Gas-phase chemistry of multiply charged bioions in analytical mass spectrometry

Enhancing Spatial Resolution in Tandem Mass Spectrometry Ion/Ion Reaction Imaging Experiments through Image Fusion

We have recently developed a charge inversion ion/ion reaction to selectively derivatize phosphatidylserine lipids via gas-phase Schiff base formation. This tandem mass spectrometry (MS/MS) workflow enables the separation and detection of isobaric lipids in imaging mass spectrometry, but the images acquired using this workflow are limited to relatively poor spatial resolutions due to the current time and limit of detection requirements for these ion/ion reaction imaging mass spectrometry experiments. This trade-off between chemical specificity and spatial resolution can be overcome by using computational image fusion, which combines complementary information from multiple images. Herein, we demonstrate a proof-of-concept workflow that fuses a low spatial resolution (i.e., 125 μm) ion/ion reaction product ion image with higher spatial resolution (i.e., 25 μm) ion images from a full scan experiment performed using the same tissue section, which results in a predicted ion/ion reaction product ion image with a 5-fold improvement in spatial resolution. Linear regression, random forest regression, and two-dimensional convolutional neural network (2-D CNN) predictive models were tested for this workflow. Linear regression and 2D CNN models proved optimal for predicted ion/ion images of PS 40:6 and SHexCer d38:1, respectively.

Implementing 1.5 mm internal diameter columns into analytical workflows

The use of smaller column diameters in liquid chromatography (LC) is often associated with capillary LC. Although there are many analytical benefits gained by adapting this format, routine use continues to be challenging due to column fragility and extra column dispersion. Bridging the gap between routinely used 2.1 mm columns and capillary bore columns allows for a sequential but far from insignificant increase in performance without the need for specialized equipment associated with very low dispersion LC systems. Moreover, an incremental decrease in column internal diameter (i.d.) allows for similar mass load (avoiding column overload that may be observed in much larger decreases in i.d. without trapping) and thus an increase in measured signal. As such, 1.5 mm i.d. columns provide an alternative intermediate dimension between the more regularly used 2.1 mm i.d. columns and 1 mm i.d. columns. These columns balance an increase in sensitivity compared to 2.1 mm i.d. columns (theoretically doubling the time-domain peak area in mass sensitive detectors for the same mass load), while mitigating the efficiency losses due to extra-column dispersion effects that are commonly observed with 1.0 mm i.d. columns. Here, the use of 1.5 mm i.d. columns was applied to LC/UV analysis of small molecules and LC/MS methods for the analysis of monoclonal antibodies. With equivalent mass load on column, the 1.5 mm i.d. columns provide two-to-threefold improvement in analyte peak area signal for small molecules as well as intact, subunit, and peptide levels of antibody analysis. Peak height was also increased using the 1.5 mm i.d. column, although the scale of increase varies between isocratic and gradient modes, likely due to differences in system dispersion effects and variation in electrospray ionization efficiency at different flow rates.

Native mass spectrometry-based metabolomics identifies metal-binding compounds

Although metals are essential for the molecular machineries of life, systematic methods for discovering metal-small molecule complexes from biological samples are limited. Here, we describe a two-step native electrospray ionization-mass spectrometry method, in which post-column pH adjustment and metal infusion are combined with ion identity molecular networking, a rule-based data analysis workflow. This method enabled the identification of metal-binding compounds in complex samples based on defined mass (m/z) offsets of ion species with the same chromatographic profiles. As this native electrospray metabolomics approach is suited to the use of any liquid chromatography-mass spectrometry system to explore the binding of any metal, this method has the potential to become an essential strategy for elucidating metal-binding molecules in biology.

