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Bell RJ, Hage DS, Dodds ED. Two-Dimensional Fourier Transform Ion Cyclotron Resonance Mass Spectrometry of N-Linked Glycopeptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1208-1216. [PMID: 38713472 DOI: 10.1021/jasms.4c00034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Glycosylation is a common modification across living organisms and plays a central role in understanding biological systems and disease. Our ability to probe the gylcome has grown exponentially in the past several decades. However, further improvements to the analytical toolbox available to researchers would allow for increased capabilities to probe structure and function of biological systems and to improve disease treatment. This article applies the developing technique of two-dimensional Fourier transform ion cyclotron resonance mass spectrometry to a glycoproteomic workflow for the standard glycoproteins coral tree lectin (CTL) and bovine ribonuclease B (BRB) to demonstrate its feasibility as a tool for glycoproteomic workflows. 2D infrared multiphoton dissociation and electron capture dissociation spectra of CTL reveal comparable structural information to their 1D counterparts, confirming the site of glycosylation and monosaccharide composition of the glycan. Spectra collected in 2D of BRB reveal correlation lines of fragment ion scans and vertical precursor ion scans for data collected using infrared multiphoton dissociation and diagonal cleavage lines for data collected by electron capture dissociation. The use of similar techniques for glycoproteomic analysis may prove valuable in instances where chromatographic separation is undesirable or quadrupole isolation is insufficient.
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Bell RJ, Hage DS, Dodds ED. Two-Dimensional Fourier Transform Ion Cyclotron Resonance Mass Spectrometry by Matrix-Assisted Laser Desorption Ionization. Anal Chem 2024; 96:6584-6587. [PMID: 38619932 DOI: 10.1021/acs.analchem.3c05601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Two-dimensional Fourier transform ion cyclotron resonance (2D FTICR) mass spectrometry is a developing form of data-independent acquisition that allows for the simultaneous fragmentation and correlation of fragment ions to their precursors across a range of m/z values. The modern usage of 2D FTICR is performed using electrospray ionization (ESI) as the dried droplet preparation for matrix-assisted laser desorption ionization (MALDI) does not produce a consistent packet of ions over a number of scans. This work uses pneumatic spray techniques from mass spectrometry imaging to create a homogeneous surface for use with MALDI as an ionization source for 2D FTICR. A mixture of peptides and matrix was deposited onto a glass slide using an HTX pneumatic sprayer. MALDI was then used to ionize the peptide mixture for use with a standard 2D FTICR pulse sequence. The generated 2D spectrum reveals comparable structural information to spectra collected in a 1D experiment. Artifacts observed in the collected 2D MALDI spectra do not significantly differ from those expected from 2D ESI spectra.
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Zhang C, Schumacher KN, Dodds ED, Hage DS. Glycoprotein analysis using lectin microcolumns and capillary electrophoresis: Characterization of alpha 1-acid glycoprotein by combined separation methods. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1179:122855. [PMID: 34274643 DOI: 10.1016/j.jchromb.2021.122855] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 07/02/2021] [Accepted: 07/05/2021] [Indexed: 11/17/2022]
Abstract
Separations based on combinations of 2.1 mm I.D. high-performance affinity microcolumns and capillary electrophoresis were developed and used to characterize the glycoforms of an intact glycoprotein. Human alpha1-acid glycoprotein (AGP) was used as a model analyte due to its heterogeneous glycosylation resulting from variations in its degree of branching, fucosylation, and number of sialic acids. Three separation formats were examined based on microcolumns that contained the lectins concanavalin A (Con A) or Aleuria aurantia lectin (AAL). These microcolumns were used with one another or in combination with capillary electrophoresis. N-Glycan analysis of the non-retained and retained AGP fractions was carried out by using PNGase F digestion and nanoflow electrospray ionization mass spectrometry. Con A microcolumns were found to selectively enrich AGP that contained bi-antennary N-glycans, while AAL microcolumns retained AGP with fucose-containing N-glycans. Results from these separation methods indicated that fucosylation of the N-linked glycans was more abundant when a high degree of branching was present in AGP. Sialic acid residues were more abundant when higher degrees of branching and more fucose residues were present in AGP. The separation and analysis methods that were developed could be used with relatively small amounts of AGP and can be adapted for use with other intact glycoproteins.
