Probing High-order Protein Complexes Using Native Mass Spectrometry and Hydrogen/Deuterium Exchange Mass Spectrometry: A Case Study Using Fresh and Commercial Hemoglobin Samples.

Native mass spectrometry (MS) analysis of protein complexes is highly susceptible to matrix effect, and addressing this predicament using buffer exchange is a common approach. Nevertheless, optimization of the buffer exchange protocol is not trivial. With the use of hemoglobin (Hb) as the model entity, it was discovered that the native mass spectrum of protein assembly is highly dependent on the buffer-exchange protocol. Given the dependence of native MS on the purification protocol, this work attempts to use hydrogen/deuterium exchange mass spectrometry (HDX-MS) for comparative studies of hemoglobin complexes in untreated fresh and commercial samples. The information obtained from the HDX study was found to correlate well with the native mass spectrometry analysis of the properly buffer-exchanged Hb samples. Both native MS and HDX-MS showed that the fresh Hb sample has retained the expected tetrameric structure, whereas the commercial Hb has largely been denatured to the dimeric form. These findings prove the complementarity of native MS and HDX-MS in the analysis of high-order protein complexes and stress the necessity to validate the integrity of the high-order structures of the proteins prior to the use of the protein samples for other biomedical studies.

A millimeter water-in-oil droplet as an alternative back exchange prevention strategy for hydrogen/deuterium exchange mass spectrometry of peptides/proteins.

Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is a versatile bioanalytical technique for protein analysis. Since the reliability of HDX-MS analysis considerably depends on the retention of deuterium labels in the post-labeling workflow, deuterium/hydrogen (D/H) back exchange prevention strategies, including decreasing the pH, temperature, and exposure time to protic sources of the deuterated samples, are widely adopted in the conventional HDX-MS protocol. Herein, an alternative and effective back exchange prevention strategy based on the encapsulation of a millimeter droplet of a labeled peptide solution in a water-immiscible organic solvent (cyclohexane) is proposed. Cyclohexane was used to prevent the undesirable uptake of water by the droplet from the atmospheric vapor through the air-water interface. Using the pepsin digest of deuterated myoglobin, our results show that back exchange kinetics of deuterated peptides is retarded in a millimeter droplet as compared to that in the bulk solution. Performing pepsin digestion directly in a water-in-oil droplet at room temperature (18-21 °C) was found to preserve more deuterium labels than that in the bulk digestion with an ice-water bath. Based on the present findings, it is proposed that keeping deuterated peptides in the form of water-in-oil droplets during the post-labelling workflow will facilitate the preservation of deuterium labels on the peptide backbone and thereby enhance the reliability of the H/D exchange data.

Determining the gas-phase structures of α-helical peptides from shape, microsolvation, and intramolecular distance data.

Mass spectrometry is a powerful technique for the structural and functional characterization of biomolecules. However, it remains challenging to accurately gauge the gas-phase structure of biomolecular ions and assess to what extent native-like structures are maintained. Here we propose a synergistic approach which utilizes Förster resonance energy transfer and two types of ion mobility spectrometry (i.e., traveling wave and differential) to provide multiple constraints (i.e., shape and intramolecular distance) for structure-refinement of gas-phase ions. We add microsolvation calculations to assess the interaction sites and energies between the biomolecular ions and gaseous additives. This combined strategy is employed to distinguish conformers and understand the gas-phase structures of two isomeric α-helical peptides that might differ in helicity. Our work allows more stringent structural characterization of biologically relevant molecules (e.g., peptide drugs) and large biomolecular ions than using only a single structural methodology in the gas phase.

CaptiveSpray Differential Ion Mobility Spectrometry Device with Enhanced Ion Transmission and Improved Resolving Power.

A performance enhanced CaptiveSpray differential ion mobility device was designed and constructed by incorporating a circular channel and a gas flow homogenizing channel (GFHC) between the CaptiveSpray ion source and planar differential ion mobility spectrometry (DMS). The GFHC was used to reduce gas flow heterogeneity prior to the entrance of the DMS device. The optimal flared entrance greatly reduces gas flow velocity at the inlet region owing to its relatively large gas inlet interface, which assists in reducing disparities between the minimum and maximum gas velocity along the x-axis. The circular electrode was machined with channels along the x- and y-axis for the passage of auxiliary gas and was applied with a potential to focus the incoming ions from the CaptiveSpray source into the DMS channel. Using reserpine as a reference standard, substantial signal enhancement was achieved with a concomitant reduction of the peak width in the ionogram.