Characterization of the Streptomyces coelicolor Glycoproteome Reveals Glycoproteins Important for Cell Wall Biogenesis

The physiological role of protein O-glycosylation in prokaryotes is poorly understood due to our limited knowledge of the extent of their glycoproteomes. In Actinobacteria, defects in protein O-mannosyl transferase (Pmt)-mediated protein O-glycosylation have been shown to significantly retard growth (Mycobacterium tuberculosis and Corynebacterium glutamicum) or result in increased sensitivities to cell wall-targeting antibiotics (Streptomyces coelicolor), suggesting that protein O-glycosylation has an important role in cell physiology. Only a single glycoprotein (SCO4142, or PstS) has been identified to date in S. coelicolor Combining biochemical and mass spectrometry-based approaches, we have isolated and characterized the membrane glycoproteome in S. coelicolor A total of ninety-five high-confidence glycopeptides were identified which mapped to thirty-seven new S. coelicolor glycoproteins and a deeper understanding of glycosylation sites in PstS. Glycosylation sites were found to be modified with up to three hexose residues, consistent with what has been observed previously in other Actinobacteria S. coelicolor glycoproteins have diverse roles and functions, including solute binding, polysaccharide hydrolases, ABC transporters, and cell wall biosynthesis, the latter being of potential relevance to the antibiotic-sensitive phenotype of pmt mutants. Null mutants in genes encoding a putative d-Ala-d-Ala carboxypeptidase (SCO4847) and an l,d-transpeptidase (SCO4934) were hypersensitive to cell wall-targeting antibiotics. Additionally, the sco4847 mutants displayed an increased susceptibility to lysozyme treatment. These findings strongly suggest that both glycoproteins are required for maintaining cell wall integrity and that glycosylation could be affecting enzyme function.IMPORTANCE In prokaryotes, the role of protein glycosylation is poorly understood due to our limited understanding of their glycoproteomes. In some Actinobacteria, defects in protein O-glycosylation have been shown to retard growth and result in hypersensitivity to cell wall-targeting antibiotics, suggesting that this modification is important for maintaining cell wall structure. Here, we have characterized the glycoproteome in Streptomyces coelicolor and shown that glycoproteins have diverse roles, including those related to solute binding, ABC transporters, and cell wall biosynthesis. We have generated mutants encoding two putative cell wall-active glycoproteins and shown them to be hypersensitive to cell wall-targeting antibiotics. These findings strongly suggest that both glycoproteins are required for maintaining cell wall integrity and that glycosylation affects enzyme function.

Investigation of Ion Transmission Effects on Intact Protein Quantification in a Triple Quadrupole Mass Spectrometer

Recently, direct intact protein quantitation using triple quadrupole mass spectrometry (QqQ-MS) and multiple reaction monitoring (MRM) was demonstrated (J. Am. Soc. Mass Spectrom. 27, 886-896 (2016)). Even though QqQ-MS is known to provide extraordinary detection sensitivity for quantitative analysis, we found that intact proteins exhibited a less than 5% ion transmission from the first quadrupole to the third quadrupole mass analyzer in the presence of zero collision energy (ZCE). With the goal to enhance intact protein quantitation sensitivity, ion scattering effects, proton transfer effects, and mass filter resolution widths were examined for their contributions to the lost signal. Protein standards myoglobin and ubiquitin along with small molecules reserpine and vancomycin were analyzed together with various collision induced dissociation (CID) gases (N₂, He, and Ar) at different gas pressures. Mass resolution settings played a significant role in reducing ion transmission signal. By narrowing the mass resolution window by 0.35 m/z on each side, roughly 75%-90% of the ion signal was lost. The multiply charged proteins experienced additional proton transfer effects, corresponding to 10-fold signal reduction. A study of increased sensitivity of the method was also conducted with various MRM summation techniques. Although the degree of enhancement was analyte-dependent, an up to 17-fold increase in sensitivity was observed for ubiquitin using a summation of multiple MRM transitions. Biological matrix, human urine, and equine plasma were spiked with proteins to demonstrate the specificity of the method. This study provides additional insight into optimizing the use and sensitivity of QqQ-MS for intact protein quantification. Graphical Abstract ᅟ.

