In-spray supercharging of peptides and proteins in electrospray ionization mass spectrometry

Desalting strategies for native mass spectrometry

In native mass spectrometry (MS) salts are indispensable for preserving the native structures of biomolecules, but detrimental to mass sensitivity, resolution, and accuracy. Such a conflict makes desalting in native MS more challenging, distinctive, and sample-dependent than in peptide-centric MS. This review first briefly introduces the charged residue mechanism whereby native-like gaseous protein ions are released from electrospray droplets, revealing a higher degree of salt adduction than denatured proteins. Subsequently, this review summarizes and explores the existing strategies, underlying mechanisms and future perspectives of desalting in native MS. These strategies mainly focus on buffer exchange into volatile salts (offline and online approaches), addition of solution additives (e.g., anion, supercharging reagent, solution phase chelator and amino acid), use of submicron electrospray emitters (down to 60 nm), and other potential approaches (e.g., induced and electrophoretic nanoelectrospray ionization). The strategies of online buffer exchange and using nanoscale electrospray emitters are highlighted. This review would not only be a valuable addition to the field of sample preparation in MS, but would also serve as a beginner's guide to desalting in native MS.

Identifying Quinones in Complex Aqueous Environmental Media (Biochar Extracts) through Tagging with Cysteine and Cysteine-Contained Peptides and High Resolution Mass Spectrometry Analysis

Quinones are among the most important components in natural organic matter (NOM) for redox reactions; however, no quinones in complex environmental media have been identified. To aid the identification of quinone-containing molecules in ultracomplex environmental samples, we developed a chemical tagging method that makes use of a Michael addition reaction between quinones and thiols (-SH) in cysteine (Cys) and cysteine-contained peptides (CCP). After the tagging, candidates of quinones in representative aqueous environmental samples (water extractions of biochar) were identified through high-resolution mass spectrometry (HRMS) analysis. The MS and UV spectra analysis showed rapid reactions between Cys/CCP and model quinones with β-carbon from the same benzene ring available for Michael addition. The tagging efficiency was not influenced by other co-occurring nonquinone representative compounds, including caffeic acid, cinnamic acid, and coumaric acid. Cys and CCP were used to tag quinones in water extractions of biochars, and possible candidates of quinones (20 and 53 based on tagging with Cys and CCP, respectively) were identified based on the HRMS features for products of reactions with Cys/CCP. This study has successfully demonstrated that such a Michael addition reaction can be used to tag quinones in complex environmental media and potentially determine their identities. The method will enable an in-depth understanding of the redox chemistry of NOM and its critical chemical compositions and structures.

Evaluating C18 stationary phases with a positively charged surface for proteomic LC-MS applications using mobile phase acidified with reduced formic acid concentration

We have recently demonstrated the ability of a C18 stationary phase with a positively charged surface (PCS-C18) to provide superior chromatographic separation of peptides using mobile phase acidified with a mere 0.01 % formic acid, significantly improving MS sensitivity. Here, we examined three columns packed with different PCS-C18 phases using the MS-favorable mobile phase acidified with low formic acid concentrations to establish the impact of separation performance and better MS sensitivity on peptide identifications. The surface charge interaction was evaluated using the retention of nitrate. The highest interaction was observed for the AdvanceBio Peptide Plus column. A surface charge-dependent shift in the retention time of peptides was confirmed with a change in formic acid concentration in the mobile phase. The separation performance of the columns with MS-favorable mobile phase acidified with low concentrations of formic acid was evaluated using well-characterized peptides. The loading capacity was assessed using a basic peptide with three lysine residues. Good chromatographic peak shapes and high loading capacity were observed for the Acquity Premier CSH C18 column, even when using a mobile phase acidified with 0.01 % formic acid. The extent of improvement in peptide identification when using reduced formic acid concentration was evaluated by analyzing the tryptic digest of trastuzumab and tryptic digest of whole bacteria cell lysate. Each column provided improved MS signal intensity and peptide identification when using the mobile phase with 0.01 % formic acid. The ability of the Acquity Premier CSH C18 column to provide better separation of peptides, even with a reduced formic acid concentration in the mobile phase, boosted MS signal intensity by 65 % and increased the number of identified peptides from the bacterial sample by 19 %. Our study confirms that significant improvement in the proteomic outputs can be achieved without additional costs only by tailoring the chemistry of the stationary phase to the composition of the mobile phase. Our results can help researchers understand the retention mechanism of peptides on the PCS-C18 stationary phases using low-ionic strength mobile phases and, more importantly, select the best-suited stationary phases for their LC-MS proteomic applications.

What is the role of current mass spectrometry in pharmaceutical analysis?

The role of mass spectrometry (MS) has become more important in most application domains in recent years. Pharmaceutical analysis is specific due to its stringent regulation procedures, the need for good laboratory/manufacturing practices, and a large number of routine quality control analyses to be carried out. The role of MS is, therefore, very different throughout the whole drug development cycle. While it dominates within the drug discovery and development phase, in routine quality control, the role of MS is minor and indispensable only for selected applications. Moreover, its role is very different in the case of analysis of small molecule pharmaceuticals and biopharmaceuticals. Our review explains the role of current MS in the analysis of both small-molecule chemical drugs and biopharmaceuticals. Important features of MS-based technologies being implemented, method requirements, and related challenges are discussed. The differences in analytical procedures for small molecule pharmaceuticals and biopharmaceuticals are pointed out. While a single method or a small set of methods is usually sufficient for quality control in the case of small molecule pharmaceuticals and MS is often not indispensable, a large panel of methods including extensive use of MS must be used for quality control of biopharmaceuticals. Finally, expected development and future trends are outlined.