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Yue H, Jiang J, Taylor AJ, Leite ADL, Dodds ED, Du L. Outer Membrane Vesicle-Mediated Codelivery of the Antifungal HSAF Metabolites and Lytic Polysaccharide Monooxygenase in the Predatory Lysobacter enzymogenes. ACS Chem Biol 2021; 16:1079-1089. [PMID: 34032403 DOI: 10.1021/acschembio.1c00260] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Lysobacter are new biocontrol agents known for their prolific production of lytic enzymes and bioactive metabolites. L. enzymogenes is a predator of fungi and produces several structurally distinct antimicrobial compounds, such as the antifungal HSAF (heat stable antifungal factor) and analogs. The mechanism by which L. enzymogenes interacts with fungal prey is not well understood. Here, we found that the production of HSAF and analogs in L. enzymogenes OH11 was significantly induced in media supplemented with ground fungal mycelia or chitin. In the OH11 genome, we identified a gene (LeLPMO10A) that was annotated to encode a chitin-binding protein. The stimulation of HSAF and analogs by chitin was diminished when LeLPMO10A was deleted. We expressed the gene in E. coli and demonstrated that purified LeLPMO10A oxidatively cleaved chitin into oligomeric products, including 1,5 δ-lactones and aldonic acids. The results revealed that LeLPMO10A encodes a lytic polysaccharide monooxygenase, which has not been reported in Lysobacter. The metabolite analysis, antifungal assay, and proteomic analysis showed that the antifungal compounds and the chitin-cleaving LeLPMO10A are colocalized in outer membrane vesicles. The enzymatic products that resulted from in vitro LeLPMO10A-cleaved chitin also significantly induced HSAF and analogs in OH11. Scanning electron microscopic analysis indicated that spherical vesicles were formed outside of OH11 cells, and fewer OH11 cells were observed to attach to fungal hyphae when LeLPMO10A was deleted. Together, the study revealed a previously uncharacterized synergistic strategy utilized by the predatory Lysobacter during interaction with fungal prey.
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Bidne KL, Rister AL, McCain AR, Hitt BD, Dodds ED, Wood JR. Maternal obesity alters placental lysophosphatidylcholines, lipid storage, and the expression of genes associated with lipid metabolism‡. Biol Reprod 2020; 104:197-210. [PMID: 33048132 DOI: 10.1093/biolre/ioaa191] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/21/2020] [Accepted: 10/09/2020] [Indexed: 02/06/2023] Open
Abstract
Dyslipidemia is a characteristic of maternal obesity and previous studies have demonstrated abnormalities in fatty acid oxidation and storage in term placentas. However, there is little information about the effect of pre-pregnancy obesity on placental lipid metabolism during early pregnancy. The objective of this study was to determine the relationship between lipid profiles and markers of metabolism in placentas from obese and lean dams at midgestation. Mice were fed a western diet (WD) or normal diet (ND) and lysophosphatidylcholines (LPCs) and/or phosphatidylcholines (PCs) were measured in dam circulation and placenta sections using liquid chromatography-tandem mass spectrometry and mass spectrometry imaging, respectively. In WD dam, circulating LPCs containing 16:1, 18:1, 20:0, and 20:3 fatty acids were increased and 18:2 and 20:4 were decreased. In WD placenta from both sexes, LPC 18:1 and PC 36:1 and 38:3 were increased. Furthermore, there were moderate to strong correlations between LPC 18:1, PC 36:1, and PC 38:3. Treatment-, spatial-, and sex-dependent differences in LPC 20:1 and 20:3 were also detected. To identify genes that may regulate diet-dependent differences in placenta lipid profiles, the expression of genes associated with lipid metabolism and nutrient transport was measured in whole placenta and isolated labyrinth using droplet digital PCR and Nanostring nCounter assays. Several apolipoproteins were increased in WD placentas. However, no differences in nutrient transport or fatty acid metabolism were detected. Together, these data indicate that lipid storage is increased in midgestation WD placentas, which may lead to lipotoxicity, altered lipid metabolism and transport to the fetus later in gestation.
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Kelly MI, Dodds ED. Parallel Determination of Polypeptide and Oligosaccharide Connectivities by Energy-Resolved Collison-Induced Dissociation of Protonated O-Glycopeptides Derived from Nonspecific Proteolysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:624-632. [PMID: 32126781 PMCID: PMC7164384 DOI: 10.1021/jasms.9b00065] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Collision-induced dissociation (CID) is by far the most broadly applied dissociation method used for tandem mass spectrometry (MS/MS). This includes MS/MS-based structural interrogation of glycopeptides for applications in glycoproteomics. The end goal of such measurements is to determine the monosaccharide connectivity of the glycan, the amino acid sequence of the peptide, and the site of glycosylation for each glycopeptide of interest. In turn, this allows inferences with respect to the glycoprofile of the intact glycoprotein. For glycopeptide analysis, CID is best known for the ability to determine glycosidic topology of the oligosaccharide group; however, CID has also been shown to produce amide bond cleavage of the polypeptide group. Whether structural information is obtained for the glycan or the peptide has been found to depend on the applied collision energy. While these energy-resolved fragmentation pathways have been the subject of several studies on N-linked glycopeptides, there remains a dearth of similar work on O-linked glycopeptides. In this study, MS/MS via CID was shown to provide substantial peptide backbone fragmentation, in addition to glycosidic fragmentation, in an energy-dependent manner. While qualitatively similar to previous findings for N-glycopeptides, the energy-resolved CID (ER-CID) of O-glycopeptides was found to be substantially more sensitive to the collision energy setting. Thus, deliberately obtaining either glycan or peptide dissociation is a more delicate undertaking for O-glycopeptides. Establishing a more complete understanding of O-glycopeptide ER-CID is likely to have a substantive impact on how O-glycoproteomic analysis is approached in the future.