Use of group IIB metal ions as charge carriers for collision-induced dissociation of glycopeptide and glycan.

RATIONALE: Dissociation of biomolecules by tandem mass spectrometry (MS/MS) generates a variety of fragment ions which provide useful information for the structural characterization of biomolecules. Different fragmentation strategies result in different mass spectra for the same molecule and thus provide distinct features. Charge carriers play important roles in determining the dissociation pathways of the target precursor ions. The use of various transition metals ions as charge carriers of glycopeptide and glycan might provide additional structural information and needs to be investigated. METHODS: A 9.4 T SolariX FTICR mass spectrometer was used for collision-induced dissociation (CID) of glycopeptide and glycan. Group IIB metal ions, including Zn2+ , Cd2+ and Hg2+ , were used as charge carriers. Glycopeptide NLTK-M5 G2 and glycan G1F were used as the model systems. RESULTS: For Zn2+ - and Cd2+ -adducted species, cross-ring cleavages, glycosidic cleavages and cleavages along the peptide backbone could be obtained. There is a high degree of similarity in their CID spectra with that of Mg2+ ion-adducted glycopeptide species. For Hg2+ -adducted species, only glycosidic cleavages were observed in high abundance. The formation of doubly-charged ions (M2+ ) and a series of [f-H]+ fragments indicated unique dissociation pathways for Hg2+ -adducted glycopeptide. CONCLUSIONS: Zn2+ and Cd2+ -adducted glycopeptide species produced similar dissociation CID spectra, whereas Hg2+ -adducted species produced significantly different CID spectra. Similar CID dissociation features were also observed for Group IIB metal ions adducted glycan species. These results demonstrated that different metal ions might be used to tune the dissociation behaviors of glycopeptides and glycans.

Tandem Mass Spectrometry for Structural Characterization of Doubly-Charged N-Linked Glycopeptides.

Three dissociation methods, including collision-induced dissociation (CID), electron capture dissociation (ECD), and electronic excitation dissociation (EED), were systematically compared for structural characterization of doubly charged glycopeptide. CID produced distinctively different tandem mass spectra for glycopeptide adducted with different charge carriers. Protonated species produced mainly glycosidic cleavages in high abundance. CID of magnesiated glycopeptide formed more cross-ring cleavages, whereas doubly sodiated species produced cleavages at both glycan and peptide moieties. The effect of charge carriers on the fragmentation in ECD and EED was lower than that in CID. ECD produced mainly peptide backbone cleavages but limited cleavages at the glycan moiety, whereas EED of glycopeptide resulted in extensive fragmentation throughout the molecular ion regardless of the charge carriers. Magnesiated species gave, however, more cross-ring cleavages than other charge carriers did. These results demonstrated that EED of magnesiated species could be used as a one-step dissociation method for comprehensive structural analysis of glycopeptides.

Dissociation of Mannose-Rich Glycans Using Collision-Based and Electron-Based Ion Activation Methods.

Three dissociation methods, including collision-induced dissociation (CID), electron capture dissociation (ECD), and electronic excitation dissociation (EED), were evaluated for the dissociation of doubly charged glycans using sodium or magnesium ions as charge carriers. CID produced mainly glycosidic cleavages, although more cross-ring fragment ions could be obtained at higher intensities when magnesium ions were used as charge carriers [M + Mg]2+. The 0,2A3, 0,3A3, and 0,4A3 ions provided structural information on the 3 → 1 and 6 → 1 linkages of the mannoses. Some internal fragment ions, such as 2,4A5_Y3ß, were also produced in high abundance, thus providing additional information on the glycan structure. ECD produced limited fragments compared to other dissociation methods when either of the metal ions were used as charge carriers. Cross-ring fragments were obtained in relatively high abundance, with the charge mainly retained on the nonreducing end. EED produced extensive glycosidic and cross-ring cleavages when either metal charge carrier was used. A higher fragmentation efficiency was achieved and more structural-specific fragments were produced when Na+ was used as the charge carrier. Of the 31 possible cross-ring cleavages, including 0,2-, 0,4-, 1,5-, 2,4-, and 3,5-cleavages, 25 were found, thus providing extensive linkage information. A wide range of fragment ions could be obtained in all dissociation methods when Mg2+ was used as the charge carrier. Two specific analytical approaches were found to produce extensively structural-specific information on the glycans studied, namely CID of magnesiated glycans and EED of sodiated glycans. These two methods were selected to further analyze the larger mannose-rich glycans Man6GlcNAc2 and Man8GlcNAc2 and generated extensive structural information.