Charge site manipulation to enhance top-down fragmentation efficiency

In recent years, top-down mass spectrometry has become a widely used approach to study proteoforms; however, improving sequence coverage remains an important goal. Here, two different proteins, α-synuclein and bovine carbonic anhydrase, were subjected to top-down collision-induced dissociation (CID) after electrospray ionisation. Two high-boiling solvents, DMSO and propylene carbonate, were added to the protein solution in low concentration (2%) and the effects on the top-down fragmentation patterns of the proteins were systematically investigated. Each sample was measured in triplicate, which revealed highly reproducible differences in the top-down CID fragmentation patterns in the presence of a solution additive, even if the same precursor charge state was isolated in the quadrupole of the instrument. Further investigation supports the solution condition-dependent selective formation of different protonation site isomers as the underlying cause of these differences. Higher sequence coverage was often observed in the presence of additives, and the benefits of this approach became even more evident when datasets from different solution conditions were combined, as increases up to 35% in cleavage coverage were obtained. Overall, this approach therefore represents a promising opportunity to increase top-down fragmentation efficiency.

Top-Down Proteomics and the Challenges of True Proteoform Characterization

Top-down proteomics (TDP) aims to identify and profile intact protein forms (proteoforms) extracted from biological samples. True proteoform characterization requires that both the base protein sequence be defined and any mass shifts identified, ideally localizing their positions within the protein sequence. Being able to fully elucidate proteoform profiles lends insight into characterizing proteoform-unique roles, and is a crucial aspect of defining protein structure-function relationships and the specific roles of different (combinations of) protein modifications. However, defining and pinpointing protein post-translational modifications (PTMs) on intact proteins remains a challenge. Characterization of (heavily) modified proteins (>∼30 kDa) remains problematic, especially when they exist in a population of similarly modified, or kindred, proteoforms. This issue is compounded as the number of modifications increases, and thus the number of theoretical combinations. Here, we present our perspective on the challenges of analyzing kindred proteoform populations, focusing on annotation of protein modifications on an "average" protein. Furthermore, we discuss the technical requirements to obtain high quality fragmentation spectral data to robustly define site-specific PTMs, and the fact that this is tempered by the time requirements necessary to separate proteoforms in advance of mass spectrometry analysis.

Variable Mixing with Theta Emitter Mass Spectrometry: Changing Solution Flow Rates with Emitter Position

Two solutions can be rapidly mixed using theta glass emitters, with products measured using electrospray ionization mass spectrometry. The relative flow rates of the two emitter channels can be measured using different calibration compounds in each channel, or the flow rates are often assumed to be the same. The relative flow rates of each channel can be essentially the same when the emitters are positioned directly in front of the capillary entrance of a mass spectrometer, but the relative flow rates can be varied by up to 3 orders of magnitude by moving the position of the emitter tip ±1 cm in a direction that is perpendicular to the inner divider. Results of the emitter position on the different concentrations of reagents in the initially formed electrospray droplets are demonstrated through protein denaturation using a supercharging reagent as well as two different bimolecular reactions. The average charge state of myoglobin changed from +7.8 to +13.8 when 2.5% sulfolane was mixed with a 200 mM ammonium acetate solution containing the protein when the position of the emitter was scanned in front of the mass spectrometer inlet. The conversion ratio of a bimolecular reaction was changed from 0.98 to 0.04 with varying emitter positions. These results show that the relative flow rates must be carefully monitored because the droplet composition depends strongly on the position of the theta glass emitters. This method can be used to measure the dependence of reaction kinetics on different solution concentrations by using a single emitter and only two solutions.

Recent advances in top-down proteome sample processing ahead of MS analysis

Top-down proteomics is emerging as a preferred approach to investigate biological systems, with objectives ranging from the detailed assessment of a single protein therapeutic, to the complete characterization of every possible protein including their modifications, which define the human proteoform. Given the controlling influence of protein modifications on their biological function, understanding how gene products manifest or respond to disease is most precisely achieved by characterization at the intact protein level. Top-down mass spectrometry (MS) analysis of proteins entails unique challenges associated with processing whole proteins while maintaining their integrity throughout the processes of extraction, enrichment, purification, and fractionation. Recent advances in each of these critical front-end preparation processes, including minimalistic workflows, have greatly expanded the capacity of MS for top-down proteome analysis. Acknowledging the many contributions in MS technology and sample processing, the present review aims to highlight the diverse strategies that have forged a pathway for top-down proteomics. We comprehensively discuss the evolution of front-end workflows that today facilitate optimal characterization of proteoform-driven biology, including a brief description of the clinical applications that have motivated these impactful contributions.

Supercharging reagents in LC-MS/MS hormone analyses: Enhancing ionization, not limit of quantification

One of the critical steps during LC-MS/MS hormone analyses that affects the sensitivity of the assay is the ionization process. Enhancing ionization efficiencies by the addition of supercharging reagents might be one way to improve sensitivity and reduce the limit of quantification (LOQ). Therefore, we investigated whether the addition of the supercharging reagents m-nitrobenzyl alcohol (m-NBA), sulfolane, propylene carbonate, and o-nitroanisole (o-NA) increased ionization efficiency and improved assay LOQ of insulin, oxytocin, sex steroids, and corticosteroids in test solutions. Additionally, the influence of the supercharging reagents was tested in serum samples after sample pretreatment to determine whether ionization would be enhanced similarly in routine analyses and, subsequently, lead to improved sensitivity. The screening experiments showed that the impact of the supercharging reagents varied for each hormone; although the addition of m-NBA increased the signal of all hormones, the other reagents only enhanced ionization efficiencies for some hormones. While the addition of 0.05 v/v% m-NBA and 0.05 v/v% o-NA did result in an increase in peak area in both test solutions and serum samples, it did not significantly improve the signal-to-noise ratio, as a simultaneous increase in noise was observed. In conclusion, even though supercharging reagents can enhance ionization efficiencies of hormones significantly, the addition of these reagents does not result in an improved LOQ for hormone measurements with LC-MS/MS.

Dual Electrospray Ionization Enhancement of Proteins Enabled by DMSO Supercharging Reagent

Supercharging reagents assist protein ionization by producing higher charge states and increasing signal intensities, thus improving sensitivity. Described here is an approach to employ a dual-spray ionization source with DMSO as a supercharging reagent to expand in-source supercharging. Under denaturing conditions, dual-source supercharging enhances ionization up to an order of magnitude for proteins of various properties and sizes, but the effect is not uniform. Efficient mixing of solutions from two nebulizing plumes was observed, which allowed sufficient transfer of supercharging molecules to a protein. The described method and proposed mechanism require at least 2.5% of DMSO to produce visible enhancement.