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Gelb AS, Lai R, Li H, Dodds ED. Composition and charge state influence on the ion-neutral collision cross sections of protonated N-linked glycopeptides: an experimental and theoretical deconstruction of coulombic repulsion vs. charge solvation effects. Analyst 2020; 144:5738-5747. [PMID: 31453603 DOI: 10.1039/c9an00875f] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Ion mobility spectrometry (IMS) is of significant interest as a platform for glycoanalysis. While much attention has been focused on the resolution of isomeric carbohydrates and glycoconjugates, another appealing aspect of IMS is the ability to sort different classes of biomolecules into distinct regions of mass vs. mobility space. This capability has potential to greatly simplify glycoproteomic analyses, as glycosylated and non-glycosylated peptides can be rapidly partitioned in the gas phase. Nevertheless, the physical and chemical characteristics of glycopeptides that dictate their mass vs. mobility loci have yet to be systematically investigated. This report presents an IMS study of model protonated glycopeptide ions with systematically varied oligosaccharide topologies, polypeptide sequences, and charge states. In all, over 110 ion-neutral collision cross sections (CCSs) were measured and analyzed in the context of the physicochemical characteristics of the analytes. Glycan size and composition emerged as a decisive factor in dictating the CCS space occupied by the glycopeptides and exerted this influence in a charge state dependent fashion. Furthermore, elongation of the glycan group was found to either increase or decrease glycopeptide CCSs depending on the ion charge state and the size of the glycan. Molecular dynamics (MD) simulations of the gas phase structures and CCSs of selected glycopeptides revealed that the experimental observations were consistent with a glycan size and charge state dependent interplay between destabilizing coulombic repulsion effects (tending to result in more extended structures) and stabilizing charge solvation effects in which the glycan plays a major role (tending to result in more compact structures). Taken together, these IMS and MD findings suggest the possibility of predicting and delineating glycopeptide-enriched regions of mass vs. mobility space for applications in glycoproteomics.
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Rister AL, Dodds ED. Steroid analysis by ion mobility spectrometry. Steroids 2020; 153:108531. [PMID: 31672629 PMCID: PMC6986338 DOI: 10.1016/j.steroids.2019.108531] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/16/2019] [Accepted: 10/24/2019] [Indexed: 12/26/2022]
Abstract
Steroids are an important biomolecule class for analysis due to their promise as biomarkers for various diseases and their abuse as performance enhancers in sports. Current analytical methods, including chromatography and nuclear magnetic resonance spectroscopy, fall short of being able to confidently analyze steroids, partly due to the large number of steroid isomers. Ion mobility spectrometry (IMS), a gas-phase ion separator, has shown potential for steroid analysis both in conjunction with liquid chromatography (LC) and as a stand-alone technique. This review will examine the current literature on IMS analysis of steroids. Analysis by LC-IMS will include examination of steroids and steroid glucuronides in human urine and serum samples for enhanced signal-to-noise ratios and higher confidence of identification. The stand-alone IMS analysis will examine the use of derivatization of steroids and formation of multimers to enhance resolution for steroid isomers analysis, where both methods have been shown to greatly increase the separation of steroid isomer species. However, these methods have not been applied to biological mixtures to assess their applicability to medical and forensic applications, which should be a future direction of this field.
