁺ peptide ions are observed predominantly as a relatively compact conformer type. Upon subjecting these ions to electron transfer dissociation (ETD), the level of protection for each amino acid residue in the peptide sequence is assessed. The overall per-residue deuterium uptake is observed to be relatively more efficient for the neutral residues than for the model peptide acetyl-PAAAAKAAAAKAAAAKAAAAK. In comparison, the N-terminal and C-terminal regions of the serine peptide show greater relative protection compared with interior residues. Molecular dynamics (MD) simulations have been used to generate candidate structures for collision cross section and HDX reactivity matching. Hydrogen accessibility scoring (HAS) for select structural candidates from MD simulations has been used to suggest conformer types that could contribute to the observed HDX patterns. The results are discussed with respect to recent studies employing extensive MD simulations of gas-phase structure establishment of a peptide system.

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The Effects of Added Hydrogen on a Helium Atmospheric-Pressure Plasma Jet Ambient Desorption/Ionization Source

We present mass spectrometric data demonstrating the effect that hydrogen has on a helium-based dielectric-barrier discharge (DBD) atmospheric-pressure plasma jet used as an ambient desorption/ionization (ADI) source. The addition of 0.9 % hydrogen to the helium support gas in a 35-W plasma jet increased signals for a range of test analytes, with enhancement factors of up to 68, without proportional increases in background levels. The changes in signal levels result from a combination of changes in the desorption kinetics from the surface and increased ion production in the gas phase. The enhancement in ADI-MS performance despite the quenching of key plasma species reported in earlier studies suggests that ionization with a H₂/He plasma jet is the result of an alternate mechanism involving the direct generation of ionized hydrogen.      

Analysis of the Formation Process of Gold Nanoparticles by Surface-Assisted Laser Desorption/Ionization Mass Spectrometry

Chemical reactions of reducing agents in the gold nanoparticle (AuNP) formation process were characterized using surface-assisted laser desorption/ionization mass spectrometry (SALDI-MS). As the reaction of the AuNPs progresses, the produced AuNPs can serve as an efficient SALDI substrate. SALDI-MS revealed that the reducing agents and their oxidation products can be determined in the mass spectra. With respect to the transmission electron microscopic and UV-Vis spectroscopic examination of AuNPs, SALDI-MS results confirm not only the tendency toward AuNPs formation, but also reflect the information of the redox reaction process. Our results provide useful information for developing SALDI-MS methods to explore the chemical information regarding the surface behavior between adsorbates and nanomaterials.      

Tuning a High Transmission Ion Guide to Prevent Gas-Phase Proton Exchange During H/D Exchange MS Analysis

Hydrogen/deuterium exchange (HDX) mass spectrometry (MS) for protein structural analysis has been adopted for many purposes, including biopharmaceutical development. One of the benefits of examining amide proton exchange by mass spectrometry is that it can readily resolve different exchange regimes, as evidenced by either binomial or bimodal isotope patterns. By careful analysis of the isotope pattern during exchange, more insight can be obtained on protein behavior in solution. However, one must be sure that any observed bimodal isotope patterns are not artifacts of analysis and are reflective of the true behavior in solution. Sample carryover and certain stationary phases are known as potential sources of bimodal artifacts. Here, we describe an additional undocumented source of deuterium loss resulting in artificial bimodal patterns for certain highly charged peptides. We demonstrate that this phenomenon is predominantly due to gas-phase proton exchange between peptides and bulk solvent within the initial stages of high-transmission conjoined ion guides. Minor adjustments of the ion guide settings, as reported here, eliminate the phenomenon without sacrificing signal intensity. Such gas-phase deuterium loss should be appreciated for all HDX-MS studies using such ion optics, even for routine studies not focused on interpreting bimodal spectra.

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Gas-Phase Fragmentation of Oligoproline Peptide Ions Lacking Easily Mobilizable Protons

The fragmentation of peptides containing quaternary ammonium group, but lacking easily mobilizable protons, was examined with the aid of deuterium-labeled analogs and quantum-chemical modeling. The fragmentation of oligoproline containing quaternary ammonium group involves the mobilization of hydrogens localized at α- and γ- or δ-carbon atoms in the pyrrolidine ring of proline. The study of the dissociation pattern highlights the unusual proline residue behavior during MS/MS experiments of peptides.      

Three–step method to determine the eutectic composition of binary and ternary mixtures

A three-step method to determine the eutectic composition of a binary or ternary mixture is introduced. The method consists in creating a temperature–composition diagram, validating the predicted eutectic composition via differential scanning calorimetry and subsequent T-History measurements. To test the three-step method, we use two novel eutectic phase change materials based on \(\mathrm{Zn}(\hbox {NO}_3)_2\cdot 6\mathrm{H}_{2}{\mathrm O}\) and \(\mathrm{NH}_4\mathrm{NO}_3\)   respectively \(\mathrm{Mn}(\hbox {NO}_3)_2\cdot 6\mathrm{H}_{2}{\hbox {O}}\) and \(\mathrm{NH}_4\mathrm{NO}_3\) with equilibrium liquidus temperatures of 12.4 and 3.9  \(\,^{\circ }\mathrm {C}\) respectively with corresponding melting enthalpies of 135 J \(\mathrm{g}^{-1}\) (237 J \(\mathrm{cm}^{-3}\) ) respectively 133 J \(\mathrm{g}^{-1}\) (225 J \(\mathrm{cm}^{-3}\) ). We find eutectic compositions of 75/25 mass% for \(\mathrm{Zn}(\hbox {NO}_3)_2\cdot \mathrm{6H}_{2}{\mathrm{O}}\) and \(\mathrm{NH}_4\mathrm{NO}_3\) and 73/27 mass% for \(\mathrm{Mn}(\hbox {NO}_3)_2\cdot 6\mathrm{H}_{2}{\mathrm{O}}\) and \(\mathrm{NH}_4\mathrm{NO}_3\) . Considering a temperature range of 15 K around the phase change, a maximum storage capacity of about 172 J \(\mathrm{g}^{-1}\) (302 J \(\mathrm{cm}^{-3}\) ) respectively 162 J \(\mathrm{g}^{-1}\) (274 J \(\mathrm{cm}^{-3}\) ) was determined for \(\mathrm{Zn}(\hbox {NO}_3)_2\cdot \mathrm{6H}_{2}{\mathrm{O}}\) and \(\mathrm{NH}_4\mathrm{NO}_3\) respectively \(\mathrm{Mn}(\hbox {NO}_3)_2\cdot \mathrm{6H}_{2}{\mathrm{O}}\) and \(\mathrm{NH}_4\mathrm{NO}_3\) .     

Overtone Mobility Spectrometry: Part 5. Simulations and Analytical Expressions Describing Overtone Limits

Mathematical expressions for the analytical duty cycle associated with different overtones in overtone mobility spectrometry are derived from the widths of the transmitted packets of ions under different instrumental operating conditions. Support for these derivations is provided through ion trajectory simulations. The outcome of the theory and simulations indicates that under all operating conditions there exists a limit or maximum observable overtone that will result in ion transmission. Implications of these findings on experimental design are discussed.