Immunodetection of rainbow trout IL-8 cleaved-peptide: Tissue bioavailability and potential antibacterial activity in a bacterial infection context

Chemokines such as IL-8 are part of an important group of proinflammatory response molecules, as well as cell recruitment. However, it has been described in both higher vertebrates and fish that IL-8 has an additional functional role by acting as an antimicrobial effector, either directly or by cleavage of a peptide derived from its C-terminal end. Nevertheless, it is still unknown whether this fragment is released in the context of infection by bacterial pathogens and if it could be immunodetected in tissues of infected salmonids. Therefore, the objective of this research was to demonstrate that the C-terminal end of IL-8 from Oncorhynchus mykiss is cleaved, retaining its antibacterial properties, and that is detectable in tissues of infected rainbow trout. SDS-PAGE and mass spectrometry demonstrated the cleavage of a fragment of about 2 kDa when the recombinant IL-8 was subjected to acidic conditions. By chemical synthesis, it was possible to synthesize this fragment called omIL-8α_80-97 peptide, which has antibacterial activity against Gram-negative and Gram-positive bacteria at concentrations over 10 μM. Besides, by fluorescence microscopy, it was possible to locate the omIL-8α_80-97 peptide both on the cell surface and in the cytoplasm of the bacteria, as well as inside the monocyte/macrophage-like cell. Finally, by indirect ELISA, Western blot, and mass spectrometry, the presence of the fragment derived from the C-terminal end of IL-8 was detected in the spleen of trout infected with Piscirickettsia salmonis. The results reported in this work present the first evidence about the immunodetection of an antibacterial, and probably cell-penetrating peptide cleaved from the C-terminal end of IL-8 in monocyte/macrophage-like cell and tissue of infected rainbow trout.

Dissecting the Flash Chemistry of Electrogenerated Reactive Intermediates by Microdroplet Fusion Mass Spectrometry

A novel mass spectrometric method for probing the flash chemistry of electrogenerated reactive intermediates was developed based on rapid collision mixing of electrosprayed microdroplets by using a theta-glass capillary. The two individual microchannels of the theta-glass capillary are asymmetrically or symmetrically fabricated with a carbon bipolar electrode to produce intermediates in situ. Microdroplets containing the newly formed intermediates collide with those of the invoked reactants at sub-10 microsecond level, making it a powerful tool for exploring their ultrafast initial transformations. As a proof-of-concept, we present the identification of the key radical cation intermediate in the oxidative dimerization of 8-methyl-1,2,3,4-tetrahydroquinoline and also the first disclosure of previously hidden nitrenium ion involved reaction pathway in the C-H/N-H cross-coupling between N,N'-dimethylaniline and phenothiazine.

Probing Polyester Branching by Hybrid Trapped Ion-Mobility Spectrometry-Tandem Mass Spectrometry

Trapped ion-mobility spectrometry combined with quadrupole time-of-flight mass spectrometry (TIMS-QTOFMS) was evaluated as a tool for resolving linear and branched isomeric polyester oligomers. Solutions of polyester samples were infused directly into the ion source employing electrospray ionization (ESI). TIMS-MS provides both mobility and m/z data on the formed ions, allowing construction of extracted-ion mobilograms (EIMs). EIMs of polyester molecules showed multimodal patterns, indicating conformational differences among isomers. Subsequent TIMS-MS/MS experiments indicated mobility differences to be caused by (degree of) branching. These assignments were supported by liquid chromatography-TIMS-MS/MS analysis, confirming that direct TIMS-MS provided fast (500 ms/scan) distinction between linear and branched small oligomers. Observing larger oligomers (up to 3000 Da) using TIMS required additional molecular charging to ensure ion entrapment within the mobility window. Molecular supercharging was achieved using m-nitrobenzyl alcohol (NBA). The additional charges on the oligomer structures enhanced mobility separation of isomeric species but also added to the complexity of the obtained fragmentation mass spectra. This complexity could be partly reduced by post-TIMS analyte-decharging applying collision-induced dissociation (CID) prior to Q1 with subsequent isolation of the singly charged ions for further fragmentation. The as-obtained EIM profiles were still quite complex as larger molecules possess more possible structural isomers. Nevertheless, distinguishing between linear and symmetrically branched oligomers was possible based on measured differences in collisional cross sections (CCSs). The established TIMS-QTOFMS approach reliably allows branching information on isomeric polyester molecules up to 3000 Da to be obtained in less than 1 min analysis time.

Evaluation of strategies for overcoming trifluoroacetic acid ionization suppression resulted in single-column intact level, middle-up, and bottom-up reversed-phase LC-MS analyses of antibody biopharmaceuticals

A wide range of strategies for efficient chromatography and high MS sensitivity in reversed-phase LC-MS analysis of antibody biopharmaceuticals and their large derivates has been evaluated. They included replacing trifluoroacetic acid with alternative acidifiers, relevancy of elevated column temperature, use of dedicated stationary phases, and counteraction of the suppression effect of trifluoroacetic acid in electrospray ionization. At the column temperature of 60 °C, which significantly reduces in-column protein degradation, the BioResolve RP mAb Polyphenyl, BioShell IgG C₄ columns performed best using mobile phases with full or partial replacement of trifluoroacetic acid with difluoroacetic acid in the analysis of intact antibodies. Similarly, 0.03% trifluoroacetic acid in combination with 0.07% formic acid is a good alternative in analyzing antibody chains at 60 °C. Collectively, the addition of 3% 1-butanol to the mobile phase acidified with 0.1% formic acid was the most efficient approach to simultaneously achieving good chromatographic separation and MS sensitivity for intact and reduced antibody biopharmaceuticals. Moreover, this mobile phase combined with the BioResolve RP mAb Polyphenyl column was subsequently demonstrated to provide excellent results for peptide mapping of antibody biopharmaceuticals fully comparable with those obtained using a state-of-the-art column for peptide separation, thus opening an avenue for a single-column multilevel analysis of these biotherapeutics.