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Rister AL, Dodds ED. Liquid chromatography-ion mobility spectrometry-mass spectrometry analysis of multiple classes of steroid hormone isomers in a mixture. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1137:121941. [PMID: 31877426 DOI: 10.1016/j.jchromb.2019.121941] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/08/2019] [Accepted: 12/13/2019] [Indexed: 10/25/2022]
Abstract
Methods for the analysis of steroids have long been of interest due to the multiple uses for such methods in medical applications, sports monitoring, and environmental science. The analysis of steroids involves inherent analytical hurdles due to their low biological concentrations, poor ionization efficiencies, and frequent occurrence of isomerism. One analytical technique that has been recently applied to steroid analysis is ion mobility spectrometry (IMS). While previous work has focused on the use of metal adduction and multimer formation to enhance separation through IMS analysis coupled to mass spectrometry (MS), this work furthers this approach by coupling IMS-MS with liquid chromatography (LC). Three different LC methods with varying tradeoffs between chromatographic resolution and run time were developed, with one of these achieving a resolution above 1.5 for all steroid isomers. These results also indicate that the coupling of LC to IMS-MS can increase the overall resolution of steroid isomers relative to what can be achieved by either LC or IMS alone. Furthermore, the use of LC and IMS in concert can allow for a more rapid analysis of steroid isomers than can be achieved by LC-MS alone. Finally, the IMS dimension provided for measurements of ion-neutral collision cross sections (CCSs), which were found to be in good agreement with previously reported measurements. Thus, this approach provides three complementary quantitative parameters (retention time, CCS, and mass-to-charge ratio) that can contribute the identification of analytes. Overall, the work presented here demonstrates the potential of coupling LC, IMS, and MS for the analysis of isomeric steroid hormones.
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Rister AL, Bidne KL, Wood JR, Dodds ED. MICROSCALE SERUM EXTRACTION METHOD FOR THE SIMULTANEOUS ANALYSIS OF CORTICOSTERONE AND LIPIDS. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2019; 11:5746-5749. [PMID: 32148562 PMCID: PMC7059636 DOI: 10.1039/c9ay01757g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Corticosterone is an important steroid for the regulation of metabolism and stress response. Existing methods for the measurement of corticosterone include radioimmunoassay (RIA), enzyme linked immunosorbent assay (ELISA), and liquid chromatography-mass spectrometry (LC-MS). While each of these approaches have their advantages, RIAs use radioactive isotopes that necessitate specially regulated usage and disposal. Furthermore, both ELISAs and RIAs require expensive kits and can only measure a single analyte. In this study, we establish a new sample preparation technique based on a modified Folch extraction that allows for the simultaneous isolation of corticosterone and lipids from serum. The extract is then analyzed by LC-MS. Using only 5 µL of serum, quantification of corticosterone was achieved with coefficients of variation at 3% or less and a detection limit of 0.12 µM. Overall, the results of this study should be beneficial to the measurement of circulating corticosterone and lipids for a variety of studies using small volumes of samples.
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Rister AL, Dodds ED. Ion Mobility Spectrometry and Tandem Mass Spectrometry Analysis of Estradiol Glucuronide Isomers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2037-2040. [PMID: 31385258 PMCID: PMC6812596 DOI: 10.1007/s13361-019-02272-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 06/11/2019] [Accepted: 06/18/2019] [Indexed: 05/31/2023]
Abstract
Estradiol is an estrogenic steroid that can undergo glucuronidation at two different sites, which results in two estradiol glucuronide regioisomers. These isomers can be produced by different enzymes and can have different biological activities before being eliminated from the body. Although there have been previous methods that can distinguish the two isomers, these methods often have long acquisition times or high cost per analysis. In this study, traveling wave ion mobility spectrometry (TWIMS) coupled with mass spectrometry (MS) was employed to separate estradiol glucuronides using alkali metal adduction in positive ion mode, where the sodiated dimer adduct provided adequate separation both in single-component standards and in two-component mixtures. Additionally, in negative ion mode, tandem mass spectrometry (MS/MS) was used to quantitatively determine the relative composition of the two isomers. This was possible due to differences in the energetic requirements for loss of the glucuronic acid, which was characterized by energy-resolved collision-induced dissociation (CID). This work demonstrated that the intensity of the glucuronic acid neutral loss product as compared with the intensity of the intact precursor ion can be used to determine the percentage of each isomer present in a mixture. Overall, TWIMS successfully separated estradiol glucuronide isomers in positive ion mode and MS/MS via CID enables relative quantitation of each isomer in negative ion mode.