Flame Atmospheric Pressure Chemical Ionization Coupled with Negative Electrospray Ionization Mass Spectrometry for Ion Molecule Reactions

Flame atmospheric pressure chemical ionization (FAPCI) combined with negative electrospray ionization (ESI) mass spectrometry was developed to detect the ion/molecule reactions (IMRs) products between nitric acid (HNO₃) and negatively charged amino acid, angiotensin I (AI) and angiotensin II (AII), and insulin ions. Nitrate and HNO₃-nitrate ions were detected in the oxyacetylene flame, suggesting that a large quantity of nitric acid (HNO₃) was produced in the flame. The HNO₃ and negatively charged analyte ions produced by a negative ESI source were delivered into each arm of a Y-shaped stainless steel tube where they merged and reacted. The products were subsequently characterized with an ion trap mass analyzer attached to the exit of the Y-tube. HNO₃ showed the strongest affinity to histidine and formed (M_histidine-H+HNO₃)^- complex ions, whereas some amino acids did not react with HNO₃ at all. Reactions between HNO₃ and histidine residues in AI and AII resulted in the formation of dominant [M_AI-H+(HNO₃)]^- and [M_AII-H+(HNO₃)]^- ions. Results from analyses of AAs and insulin indicated that HNO₃ could not only react with basic amino acid residues, but also with disulfide bonds to form [M-3H+(HNO₃)_n]^3- complex ions. This approach is useful for obtaining information about the number of basic amino acid residues and disulfide bonds in peptides and proteins. Graphical Abstract ᅟ.

Design of a TW-SLIM Module for Dual Polarity Confinement, Transport, and Reactions

Here we describe instrumental approaches for performing dual polarity ion confinement, transport, ion mobility separations, and reactions in structures for lossless ion manipulations (SLIM). Previous means of ion confinement in SLIM, based upon rf-generated pseudopotentials and DC fields for lateral confinement, cannot trap ions of opposite polarity simultaneously. Here we explore alternative approaches to provide simultaneous lateral confinement of both ion polarities. Traveling wave ion mobility (IM) separations experienced in such SLIM cause ions of both polarities to migrate in the same directions and exhibit similar separations. The ion motion (and relative motion of the two polarities) under both surfing and IM separation conditions are discussed. In surfing conditions the two polarities are transported losslessly and non-reactively in their respective potential minima (higher absolute voltage regions confine negative polarities, and lower absolute potential regions are populated by positive polarities). In separation mode, where ions roll over an overtaking traveling wave, the two polarities can interact during the rollovers. Strategies to minimize overlap of the two ion populations to prevent reactive losses during separations are presented. A theoretical treatment of the time scales over which two populations (injected into a DC field-free region of the dual polarity SLIM device) interact is considered, and SLIM designs for allowing ion/ion interactions and other manipulations with dual polarities at 4 Torr are presented. Graphical Abstract ᅟ.

Bacterial Electron Transfer Chains Primed by Proteomics

Electron transport phosphorylation is the central mechanism for most prokaryotic species to harvest energy released in the respiration of their substrates as ATP. Microorganisms have evolved incredible variations on this principle, most of these we perhaps do not know, considering that only a fraction of the microbial richness is known. Besides these variations, microbial species may show substantial versatility in using respiratory systems. In connection herewith, regulatory mechanisms control the expression of these respiratory enzyme systems and their assembly at the translational and posttranslational levels, to optimally accommodate changes in the supply of their energy substrates. Here, we present an overview of methods and techniques from the field of proteomics to explore bacterial electron transfer chains and their regulation at levels ranging from the whole organism down to the Ångstrom scales of protein structures. From the survey of the literature on this subject, it is concluded that proteomics, indeed, has substantially contributed to our comprehending of bacterial respiratory mechanisms, often in elegant combinations with genetic and biochemical approaches. However, we also note that advanced proteomics offers a wealth of opportunities, which have not been exploited at all, or at best underexploited in hypothesis-driving and hypothesis-driven research on bacterial bioenergetics. Examples obtained from the related area of mitochondrial oxidative phosphorylation research, where the application of advanced proteomics is more common, may illustrate these opportunities.