Solution Condition-Dependent Formation of Gas-Phase Protomers of Alpha-Synuclein in Electrospray Ionization

One of the main characteristics of biomolecular ions in mass spectrometry is their net charge, and a range of approaches exist to either increase or decrease this quantity in the gas phase. In the context of small molecules, it is well known that, in addition to the charge state, the charge site also has a profound effect on an ion's gas-phase behavior; however, this effect has been far less explored for peptides and intact proteins. Methods exist to determine charge sites of protein ions, and others have observed that the interplay of electrostatic repulsion and inherent basicity leads to different sites gaining or losing a charge depending on the total net charge. Here, we report two distinct protonation site isomers ("protomers") of α-synuclein occurring at the same charge state. The protomers showed important differences in their gas-phase fragmentation behavior and were furthermore distinguishable by ion mobility spectrometry. One protomer was produced under standard electrospray conditions, while the other was observed after addition of 10% dimethyl sulfoxide to the protein solution. Charge sites for both protomers were determined using ultraviolet photodissociation.

Charge Retention/Charge Depletion in ESI-MS: Experimental Evidence

The effects of liquid and gas phase additives (chemical modifiers) on the ion signal distribution for Substance P (SP), recorded with a nanoelectrospray setup, are evaluated. Depletion of the higher charge state of Substance P ([SP+3H]³⁺) is observed with polar protic gas phase modifiers. This is attributed to their ability to form larger hydrogen-bonded clusters, whose proton affinity increases with cluster size. These clusters are able to deprotonate the higher charge state. "Supercharging agents" (SCAs) as well as aprotic polar gas phase modifiers, which promote the retention of the higher charge state of Substance P, do not form such large clusters under the given conditions and are therefore not able to deprotonate Substance P. Both SCAs and aprotic modifiers form clusters with the higher charge state, leading to stabilization of the charge. Whereas supercharging agents have low vapor pressures and are therefore enriched in late-stage electrospray droplets, the gas phase modifiers are volatile organic solvents. Collision induced dissociation experiments revealed that the addition of a modifier significantly delays the droplet evaporation and ion release process. This indicates that the droplet takes up the gas phase modifier to a certain extent (accommodation). Depending on the modifier's properties either charge depletion or retention may eventually be promoted.

Study on properties of wooden capillary electrospray ionization mass spectrometry

RATIONALE

In view of the unique properties of wooden materials as electrospray emitters, a novel wooden capillary electrospray ionization (WC-ESI) device was fabricated. The performance of a wooden capillary as an electrospray emitter was investigated by using a wooden capillary instead of the metal emitter of commercial ESI sources.

METHODS

The mass spectrometric measurement of baicalein, emodin and myoglobin was carried out by using wooden capillary (WC) and metal capillary (MC) ESI sources. Contrasting analysis of signal intensity between WC and MC electrospray ionization mass spectrometry (ESI-MS) was implemented at different sample flow rates. The effect of WC-ESI-MS and MC-ESI-MS was evaluated experimentally with electrospray solutions in different solvent ratios.

RESULTS

Generally, the signal generated by WC-ESI-MS was much stronger than that obtained by MC-ESI-MS. In particular, the MS signal in negative ion mode was very strong, which may solve the long-standing problem of low MS signals in negative ion mode, and fully improve the detection efficiency of ESI-MS.

CONCLUSIONS

The signal intensity produced by WC-ESI-MS is significantly higher than that from MC-ESI-MS, and polymerization and electrolysis are reduced; therefore, the spectra become simpler. In addition, it is also tolerant to high flow rates and high aqueous phase samples.

Strong Acid Anions Significantly Increasing the Charge State of Proteins during Electrospray Ionization

Regulation of protein's charge state in electrospray is of great importance to the analysis of proteins. Different methods have been developed so far to increase the charge state of proteins. In this work, we investigated the influence of different anions on the charge state of proteins. Both strong acid anions and weak acid anions were taken into consideration. The results showed that the presence of 5 mM strong acid anions in acidic solutions could significantly increase the charge state of proteins. In comparison, weak acid anions with the same concentration in solution had little impact on the charge state of proteins. The species of the cations in the samples had very limited influence on the charge state. The presence of a certain amount of acid in sample solution was critical to the effect of strong acid anions. Almost no increase of the charge state was observed when no acid was added to the samples. However, remarkable increase of the charge state of myoglobin (Mb) was observed when 0.001% (v/v) acetic acid (HAc) was added to the sample together with 5 mM sodium chloride (NaCl). A higher concentration of acid in samples would further enhance the effect of strong acid anions on the increase of the charge state. Further investigations into the mechanism revealed that the effect of the strong acid anions on the charge state of proteins was based on the unfolding of the protein molecules during electrospray ionization (ESI). The interactions among H⁺, anions, and protein molecules were so strong that it caused the unfolding of protein molecules and resulted in the increasing of proteins' charge states. The key factor that made strong acid anions and weak acid anions different in the results was the hydrolysis of the weak acid anions in acidic solutions. The present work furthers our understanding about electrospray, as well as the regulation of protein charge state. The presence of strong acid anions in acidic solutions can significantly influence the charge state of proteins in electrospray. Attention should be paid to this when regulating the charge state of proteins.

Overcharging Effect in Electrospray Ionization Mass Spectra of Daunomycin-Tuftsin Bioconjugates

Peptide-based small molecule drug conjugates for targeted tumor therapy are currently in the focus of intensive research. Anthracyclines, like daunomycin, are commonly used anticancer drug molecules and are also often applied in peptide-drug conjugates. However, lability of the O-glycosidic bond during electrospray ionization mass spectrometric analysis hinders the analytical characterization of the constructs. “Overprotonation” can occur if daunomycin is linked to positively charged peptide carriers, like tuftsin derivatives. In these molecules, the high number of positive charges enhances the in-source fragmentation significantly, leading to complex mass spectra composed of mainly fragment ions. Therefore, we investigated different novel tuftsin-daunomycin conjugates to find an appropriate condition for mass spectrometric detection. Our results showed that shifting the charge states to lower charges helped to keep ions intact. In this way, a clear spectrum could be obtained containing intact protonated molecules only. Shifting of the protonation states to lower charges could be achieved with the use of appropriate neutral volatile buffers and with tuning the ion source parameters.