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Rister AL, Martin TL, Dodds ED. Formation of multimeric steroid metal adducts and implications for isomer mixture separation by traveling wave ion mobility spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2019; 54:429-436. [PMID: 30860640 PMCID: PMC6556764 DOI: 10.1002/jms.4350] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 01/25/2019] [Accepted: 03/04/2019] [Indexed: 05/03/2023]
Abstract
Steroid analysis is essential to the fields of medicine and forensics, but such analyses can present some complex analytical challenges. While chromatographic methods require long acquisition times and often provide incomplete separation, ion mobility spectrometry (IMS) as coupled to mass spectrometry (MS) has demonstrated significant promise for the separation of steroids, particularly in concert with metal adduction and multimerization. In this study, traveling wave ion mobility spectrometry (TWIMS) was employed to separate multimer steroid metal adducts of isomers in mixtures. The results show the ability to separate steroid isomers with a decrease in resolution compared with single component standards because of the formation of heteromultimers. Additionally, ion-neutral collision cross sections (CCS) of the species studied were measured in the mixtures and compared with CCSs obtained in single component standards. Good agreement between these values suggests that the CCS may aid in identification of unknowns. Furthermore, a complex mixture composed of five sets of steroid isomers were analyzed, and distinct features for each steroid component were identified. This study further demonstrated the potential of TWIMS-MS methods for the rapid and isomer-specific study of steroids in biological samples for use either in tandem with or without chromatographic separation.
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Rister AL, Martin TL, Dodds ED. Application of Group I Metal Adduction to the Separation of Steroids by Traveling Wave Ion Mobility Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:248-255. [PMID: 30414066 PMCID: PMC6551524 DOI: 10.1007/s13361-018-2085-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 08/09/2018] [Accepted: 08/10/2018] [Indexed: 05/04/2023]
Abstract
Steroids represent an interesting class of small biomolecules due to their use as biomarkers and their status as scheduled drugs. Although the analysis of steroids is complicated by the potential for many isomers, ion mobility spectrometry (IMS) has previously shown promise for the rapid separation of steroid isomers. This work is aimed at the further development of IMS separation for the analysis of steroids. Here, traveling wave ion mobility spectrometry (TWIMS) was applied to the study of group I metal adducted steroids and their corresponding multimers for five sets of isomers. Each set of isomers had a minimum of one dimeric metal ion adduct that exhibited a resolution greater than one (i.e., approaching baseline resolution). Additionally, ion-neutral collision cross sections (CCSs) were measured using polyalanine as a calibrant, which may provide an additional metric contributing to analyte identification. Where possible, measured CCSs were compared to previously reported values. When measuring CCSs of steroid isomers using polyalanine as the calibrant, nitrogen CCS values were within 1.0% error for monomeric sodiated adducts and slightly higher for the dimeric sodiated adducts. Overall, TWIMS was found to successfully separate steroids as dimeric adducts of group I metals. Graphical Abstract ᅟ.
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Bhinderwala F, Lei S, Woods J, Rose J, Marshall DD, Riekeberg E, Leite ADL, Morton M, Dodds ED, Franco R, Powers R. Metabolomics Analyses from Tissues in Parkinson's Disease. Methods Mol Biol 2019; 1996:217-257. [PMID: 31127560 DOI: 10.1007/978-1-4939-9488-5_19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Metabolomics has been successfully applied to study neurological and neurodegenerative disorders including Parkinson's disease for (1) the identification of potential biomarkers of onset and disease progression; (2) the identification of novel mechanisms of disease progression; and (3) the assessment of treatment prognosis and outcome. Reproducible and efficient extraction of metabolites is imperative to the success of any metabolomics investigation. Unlike other omics techniques, the composition of the metabolome can be negatively impacted by the preparation, processing, and handling of these samples. The proper choice of data collection, preprocessing, and processing protocols is similarly important to the design of an effective metabolomics experiment. Likewise, the correct application of univariate and multivariate statistical methods is essential for providing biologically relevant insights. In this chapter, we have outlined a detailed metabolomics workflow that addresses all of these issues. A step-by-step protocol from the preparation of neuronal cells and metabolomic tissue samples to their metabolic analyses using nuclear magnetic resonance, mass spectrometry, and chemometrics is presented.
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Kolli V, Schumacher KN, Dodds ED. Ion mobility-resolved collision-induced dissociation and electron transfer dissociation of N-glycopeptides: gathering orthogonal connectivity information from a single mass-selected precursor ion population. Analyst 2018; 142:4691-4702. [PMID: 29119999 DOI: 10.1039/c7an01196b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Glycopeptide-level mass spectrometry (MS) and tandem mass spectrometry (MS/MS) analyses are commonly performed to establish site-specific protein glycosylation profiles that are of central importance to gaining structure-function insights on glycoproteins. Confoundingly, the complete characterization of glycopeptide connectivity usually requires the acquisition of multiple MS/MS fragmentation spectra. Complementary ion fragmentation techniques such as collision-induced dissociation (CID) and electron transfer dissociation (ETD) are often applied in concert to address this need. While structurally informative, the requirement for acquisition of two MS/MS spectra per analyte places considerable limitations upon the breadth and depth of large-scale glycoproteomic inquiry. Here, a previously developed method of multiplexing CID and ETD is applied to the study of glycopeptides for the first time. Integration of the two dissociation methods was accomplished through addition of an ion mobility (IM) dimension that disperses the two stages of MS/MS in time. This allows the two MS/MS spectra to be acquired within a few milliseconds of one another, and to be deconvoluted in post-processing. Furthermore, the method allows both fragmentation readouts to be obtained from the same precursor ion packet, thus reducing the inefficiencies imposed by separate CID and ETD acquisitions and the relatively poor precursor ion to fragment ion conversion typical of ETD. N-Linked glycopeptide ions ranging in molecular weight from 1.8 to 6.5 kDa were generated from four model glycoproteins that collectively encompassed paucimannosidic, high mannose, and complex types of N-glycosylation. In each case, IM-resolved CID and ETD events provided complete coverage of the glycan topology and peptide sequence coverages ranging from 48.4% (over 32 amino acid residues) to 85.7% (over eight amino acid residues). The potential of this method for large-scale glycoproteomic analysis is discussed.