Development of a Matrix Sublimation Device with Controllable Crystallization Temperature for MALDI Mass Spectrometry Imaging.

The size and distribution of matrix crystals deposited on the surface of a tissue section play a key role in the performance of MALDI mass spectrometry imaging (MALDI-MSI). In this study, uniform distribution and a restricted size of matrix crystals were achieved via a homemade matrix sublimation device with controllable crystallization temperature. The crystallization temperature was stably controlled at a subzero temperature, and homogeneous matrix crystals with diameters <0.2 µm were generated on the sample surface. Typical MALDI-MSI experiments of endogenous and exogenous components in the tissues of strawberries, kidneys, and mussels were conducted to examine the performance of the sublimator. Good reproducibility of MALDI-MSI was achieved, and the quality of ion images was significantly improved. These results demonstrate that the developed sublimator should have potential in matrix deposition for further high resolution MALDI-MSI application.

Development of an All-in-One Protein Digestion Platform Using Sorbent-Attached Membrane Funnel-Based Spray Ionization Mass Spectrometry.

In this work, the sorbent-attached microfunnels used in funnel-based spray ionization mass spectrometry were evaluated for the all-in-one digestion of proteins. Sorbent materials, including C18 and TiO2 powders, were used as substrates to support in-funnel digestion and subsequent solid-phase extraction and purification of the digested products. In-funnel digestion protocols with and without reductive alkylation were developed for the analysis of proteins with and without disulfide linkages. Compared with in-solution digestion of the same loadings, the sequence coverage of in-funnel digestion of ovalbumin (with one disulfide bond) and ovocystatin (with two disulfide bonds) increased from 36% to 65% and from 21% to 81%, respectively. Loading 100 fmol of ovalbumin was sufficient to generate detectable tryptic fragments on C18-attached funnels. Notably, some phosphorylated digestion fragments were solely detected on C18-attached funnels and some nonphosphorylated digestion fragments were detected only on TiO2-attached funnels. Complex biological protein mixtures (i.e., bovine milk) and mouse liver protein extract could also be digested on C18- and TiO2-attached funnels. Using this platform, 30 samples were digested at the same time with enhanced digestion efficiency and were analyzed by funnel-based spray ionization mass spectrometry. This approach is potentially useful for sensitive and high-throughput bottom-up proteomic studies of complex biological samples.

Magnetic solid-phase extraction of sulfonamide antibiotics in water and animal-derived food samples using core-shell magnetite and molybdenum disulfide nanocomposite adsorbent.

A molybdenum disulfide(MoS2)-based core-shell magnetic nanocomposite (Fe3O4@MoS2) was synthesized by the stepwise hydrothermal method. Two-dimension ultrathin MoS2 sheets with a thickness of approximately 20 nm were grown in situ on the surface of Fe3O4 (∼200 nm). They were employed as an adsorbent for the magnetic solid-phase extraction (MSPE) of sulfonamide antibiotics (SAs) from water samples. High-performance liquid chromatography tandem mass spectrometry (HPLC-MS/MS) was used for SA quantitation. Extraction parameters, including the pH effect, amount of Fe3O4@MoS2, extraction time, temperature, and desorption conditions, were systematically investigated. The electrostatic interaction between the positively charged SAs and negatively charged MoS2 nanoparticles in the optimal extraction conditions enhanced the adsorption of SAs on the sorbent surface. Under chosen conditions, the proposed strategy achieved wide linear range of 1.0-1000 ng·L-1 SAs, low limits of detection (LOD, 0.20-1.15 ng·L-1, S/N = 3:1), good trueness (recoveries between 85.50-111.5%), satisfactory repeatability and reproducibility (relative standard deviation, <10%, n = 5), and excellent recoveries between 80.20% and 108.6% for SAs determination in spiked waste water samples. The proposed strategy was validated and successfully applied for the analysis of water, milk, pork meat and fish meat. The nanocomposites, which have the combined advantages of magnetic separation and high adsorption affinity toward SAs, are a promising sorbent for antibiotics extraction from real samples.

Rapid Differentiation of Asian and American Ginseng by Differential Ion Mobility Spectrometry-Tandem Mass Spectrometry Using Stepwise Modulation of Gas Modifier Concentration.