Enhancing Sensitivity of Microflow-Based Bottom-Up Proteomics through Postcolumn Solvent Addition

The introduction of more sensitive mass spectrometers allows researchers to adapt front-end liquid chromatography (LC) to individual needs for the analysis of complex proteomes. Where absolute sensitivity is not paramount, it is advantageous to switch from a highly sensitive nanoflow-LC setup, the de facto standard platform in mass-spectrometry (MS)-based discovery proteomics, to a more robust, high-throughput-compatible microflow or conventional-flow setup. To enhance the microflow-LC-MS electrospray process of complex proteomic samples, we tested the effects of different solvents, including 2-propanol, methanol, and acetonitrile, pure or as mixture with dimethyl sulfoxide, which were added postcolumn to the eluting sample. Postcolumn addition of organic solvents strongly enhanced the electrospray efficiency in microflow-LC-MS experiments and improved the sensitivity across the entire gradient and for early eluting peptides by up to 10-fold. Postcolumn solvent addition did not negatively affect chromatographic performance and resulted in an overall 28-36% increase in identifications at both the protein and peptide levels. The presented microflow-LC-MS workflow, including postcolumn solvent addition, can be easily adopted on any LC-MS/MS platform.

A comparative study of the electrospray ionization response of β-O-4' lignin model compounds

Electrospray ionization mass spectrometry has recently become the technique of choice for rapid characterization of lignin degradation products. However, the fundamental question of the relationship between lignin structure and ionization efficiency has not been explored. In this work, we studied the electrospray ionization response of five structurally similar β-O-4' model lignin compounds using lithium cationization in the positive electrospray ionization mode. The studied compounds have the same β-O-4' backbone structure but differ at the α-position by increasing nonpolar side chains. Our results show a correlation between the ionization response and the length of the nonpolar side chain, with analytes having the longest side chain recording the highest ESI response in the full scan mode. Factors affecting the formation of analyte ions and analyte cluster ions were also studied. We have shown for the first time in this work that the introduction of a nonpolar group onto a β-O-4' lignin compound can increase the lithium cationization ESI response in the positive ion mode.

Toward highly sensitive and reproducible LC-MS/MS analysis of MK-8591 phosphorylated anabolites in human peripheral blood mononuclear cells

Aim: MK-8591 (EFdA), a novel anti-HIV nucleoside analog, is converted to mono-, di- and tri-phosphates (MK-8591-MP, MK-8591-DP and MK-8591-TP) intracellularly, among which MK-8591-TP is the active pharmacological form. An ultrasensitive LC-MS/MS assay was required to measure MK-8591-DP and MK-8591-TP levels in human peripheral blood mononuclear cells (PBMCs). Sensitivity and reproducibility were major bottlenecks in these analyses. Materials and methods: Human PBMCs were isolated from blood and lysed with 70/30 methanol/RPMI-1640. An LC-MS/MS method was developed to simultaneously quantify MK-8591-DP and MK-8581-TP in PBMC lysates. Results: Low flow LC and dimethyl sulfoxide mediated signal enhancement enabled an extreme sensitivity with limit of quantitation at 0.1 ng/ml. Assay accuracy was 92.5-106% and precision was 0.7-12.1% for a linear curve range of 0.1-40 ng/ml. Matrix variability and interference liability were comprehensively evaluated. Conclusion: Our study findings and steps taken in addressing clinical sample issues help understand and overcome the challenges facing intracellular nucleotide analog analysis.

Supercharging of Proteins by Salts during Polarity Reversed Nano-Electrospray Ionization

Supercharging is beneficial in many ways to the analysis of proteins by mass spectrometry (MS). In this work, a novel supercharging method was developed. It made use of our previously developed ionization technique: namely, polarity reversed nanoelectrospray ionization (PR-nESI) for the ionization of proteins. Supercharging of proteins was achieved by just adding 1-10 mM of a salt to the sample, such as sodium chloride (NaCl). The charge state of proteins obtained by our method was significantly higher than that by nano-ESI with 1% (v/v) acetic acid (HAc). Different kinds of salts were investigated. Salts with  strong acid anions were capable of supercharging proteins, including chlorides, bromides, iodides, and nitrates. The signal intensity and signal to noise ratio ( S/ N) of proteins were increased at the same time. Phosphates were also found to have a supercharging effect, due to the fact that phosphoric acid was a medium-strong acid. In comparison, salts with weak acid anions had no supercharging effect, such as carbonates, sulfides, acetates, and formates. The species of the salt anion was critical to the supercharging effect, while the species of the salt cation showed little influence on the supercharging effect. Investigations were made into the mechanism of our method. The supercharging effect was caused by interactions between protein molecules and salt anions, as well as the influence of protons. The present work offered us an alternative way for the supercharging of proteins. The use of common salts for supercharging made the procedure more convenient. The concentration of salts needed for supercharging was much lower than those conventionally used for supercharging reagents. Taking into consideration the fact that many biological samples are buffered with phosphates and chlorides, these samples could be directly supercharged by our method without any additional additives. Furthermore, as many salts are nontoxic and can easily be found in a chemical laboratory, the use of salts for supercharging would be a much more practical and economical choice. In addition, the present work also furthered our understandings about the mechanism of supercharging, as well as electrospray.

Enhanced-Fluidity Liquid Chromatography-Mass Spectrometry for Intact Protein Separation and Characterization

Recent advances in the analysis of proteins have increased the demand for more efficient techniques to separate intact proteins. Enhanced-fluidity liquid chromatography (EFLC) involves the addition of liquefied CO₂ to conventional liquid mobile phases. The addition of liquefied CO₂ increases diffusivity and decreases viscosity, which inherently leads to a more efficient separation. Herein, EFLC is applied to hydrophobic interaction chromatography (HIC) stationary phases for the first time to study the impact of liquefied CO₂ to the chromatographic behavior of proteins. The effects of liquefied CO₂ on chromatographic properties, charge state distributions (CSDs), and ionization efficiencies were evaluated. EFLC offered improved chromatographic performance compared to conventional liquid chromatography (LC) methods including a shorter analysis time, better peak shapes, and higher plate numbers. The addition of liquefied CO₂ to the mobile phase provided an electrospray ionization (ESI)-friendly and "supercharging" reagent without sacrificing chromatographic performance, which can be used to improve peptide and protein identification in large-scale application.