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Stewart KL, Rathore D, Dodds ED, Cordes MHJ. Increased sequence hydrophobicity reduces conformational specificity: A mutational case study of the Arc repressor protein. Proteins 2018; 87:23-33. [PMID: 30315592 DOI: 10.1002/prot.25613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 10/06/2018] [Accepted: 10/08/2018] [Indexed: 11/08/2022]
Abstract
The amino-acid sequences of soluble, globular proteins must have hydrophobic residues to form a stable core, but excess sequence hydrophobicity can lead to loss of native state conformational specificity and aggregation. Previous studies of polar-to-hydrophobic mutations in the β-sheet of the Arc repressor dimer showed that a single substitution at position 11 (N11L) leads to population of an alternate dimeric fold in which the β-sheet is replaced by helix. Two additional hydrophobic mutations at positions 9 and 13 (Q9V and R13V) lead to population of a differently folded octamer along with both dimeric folds. Here we conduct a comprehensive study of the sequence determinants of this progressive loss of fold specificity. We find that the alternate dimer-fold specifically results from the N11L substitution and is not promoted by other hydrophobic substitutions in the β-sheet. We also find that three highly hydrophobic substitutions at positions 9, 11, and 13 are necessary and sufficient for oligomer formation, but the oligomer size depends on the identity of the hydrophobic residue in question. The hydrophobic substitutions increase thermal stability, illustrating how increased hydrophobicity can increase folding stability even as it degrades conformational specificity. The oligomeric variants are predicted to be aggregation-prone but may be hindered from doing so by proline residues that flank the β-sheet region. Loss of conformational specificity due to increased hydrophobicity can manifest itself at any level of structure, depending upon the specific mutations and the context in which they occur.
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Aboufazeli F, Dodds ED. Precursor ion survival energies of protonated N-glycopeptides and their weak dependencies on high mannose N-glycan composition in collision-induced dissociation. Analyst 2018; 143:4459-4468. [PMID: 30151520 PMCID: PMC6131044 DOI: 10.1039/c8an00830b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Fully realizing the capabilities of tandem mass spectrometry (MS/MS) for analysis of glycosylated peptides will require further understanding of the unimolecular dissociation chemistry that dictates their fragmentation pathways. In this context, the overall composition of a given glycopeptide ion is a key characteristic; however, the extent to which the carbohydrate moiety influences the preferred dissociation channels has received relatively little study. Here, the effect of glycan composition on energy-resolved collision-induced dissociation (CID) behavior was studied for a select menu of 30 protonated high mannose type N-linked glycopeptide ions. Groups of analytes which shared a common charge state, polypeptide sequence, and glycosylation site exhibited 50% precursor ion survival energies that varied only slightly as the size and composition of the oligosaccharide was varied. This was found to be true regardless of whether the precursor ion survival energies were normalized for the number of available vibrational degrees of freedom. The practical consequence of this was that a given collision energy brought about highly similar levels of precursor ion depletion and structural information despite systematic variation of the glycan identity. This lack of sensitivity to oligosaccharide composition stands in contrast to other physicochemical properties of glycopeptide ions (e.g., polypeptide composition, charge state, charge carrier) which sharply influence their energy-resolved CID characteristics. On the whole, these findings imply that the deliberate selection of CID energies to bring about a desired range of fragmentation pathways does not necessarily hinge on the nature of the glycan.