This study reports a rapid and robust method for the differentiation of Asian and American ginseng samples based on differential ion mobility spectrometry-tandem mass spectrometry (DMS-MS/MS). Groups of bioactive ginsenoside/pseudo-ginsenoside isomers, including Rf/Rg1/F11, Rb2/Rb3/Rc, and Rd/Re, in the ginseng extracts were sequentially separated using DMS with stepwise changes in the gas modifier concentration prior to MS analysis. The identities of the spatially separated ginsenoside/pseudo-ginsenoside isomers were confirmed by their characteristic compensation voltages at specific modifier loading and MS/MS product ions. As expected, Asian ginseng samples contained some Rf and an insignificant amount of F11, whereas American ginseng samples had a high level of F11 but no Rf. The origin of the whole and sliced ginseng could further be confirmed using the quantitative ratios of three sets of ginsenoside markers, namely, Rg1/Re, Rb1/Rg1, and Rb2/Rc. Based on our results, new benchmark ratios of Rg1/Re < 0.15, Rb1/Rg1 > 2.15, and Rb2/Rc < 0.26 were proposed for American ginseng (as opposed to Asian ginseng).

Water-dispersible pH/thermo dual-responsive microporous polymeric microspheres as adsorbent for dispersive solid-phase extraction of fluoroquinolones from environmental water samples and food samples.

Multifunctional polymeric microspheres were prepared using hyper-cross-linking chemistry combined with surface-initiated atom transfer radical polymerization. The synthesized microspheres exhibited good water dispersibility, a high surface area, and pH/thermo dual-responsiveness. Fluoroquinolones (FQs), which contains a hydrophilic piperazine ring and hydrophobic fluorine atoms, were used as target analytes to assess the performance of the microspheres as a sorbent for dispersive solid-phase extraction (d-SPE). The d-SPE experimental parameters, including extraction time, amount of microspheres, extraction temperature, and sample solution pH, as well as the desorption conditions, were systematically studied. Coupled with LCMS/MS, an analytical method for analysis of trace-level FQs in water samples was developed and validated. Under optimal conditions, linearity with correlation coefficients (r) of >0.99 was achieved in the concentration range of 0.02-10 µg L-1. The limits of detection and quantification for the selected FQs were 5.0-6.7 and 12-20 ng L-1, respectively. High recovery values (93.1%-97.2%), a high enrichment factor (˜180), and good precision (RSD < 8%, n = 6) were obtained for FQ determination in spiked purified water samples. It was proposed that hydrophilic-hydrophobic transition induced by stretching and shrinking of polymer chains under different pH and temperature conditions offered good control of the surface wettability and altered the extraction behavior. The developed method was validated and was successfully applied to the analysis of FQs in environmental water samples, meat and milk samples. These results demonstrated that the water-dispersible polymeric microspheres have good potential for use in separation and extraction techniques.

Determination of fluoroquinolones in food samples by magnetic solid-phase extraction based on a magnetic molecular sieve nanocomposite prior to high-performance liquid chromatography and tandem mass spectrometry.

In this study, a magnetic molecular sieve material (Fe3O4@MCM-48) was synthesized by a combination of solvothermal and self-assembly methods. The physicochemical properties of the magnetic molecular sieve material were characterized by scanning electron microscopy, energy-dispersive spectroscopy, magnetic hysteresis loop measurements, transmission electron microscopy, powder X-ray diffraction, N2 adsorption-desorption analysis, and Fourier transform infrared spectroscopy. The as-synthesized nanocomposite showed various advantages, including easy magnetic-assisted separation, high specific surface area, and a highly interwoven and branched mesoporous structure. The Fe3O4@MCM-48 nanocomposite was then used as an effective adsorbent material for magnetic solid-phase extraction of fluoroquinolones (FQs) from water samples. The FQs in the extract were determined via liquid chromatography-tandem mass spectrometry. Adsorption and desorption factors that affected the extraction performance were systematically optimized using spiked purified water samples. Good linearity (with R2 > 0.99) was shown by this FQ detection system for FQ concentrations from 5 to 1000 ng L-1. Moreover, low detection limits (0.7-6.0 ng L-1) and quantitation limits (2.5-20.0 ng L-1) and satisfactory repeatability (relative standard deviation < 10%, n = 6) were achieved for water samples. The developed method was also validated for the analysis of FQs in meat and milk samples. Finally, FQs in food and drinking water samples were successfully determined using the developed method. Graphical abstract.

Performance Enhancements in Differential Ion Mobility Spectrometry-Mass Spectrometry (DMS-MS) by Using a Modified CaptiveSpray Source.