Analytical barriers in clinical B-type natriuretic peptide measurement and the promising analytical methods based on mass spectrometry technology

B-type natriuretic peptide (BNP) is a circulating biomarker that is mainly applied in heart failure (HF) diagnosis and to monitor disease progression. Because some identical amino acid sequences occur in the precursor and metabolites of BNP, undesirable cross-reactions are common in immunoassays. This review first summarizes current analytical methods, such as immunoassay- and mass spectrometry (MS)-based approaches, including the accuracy of measurement and the inconsistency of the results. Second, the review presents some promising approaches to resolve the current barriers in clinical BNP measurement, such as how to decrease cross-reactions and increase the measurement consistency. Specific approaches include research on novel BNP assays with higher-specificity chemical antibodies, the development of International System of Units (SI)-traceable reference materials, and the development of structure characterization methods based on state-of-the-art ambient and ion mobility MS technologies. The factors that could affect MS analysis are also discussed, such as biological sample cleanup and peptide ionization efficiency. The purpose of this review is to explore and identify the main problems in BNP clinical measurement and to present three types of approaches to resolve these problems, namely, materials, methods and instruments. Although novel approaches are proposed here, in practice, it is worth noting that the BNP-related peptides including unprocessed proBNP were all measured in clinical BNP assays. Therefore, approaches that aimed to measure a specific BNP or proBNP might be an effective way for the standardization of a particular BNP form measurement, instead of the standardization of “total” immunoreactive BNP assays in clinical at present.

Coaxial Electrospray Ionization for the Study of Rapid In-source Chemistry

Coaxial electrospray has been used effectively for several dual-emitter applications, but has not been utilized for the study of rapid in-source chemistry. In this paper, we report the fabrication of a coaxial, micro-volume dual-emitter through the modification of a manufacturer's standard electrospray probe. This modification creates rapid mixing inside the Taylor cone and the ability to manipulate fast reactions using a variety of solvents and analytes. We demonstrate its potential as a low-cost, dual-emitter assembly for diverse applications through three examples: relative ionization in a biphasic electrospray, hydrogen-deuterium exchange, and protein supercharging. Graphical Abstract.

Enhancing Sensitivity of Liquid Chromatography-Mass Spectrometry of Peptides and Proteins Using Supercharging Agents

Trifluoroacetic acid (TFA) is often used as a mobile phase modifier to enhance reversed phase chromatographic performance. TFA adjusts solution pH and is an ion-pairing agent, but it is not typically suitable for electrospray ionization-mass spectrometry (ESI-MS) and liquid chromatography/MS (LC/MS) because of its significant signal suppression. Supercharging agents elevate peptide and protein charge states in ESI, increasing tandem MS (MS/MS) efficiency. Here, LC/MS protein supercharging was effected by adding agents to LC mobile phase solvents. Significantly, the ionization suppression generally observed with TFA was, for the most part, rescued by supercharging agents, with improved separation efficiency (higher number of theoretical plates) and lowered detection limits.

Phase Separation Behavior of Supercharged Proteins and Polyelectrolytes

Membraneless organelles, like membrane-bound organelles, are essential to cell homeostasis and provide discrete cellular subcompartments. Unlike classical organelles, membraneless organelles possess no physical barrier but rather arise by phase separation of the organelle components from the surrounding cytoplasm or nucleoplasm. Complex coacervation, the liquid-liquid phase separation of oppositely charged polyelectrolytes, is one of several phenomena that are hypothesized to drive the formation and regulation of some membraneless organelles. Studies of the molecular properties of globular proteins that drive complex coacervation are limited as many proteins do not form complexes with oppositely charged macromolecules at neutral pH and moderate ionic strengths. Protein supercharging overcomes this problem and drives complexation with oppositely charged macromolecules. In this work, several distinct cationic supercharged green fluorescent protein (GFP) variants were designed to examine the phase behavior with oppositely charged polyanionic macromolecules. Cationic GFP variants phase separated with oppositely charged macromolecules at various mixing ratios, salt concentrations, and pH values. Efficient protein incorporation in the macromolecule rich phase occurred over a range of protein and polymer mass fractions, but the protein encapsulation efficiency was highest at the midpoint of the phase separation regime. More positively charged proteins phase separated over broader pH and salt ranges than those of proteins with a lower charge density. Interestingly, each GFP variant phase separated at higher salt concentrations with anionic synthetic macromolecules compared to anionic biological macromolecules. Optical microscopy revealed that most variants, depending on solution conditions, formed liquid-liquid phase separations, except for GFP/DNA pairs that formed solid aggregates under all tested conditions.

A candidate liquid chromatography mass spectrometry reference method for the quantification of the cardiac marker 1-32 B-type natriuretic peptide

BACKGROUND

B-type natriuretic peptide (BNP) is a 32 amino acid cardiac hormone routinely measured by immunoassays to diagnose heart failure. While it is reported that immunoassay results can vary up to 45%, no attempt of standardization and/or harmonization through the development of certified reference materials (CRMs) or reference measurement procedures (RMPs) has yet been carried out.

METHODS

B-type natriuretic peptide primary calibrator was quantified traceably to the International System of Units (SI) by both amino acid analysis and tryptic digestion. A method for the stabilization of BNP in plasma followed by protein precipitation, solid phase extraction (SPE) and liquid chromatography (LC) mass spectrometry (MS) was then developed and validated for the quantification of BNP at clinically relevant concentrations (15-150 fmol/g).

RESULTS

The candidate reference method was applied to the quantification of BNP in a number of samples from the UK NEQAS Cardiac Markers Scheme to demonstrate its applicability to generate reference values and to preliminary evaluate the commutability of a potential CRM. The results from the reference method were consistently lower than the immunoassay results and discrepancy between the immunoassays was observed confirming previous data.