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Lai R, Dodds ED, Li H. Molecular dynamics simulation of ion mobility in gases. J Chem Phys 2018; 148:064109. [PMID: 29448783 DOI: 10.1063/1.4998955] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A force field molecular dynamics method is developed to directly simulate ion drift in buffer gases driven by an electric field. The ion mobility and collision cross sections (CCSs) with relevance to ion mobility spectrometry can be obtained from the simulated drift velocity in high-density buffer gases (pressure ∼50 bars) and high electric fields (∼107 V/m). Compared to trajectory methods, the advantage of the molecular dynamics method is that it can simultaneously sample the internal dynamic motions of the ion and the ion-gas collisions. For ions with less than 100 atoms, the simulated collision cross section values can be converged to within ±1%-2% by running a 100 ns simulation for 5-19 h using one computer core. By using a set of element-based Lennard-Jones parameters that are not tuned for different atomic types in different molecules, the simulated collision cross sections for 15 small molecular ions (number of atoms ranging from 17 to 85, mass ranging from 74.1 to 609.4 g/mol) are consistent with experimental values: the mean unsigned error is 2.6 Å2 for He buffer gas and 4.4 Å2 for N2 buffer gas. The sensitivity of the simulated CCS values to random diffusion, drift velocity, electric field strength, temperature, and buffer gas density is examined.
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19
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Matsuda R, Kolli V, Woods M, Dodds ED, Hage DS. Optimizing sequence coverage for a moderate mass protein in nano-electrospray ionization quadrupole time-of-flight mass spectrometry. Anal Biochem 2016; 509:115-117. [PMID: 27320213 DOI: 10.1016/j.ab.2016.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 06/07/2016] [Accepted: 06/08/2016] [Indexed: 10/21/2022]
Abstract
Sample pretreatment was optimized to obtain high sequence coverage for human serum albumin (HSA, 66.5 kDa) when using nano-electrospray ionization quadrupole time-of-flight mass spectrometry (nESI-Q-TOF-MS). Use of the final method with trypsin, Lys-C, and Glu-C digests gave a combined coverage of 98.8%. The addition of peptide fractionation resulted in 99.7% coverage. These results were comparable to those obtained previously with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). The sample pretreatment/nESI-Q-TOF-MS method was also used with collision-induced dissociation to analyze HSA digests and to identify peptides that could be employed as internal mass calibrants in future studies of modifications to HSA.
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Rathore D, Aboufazeli F, Dodds ED. Obtaining complementary polypeptide sequence information from a single precursor ion packet via sequential ion mobility-resolved electron transfer and vibrational activation. Analyst 2016; 140:7175-83. [PMID: 26357706 DOI: 10.1039/c5an01225b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Tandem mass spectrometry (MS/MS) is now well-known as a powerful tool for characterizing the primary structures of peptides and proteins; however, in many cases the use of but a single dissociation method provides only a partial view of the amino acid sequences and post-translational modification patterns of polypeptides. While the application of multiple fragmentation methods can be more informative, this introduces the burden of acquiring multiple MS/MS spectra per analyte, thus reducing the effective duty cycle of such methods. In this work, initial proof-of-concept is provided for a method designed to overcome these barriers. This method relies on the complementary fragmentation information that can be provided by performing collision-induced dissociation (CID) and electron transfer dissociation (ETD) in concert, while also taking advantage of an ion mobility (IM) dimension to temporally resolve the occurrence of CID and ETD when applied to a single accumulated packet of precursor ions. In this way, the significant proportion of the precursor ion population that remains unreacted in ETD experiments is subjected to CID rather than being fruitlessly discarded. In addition, the two distinct fragmentation spectra can be extracted from their corresponding IM domains to render readily interpretable individual fragmentation spectra. This scheme was demonstrated for several polypeptides ranging from 1.3 to 8.6 kDa in molecular weight. In each case, IM-resolved CID and ETD events resulted in b/y and c/z ions, respectively, which each covered both unique and overlapping sequence information. These findings demonstrate that the combination of CID and ETD can be achieved with greater utilization of the available ion population and little or no loss of duty cycle.
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21
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Huang Y, Dodds ED. Ion-neutral collisional cross sections of carbohydrate isomers as divalent cation adducts and their electron transfer products. Analyst 2016. [PMID: 26225371 DOI: 10.1039/c5an01093d] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
As the gravity of glycoscience continues to amass, a commensurate demand for rapid, sensitive, and structurally comprehensive glycoanalytical tools has arisen. Among the most elusive but desirable analytical capabilities is the ability to expeditiously and unambiguously detect, distinguish, and resolve carbohydrates that differ only in their constitutional isomerism and/or stereoisomerism. While ion mobility spectrometry (IMS) has proven a highly promising tool for such analyses, the facility of this method to discriminate larger oligosaccharides is still somewhat limited. In an effort to expand the capabilities of IMS to discriminate among carbohydrate isomers, the present investigation was focused on IMS studies of four trisaccharide isomers, four pentasaccharide isomers, and two hexasaccharide isomers, each as group II metal ion adducts and their corresponding gas-phase electron transfer (ET) products. These studies were also evaluated in the context of previously investigated group I metal ion adducts of the same saccharides. The orientationally averaged ion-neutral collisional cross sections (CCSs) of the various carbohydrate/metal ion adducts were found to be dependent on the structures of specific carbohydrate isomers, sensitive to the electronic characteristics of the bound cation, and responsive to the attachment of an additional electron (in the case of divalent metal ion adducts). Overall, these results underscore the utility of metal ions for probing carbohydrate structure in concert with IMS, and the capacity of gas-phase ion chemistry to expand the menu of such probes.