Mass spectrometry-based detection and assignment of protein posttranslational modifications

Recent advances in mass spectrometry (MS)-based proteomics allow the identification and quantitation of thousands of posttranslational modification (PTM) sites in a single experiment. This follows from the development of more effective class enrichment strategies, new high performance instrumentation and bioinformatic algorithms with rigorous scoring strategies. More widespread use of these combined capabilities have led to a vast expansion in our knowledge of the complexity of biological processes mediated by PTMs. The classes most actively pursued include phosphorylation, ubiquitination, O-GlcNAcylation, methylation, and acetylation. Very recently succinylation, SUMOylation, and citrullination have emerged. Among the some 260 000 PTM sites that have been identified in the human proteome thus far, only a few have been assigned to key regulatory and/or other biological roles. Here, we provide an update of MS-based PTM analyses, with a focus on current enrichment strategies coupled with revolutionary advances in high performance MS. Furthermore, we discuss examples of the discovery of recently described biological roles of PTMs and address the challenges of defining site-specific functions.

Gas phase reactivity of carboxylates with N-hydroxysuccinimide esters

N-hydroxysuccinimide (NHS) esters have been used for gas-phase conjugation reactions with peptides at nucleophilic sites, such as primary amines (N-terminus, ε-amine of lysine) or guanidines, by forming amide bonds through a nucleophilic attack on the carbonyl carbon. The carboxylate has recently been found to also be a reactive nucleophile capable of initiating a similar nucleophilic attack to form a labile anhydride bond. The fragile bond is easily cleaved, resulting in an oxygen transfer from the carboxylate-containing species to the reagent, nominally observed as a water transfer. This reactivity is shown for both peptides and non-peptidic species. Reagents isotopically labeled with O(18) were used to confirm reactivity. This constitutes an example of distinct differences in reactivity of carboxylates between the gas phase, where they are shown to be reactive, and the solution phase, where they are not regarded as reactive with NHS esters.

Gas phase reactivity of carboxylates with N-hydroxysuccinimide esters

N-hydroxysuccinimide (NHS) esters have been used for gas-phase conjugation reactions with peptides at nucleophilic sites, such as primary amines (N-terminus, ε-amine of lysine) or guanidines, by forming amide bonds through a nucleophilic attack on the carbonyl carbon. The carboxylate has recently been found to also be a reactive nucleophile capable of initiating a similar nucleophilic attack to form a labile anhydride bond. The fragile bond is easily cleaved, resulting in an oxygen transfer from the carboxylate-containing species to the reagent, nominally observed as a water transfer. This reactivity is shown for both peptides and non-peptidic species. Reagents isotopically labeled with O(18) were used to confirm reactivity. This constitutes an example of distinct differences in reactivity of carboxylates between the gas phase, where they are shown to be reactive, and the solution phase, where they are not regarded as reactive with NHS esters.

Top-down proteomics by means of Orbitrap mass spectrometry

Top-down proteomics has become a popular approach for the analysis of intact proteins. The term "top down" has been coined for the analysis of proteins not involving any enzymatic or chemical cleavage but rather the ionization of the protein as a sound molecule and mass analysis of intact species and fragment ions thereof produced upon dissociation inside a mass spectrometer. One or several charge states of the protein are mass-isolated and subjected to dissociation (MS/MS) in the gas phase. The obtained fragment masses, predominantly from cleavages of the protein along its amino acid backbone, are directly related to the intact protein. Using bioinformatics tools the fragment masses are matched against a known protein sequence or can alternatively be used for partial or full de novo sequencing, depending on the size of the protein and the number of fragment ions obtained. Moreover, this approach provides global information about modification states of proteins including the number and types of isoforms and their stoichiometry and allows for the precise localization of modifications within the amino acid sequence. Top-down analysis of a single, purified protein can be performed by matrix-assisted laser desorption ionization or electrospray ionization upon direct infusion without online chromatographic separation, whereas top-down analysis of complex protein mixtures makes pre-fractionation combined with an efficient front-end chromatographic separation coupled online to the mass spectrometer inevitable.