CONCLUSIONS

The application of the liquid chromatography-mass spectrometry (LC-MS) method to the UK NEQAS samples and the correlation of the results with the immunoassay results shows the potential of the method to support external quality assessment schemes, to improve understanding of the bias of the assays and to establish RMPs for BNP measurements. Furthermore, the method has the potential to be multiplexed for monitoring circulating truncated forms of BNP.

Improving sensitivity and linear dynamic range of intact protein analysis using a robust and easy to use microfluidic device

We demonstrate an integrated microfluidic LC device coupled to a QTOF capable of improving sensitivity and linearity for intact protein analysis while also tuning the charge state distributions (CSD) of whole antibodies.

Re-configurable, multi-mode contained-electrospray ionization for protein folding and unfolding on the millisecond time scale

Contained-electrospray ionization enables online selection of protein charge states by a direct infusion of reactive vapors and liquids into charged micro-droplets.

Progress and Potential of Imaging Mass Spectrometry Applied to Biomarker Discovery

Mapping provides a direct means to assess the impact of protein biomarkers and puts into context their relevance in the type of cancer being examined. To this end, mass spectrometry imaging (MSI) was developed to provide the needed spatial information which is missing in traditional liquid-based mass spectrometric proteomics approaches. Aptly described as a "molecular histology" technique, MSI gives an additional dimension in characterizing tumor biopsies, allowing for mapping of hundreds of molecules in a single analysis. A decade of developments focused on improving and standardizing MSI so that the technique can be translated into the clinical setting. This review describes the progress made in addressing the technological development that allows to bridge local protein detection by MSI to its identification and to illustrate its potential in studying various aspects of cancer biomarker discovery.

Neutral Loss Is a Very Common Occurrence in Phosphotyrosine-Containing Peptides Labeled with Isobaric Tags

While developing a multiplexed phosphotyrosine peptide quantification assay, an unexpected observation was made: significant neutral loss from phosphotyrosine (pY) containing peptides. Using a 2000-member peptide library, we sought to systematically investigate this observation by comparing unlabeled peptides with the two highest-plex isobaric tags (iTRAQ8 and TMT10) across CID, HCD, and ETD fragmentation using high resolution high mass accuracy Orbitrap instrumentation. We found pY peptide neutral loss behavior was consistent with reduced proton mobility, and does not occur during ETD. The site of protonation at the peptide N-terminus changes from a primary to a tertiary amine as a result of TMT labeling which would increase the gas phase basicity and reduce proton mobility at this site. This change in fragmentation behavior has implications during instrument method development and interpretation of MS/MS spectra, and therefore ensuing follow-up studies. We show how sites not localized to tyrosine by search and site localization algorithms can be confidently reassigned to tyrosine using neutral loss and phosphotyrosine immonium ions. We believe these findings will be of general interest to those studying pY signal transduction using isobaric tags.

Surface-Induced Protein Unfolding in Submicron Electrospray Emitters

The charging of protein ions formed by nanoelectrospray ionization (nanoESI) with tips that are between 1.5 μm and 250 nm in outer diameter is compared. More charging is obtained with the smaller tip sizes for proteins that have a net positive charge in solution, and additional high-charge-state distributions are often observed. A single charge-state distribution of holo-myoglobin ions is produced by nanoESI from a slightly acidified aqueous solution with the micron outer diameter tips, but some apo-myoglobin ions are produced with the submicron tips. In contrast, the charge-state distributions for proteins with a net negative charge in solution do not depend on tip size. Both the formation of high charge states and the appearance of higher-charge-state distributions, as well as the loss of the heme group from myoglobin, indicate that a fraction of the protein population is unfolding with the smaller tips. The increased charging with the smaller tip sizes for proteins with a net positive charge but not for proteins with a net negative charge indicates that the unfolding occurs prior to nanoelectrospray ionization as a result of Coulombic attraction between positively charged protein molecules in solution and the glass surfaces of the emitter tips that are negatively charged. These results demonstrate a novel method for producing highly charged protein ions that does not require exposing the proteins to additional chemicals either in solution or in the gas phase.

Top-down Proteomics: Technology Advancements and Applications to Heart Diseases

INTRODUCTION

Heart diseases are a leading cause of morbidity and mortality for both men and women worldwide, and impose significant economic burdens on the healthcare systems. Despite substantial effort over the last several decades, the molecular mechanisms underlying diseases of the heart remain poorly understood.

AREAS COVERED

Altered protein post-translational modifications (PTMs) and protein isoform switching are increasingly recognized as important disease mechanisms. Top-down high-resolution mass spectrometry (MS)-based proteomics has emerged as the most powerful method for the comprehensive analysis of PTMs and protein isoforms. Here, we will review recent technology developments in the field of top-down proteomics, as well as highlight recent studies utilizing top-down proteomics to decipher the cardiac proteome for the understanding of the molecular mechanisms underlying diseases of the heart. Expert commentary: Top-down proteomics is a premier method for the global and comprehensive study of protein isoforms and their PTMs, enabling the identification of novel protein isoforms and PTMs, characterization of sequence variations, and quantification of disease-associated alterations. Despite significant challenges, continuous development of top-down proteomics technology will greatly aid the dissection of the molecular mechanisms underlying diseases of the hearts for the identification of novel biomarkers and therapeutic targets.