Differential ion mobility spectrometry (DMS) spatially separates ions in the gas phase using the mobility differences of the ions under applied low and high electric fields. The use of DMS as an ion filter (or ion selector) prior to mass spectrometry analysis has been compromised by the limited ion transmission efficiency. This paper reports enhancement of the DMS-MS sensitivity and signal stability using a modified CaptiveSpray™ source. In terms of the ion sampling and transmission efficiency, the modified CaptiveSpray source swept ~ 89% of the ions generated by the tapered capillary through the DMS device (compared to ~ 10% with a conventional microspray source). The signal fluctuation improved from 11.7% (relative standard deviation, RSD) with microspray DMS-MS to 3.6% using CaptiveSpray-DMS-MS. Coupling of LC to DMS-MS via the modified CaptiveSpray source was simple and robust. Using DMS as a noise-filtering device, LC-DMS-MS performed better than conventional LC-MS for analyzing a BSA digest standard. Although LC-DMS-MS had a lower sequence coverage (55%), a higher Mascot score (283) was obtained compared to those of LC-MS (sequence coverage 65%; Mascot score 192) under the same elution conditions. The improvement in the confidence of the search result was attributed to the preferential elimination of noise ions. Graphical Abstract ᅟ.

Electron-ion reaction-based dissociation: A powerful ion activation method for the elucidation of natural product structures.

The structural elucidation of natural products (NPs) remains a challenge due to their structurally diversities and unpredictable functionalities, motifs, and scaffolds. Tandem mass spectrometry (MS/MS) is an effective method that assists the full elucidation of complicated NP structures. Ion activation methods play a key role in determining the fragmentation pathways and the structural information obtained from MS/MS. Electron-ion reaction-based dissociation (ExD) methods, including electron capture dissociation (ECD), electron transfer dissociation (ETD), electron-induced dissociation (EID), and electron detachment dissociation (EDD), can induce the breakage of specific chemical bonds and the generation of distinct fragment ions. This review article provides an overview of the mechanisms, instrumentation, and typical applications related to ExD MS/MS in the structural elucidation of NPs, primarly including lipids, oligosaccharides, glycoconjugates, metabolites, and pharmaceutical drugs. This work aims to reveal the capacity and potential of ExD mass spectrometry in analyzing NPs and consequently helping the NP communities to utilize the modern capabilities of MS/MS in the discovery and evaluation of novel NPs.

Tissue imaging with in situ solid-phase extraction micro-funnel based spray ionization mass spectrometry.

Current imaging mass spectrometry techniques are faced with a major challenge related to ion suppression effect. Data regarding low-abundance components or low-polarity compounds cannot be normally obtained presumably because of the discrimination effect of easily ionized chemical components on desorption/ionization process. In this study, a new method was proposed to obtain images of chemical components in biological tissues or sections through in situ solid-phase extraction in sorbent mounted micro-funnel based spray ionization mass spectrometry. An imprint of a strawberry section was formed by gently pressing against a 2D array of micro-funnels. The sorbent mounted micro-funnels were then subjected to in situ single-pixel solid-phase extraction to alleviate the matrix-related ion suppression effect. The achievable spatial resolution is approximately 250 µm. The imaging of the spatial distribution of low-abundance or low-polarity chemicals in the strawberry imprint could be obtained by using a gradient elution strategy. Results demonstrated that the "not observed" remark does not necessarily indicate that a specific compound is non-existent when traditional imaging mass spectrometry techniques are used. The proposed method can be applied to conduct low-abundance chemical imaging through in situ single-pixel sample pretreatment.

Structural Characterization of Intact Glycoconjugates by Tandem Mass Spectrometry Using Electron-Induced Dissociation.

Characterizing the structures of glycoconjungates is important because of glycan heterogeneity and structural complexity of aglycon. The presence of relatively weak glycosidic linkages leads to preferential cleavages that limit the acquisition of structural information under typical mass spectrometry dissociation conditions, such as collision-induced dissociation (CID) and infrared multiphoton dissociation. In this paper, we explored the dissociation behaviors of different members of glycoconjugates, including glycopeptides, glycoalkaloids, and glycolipids, under electron-induced dissociation (EID) conditions. Using CID spectra as references, we found that EID is not only a complementary method to CID, but also a method that can generate extensive fragment ions for the structural characterization of all intact glycoconjugates studied. Furthermore, isomeric ganglioside species can be differentiated, and the double bond location in the ceramide moiety of the gangliosides can be identified through the MS3 approach involving sequential CID and EID processes.