Covalent and non-covalent binding in the ion/ion charge inversion of peptide cations with benzene-disulfonic acid anions

Protonated angiotensin II and protonated leucine enkephalin-based peptides, which included YGGFL, YGGFLF, YGGFLH, YGGFLK and YGGFLR, were subjected to ion/ion reactions with the doubly deprotonated reagents 4-formyl-1,3-benzenedisulfonic acid (FBDSA) and 1,3-benzenedisulfonic acid (BDSA). The major product of the ion/ion reaction is a negatively charged complex of the peptide and reagent. Following dehydration of [M + FBDSA-H](-) via collisional-induced dissociation (CID), angiotensin II (DRVYIHPF) showed evidence for two product populations, one in which a covalent modification has taken place and one in which an electrostatic modification has occurred (i.e. no covalent bond formation). A series of studies with model systems confirmed that strong non-covalent binding of the FBDSA reagent can occur with subsequent ion trap CID resulting in dehydration unrelated to the adduct. Ion trap CID of the dehydration product can result in cleavage of amide bonds in competition with loss of the FBDSA adduct. This scenario is most likely for electrostatically bound complexes in which the peptide contains both an arginine residue and one or more carboxyl groups. Otherwise, loss of the reagent species from the complex, either as an anion or as a neutral species, is the dominant process for electrostatically bound complexes. The results reported here shed new light on the nature of non-covalent interactions in gas phase complexes of peptide ions that can be used in the rationale design of reagent ions for specific ion/ion reaction applications.

Dissociation Behavior of Tryptic and Intramolecular Disulfide-linked Peptide Ions Modified in the Gas Phase via Ion/Ion Reactions

Protonated tryptic peptides, somatostatin-14, and oxytocin have been subjected to reactions with doubly deprotonated 4-formyl-1,3-benzenedisulfonic acid (FBDSA) in the gas phase. The major product is a negatively-charged complex comprised of the peptide and the reagent. Upon dehydration of the complex, all peptides show evidence for Schiff base formation involving a primary amine of the peptide. Some peptides also show evidence for the formation of a relatively strong electrostatic interaction without Schiff base formation (i.e., a mixture of isomeric precursor ions is generated upon dehydration of the complex). Ion trap collision-induced dissociation of the dehydration products from all peptides examined gave distinct product ion spectra relative to the deprotonated and protonated forms of the peptides. The distinct behavior of the modified ions is attributed to the highly stable charge carrying sulfonate group, which tends to inhibit intramolecular proton transfer in negatively charged species. Modified anions of the peptides with an intramolecular disulfide linkage show evidence for cleavage of both the disulfide linkage and an amide bond in the loop defined by the disulfide bond. Modification of protonated peptides via charge inversion with FBDSA is a useful means for generating novel and distinct ion-types that can provide complementary structural information upon subsequent activation to that obtained from dissociation of protonated or deprotonated forms of the peptide.

Electron transfer dissociation mass spectrometry in proteomics

Mass spectrometry has rapidly evolved to become the platform of choice for proteomic analysis. While CID remains the major fragmentation method for peptide sequencing, electron transfer dissociation (ETD) is emerging as a complementary method for the characterization of peptides and post-translational modifications (PTMs). Here, we review the evolution of ETD and some of its newer applications including characterization of PTMs, non-tryptic peptides and intact proteins. We will also discuss some of the unique features of ETD such as its complementarity with CID and the use of alternating CID/ETD along with issues pertaining to analysis of ETD data. The potential of ETD for applications such as multiple reaction monitoring and proteogenomics in the future will also be discussed.

Structural Characterization of Carbohydrates by Fourier Transform Tandem Mass Spectrometry

Fourier transform tandem mass spectrometry (MS/MS) provides high mass accuracy, high sensitivity, and analytical versatility and has therefore emerged as an indispensable tool for structural elucidation of biomolecules. Glycosylation is one of the most common posttranslational modifications, occurring in ~50% of proteins. However, due to the structural diversity of carbohydrates, arising from non-template driven biosynthesis, achievement of detailed structural insight is highly challenging. This review briefly discusses carbohydrate sample preparation and ionization methods, and highlights recent developments in alternative high-resolution MS/MS strategies, including infrared multiphoton dissociation (IRMPD), electron capture dissociation (ECD), and electron detachment dissociation (EDD), for carbohydrates with a focus on glycans and proteoglycans from mammalian glycoproteins.