Ultrafast (1 μs) Mixing and Fast Protein Folding in Nanodrops Monitored by Mass Spectrometry

The use of theta-glass emitters and mass spectrometry to monitor reactions that occur as fast as one μs is demonstrated. Acidified aqueous solutions containing unfolded proteins are mixed with aqueous ammonium acetate solutions to increase the solution pH and induce protein folding during nanoelectrospray ionization. Protein charge-state distributions show the extent to which folding occurs, and reaction times are obtained from known protein folding time constants. Shorter reaction times are obtained by decreasing the solution flow rate, and reaction times between 1.0 and 22 μs are obtained using flow rates between 48 and 2880 pL/s, respectively. Remarkably similar reaction times are obtained for three different proteins (Trp-cage, myoglobin, and cytochrome c) with folding time constants that differ by more than an order of magnitude (4.1, 7, and 57 μs, respectively), indicating that the reaction times obtained using rapid mixing from theta-glass emitters are independent of protein identity. A folding time constant of 2.2 μs is obtained for the formation of a β-hairpin structure of renin substrate tetradecapeptide, which is the fastest folding event measured using a rapid mixing technique. The 1.0 μs reaction time obtained here is about an order of magnitude lower than the shortest reaction time probed using a conventional mixer (8 μs). Moreover, this fast reaction time is obtained with a 48 pL/s flow rate, which is 2000-times less than the flow rate required to obtained the 8 μs reaction time using a conventional mixer. These results indicate that rapid mixing with theta-glass emitters can be used to access significantly faster reaction times while consuming substantially less sample than in conventional mixing apparatus.

Capillary Electrophoresis-Mass Spectrometry for Clinical Metabolomics

In clinical metabolomics, capillary electrophoresis-mass spectrometry (CE-MS) has become a very useful technique for the analysis of highly polar and charged metabolites in complex biologic samples. A comprehensive overview of recent developments in CE-MS for metabolic profiling studies is presented. This review covers theory, CE separation modes, capillary coatings, and practical aspects of CE-MS coupling. Attention is also given to sample pretreatment and data analysis strategies used for metabolomics. The applicability of CE-MS for clinical metabolomics is illustrated using samples ranging from plasma and urine to cells and tissues. CE-MS application to large-scale and quantitative clinical metabolomics is addressed. Conclusions and perspectives on this unique analytic strategy are presented.

A multichannel rotating electrospray ionization mass spectrometry (MRESI): instrumentation and plume interactions

A multichannel rotating electrospray ionization (MRESI) mass spectrometry method is described. Plume interactions are also systematically studied.

Desalting protein ions in native mass spectrometry using supercharging reagents

Effects of the supercharging reagents m-NBA and sulfolane on sodium ion adduction to protein ions formed using native mass spectrometry were investigated. There is extensive sodium adduction on protein ions formed by electrospray ionization from aqueous solutions containing millimolar concentrations of NaCl, which can lower sensitivity by distributing the signal of a given charge state over multiple adducted ions and can reduce mass measuring accuracy for large proteins and non-covalent complexes for which individual adducts cannot be resolved. The average number of sodium ions adducted to the most abundant ion formed from ten small (8.6-29 kDa) proteins for which adducts can be resolved is reduced by 58% or 80% on average, respectively, when 1.5% m-NBA or 2.5% sulfolane are added to aqueous solutions containing sodium compared to without the supercharging reagent. Sulfolane is more effective than m-NBA at reducing sodium ion adduction and at preserving non-covalent protein-ligand and protein-protein interactions. Desalting with 2.5% sulfolane enables detection of several glycosylated forms of 79.7 kDa holo-transferrin and NADH bound to the 146 kDa homotetramer LDH, which are otherwise unresolved due to peak broadening from extensive sodium adduction. Although sulfolane is more effective than m-NBA at protein ion desalting, m-NBA reduces salt clusters at high m/z and can increase the signal-to-noise ratios of protein ions by reducing chemical noise. Desalting is likely a result of these supercharging reagents binding sodium ions in solution, thereby reducing the sodium available to adduct to protein ions.

Supermetallization of peptides and proteins during electrospray ionization

The formation of metal-peptide complexes during electrospray ionization (ESI) is a widely known phenomenon and is often considered to be undesirable. Such effect considerably limits the use of ESI mass spectrometry for the investigation of biologically relevant metal-peptide compounds that are present in the solution and play critical roles in many bioprocesses such as progression of neurodegenerative diseases. In the article, it is demonstrated that under specific conditions such as high temperature of the desolvating capillary, an interesting effect, which can be called as 'supermetallization', occurs. Using a model peptide Αβ amyloid domain 1-16, it was observed that an increase in the temperature of the desolvating capillary results in multiple substitutions of hydrogen atoms by Zn atoms in this peptide. At high temperatures (T ~ 400 °C), up to 11 zinc atoms can be covalently bound to (1-16) Αβ. It was observed that supermetallization of (1-16) Αβ depends on the solvent composition and pH. Supermetallization was also demonstrated for proteins, such as ubiquitin and cytochrome C. That proves that the supermetallization is a general phenomenon for peptides and proteins. For the structural investigation of supermetallized complexes, electron-capture dissociation (ECD) fragmentation was applied. The effect of hydrogen rearranging during ECD was observed. In addition, quantum chemical calculations were used to estimate the possible structures of different supermetallized complexes. These results allow a more deep understanding of the limitations of the use of ESI mass spectrometry for the investigation of biologically relevant metal-peptide complexes. Copyright © 2015 John Wiley & Sons, Ltd.

High-throughput bioconjugation for enhanced 193 nm photodissociation via droplet phase initiated ion/ion chemistry using a front-end dual spray reactor

Fast online chemical derivatization of peptides with an aromatic label for enhanced 193 nm ultraviolet photodissociation (UVPD) is demonstrated using a dual electrospray reactor implemented on the front-end of a linear ion trap (LIT) mass spectrometer. The reactor facilitates the intersection of protonated peptides with a second population of chromogenic 4-formyl-1,3-benzenedisulfonic acid (FBDSA) anions to promote real-time formation of ion/ion complexes at atmospheric pressure. Subsequent collisional activation of the ion/ion intermediate results in Schiff base formation generated via reaction between a primary amine in the peptide cation and the aldehyde moiety of the FBDSA anion. Utilizing 193 nm UVPD as the subsequent activation step in the MS(3) workflow results in acquisition of greater primary sequence information relative to conventional collision induced dissociation (CID). Furthermore, Schiff-base-modified peptides exhibit on average a 20% increase in UVPD efficiency compared to their unmodified counterparts. Due to the efficiency of covalent labeling achieved with the dual spray reactor, we demonstrate that this strategy can be integrated into a high-throughput LC-MS(n) workflow for rapid derivatization of peptide mixtures.