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22
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Kolli V, Roth HA, De La Cruz G, Fernando GS, Dodds ED. The role of proton mobility in determining the energy-resolved vibrational activation/dissociation channels of N-glycopeptide ions. Anal Chim Acta 2015; 896:85-92. [PMID: 26481991 DOI: 10.1016/j.aca.2015.09.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 09/04/2015] [Accepted: 09/05/2015] [Indexed: 12/21/2022]
Abstract
Site-specific glycoproteomic analysis largely hinges on the use of tandem mass spectrometry (MS/MS) to identify glycopeptides. Experiments of this type are usually aimed at drawing connections between individual oligosaccharide structures and their specific sites of attachment to the polypeptide chain. These determinations inherently require ion dissociation methods capable of interrogating both the monosaccharide and amino acid connectivity of the glycopeptide. Collision-induced dissociation (CID) shows potential to satisfy this requirement, as the vibrational activation/dissociation of protonated N-glycopeptides has been observed to access cleavage of either glycosidic bonds of the glycan or amide bonds of the peptide in an energy-resolved manner. Nevertheless, the relative energy requirement for these fragmentation pathways varies considerably among analytes. This research addresses the influence of proton mobility on the vibrational energy necessary to achieve either glycan or peptide cleavage in a collection of protonated N-glycopeptide ions. While greater proton mobility of the precursor ion was found to correlate with lower energy requirements for precursor ion depletion and appearance of glycosidic fragments, the vibrational energy deposition necessary for appearance of peptide backbone fragments showed no relation to the precursor ion proton mobility. These results are consistent with observations suggesting that peptide fragments arise from an intermediate fragment which is generally of lower proton mobility than the precursor ion. Such findings have potential to facilitate the rational selection of CID conditions which are best suited to provide either glycan or peptide cleavage products in MS/MS based N-glycoproteomic analysis.
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Huang Y, Dodds ED. Discrimination of Isomeric Carbohydrates as the Electron Transfer Products of Group II Cation Adducts by Ion Mobility Spectrometry and Tandem Mass Spectrometry. Anal Chem 2015; 87:5664-8. [PMID: 25955237 DOI: 10.1021/acs.analchem.5b00759] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The rapid and unambiguous distinction of isomeric carbohydrate structures persists as a tremendous analytical challenge. This paper reports the first exploitation of carbohydrate/metal ion interactions in concert with gas-phase ion chemistry to improve discrimination of oligosaccharide isomers by both ion mobility spectrometry and tandem mass spectrometry. This is demonstrated for two isomeric pentasaccharides and two isomeric hexasaccharides, each studied in an underivatized form as their calcium ion adducts, barium ion adducts, and gas-phase electron transfer products thereof. With appropriate selection of the charge carrier, transfer of a single electron to the carbohydrate metal ion adducts resulted in isomer-distinguishing shifts in their ion/neutral collision cross sections and the appearance of unique features in their vibrational activation/dissociation spectra. These findings suggest novel and elegant gas-phase strategies for rapid differentiation of isomeric oligosaccharides.
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Aboufazeli F, Kolli V, Dodds ED. A comparison of energy-resolved vibrational activation/dissociation characteristics of protonated and sodiated high mannose N-glycopeptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:587-595. [PMID: 25582509 DOI: 10.1007/s13361-014-1070-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 12/11/2014] [Accepted: 12/16/2014] [Indexed: 06/04/2023]
Abstract
Fragmentation of glycopeptides in tandem mass spectrometry (MS/MS) plays a pivotal role in site-specific protein glycosylation profiling by allowing specific oligosaccharide compositions and connectivities to be associated with specific loci on the corresponding protein. Although MS/MS analysis of glycopeptides has been successfully performed using a number of distinct ion dissociation methods, relatively little is known regarding the fragmentation characteristics of glycopeptide ions with various charge carriers. In this study, energy-resolved vibrational activation/dissociation was examined via collision-induced dissociation for a group of related high mannose tryptic glycopeptides as their doubly protonated, doubly sodiated, and hybrid protonated sodium adduct ions. The doubly protonated glycopeptide ions with various compositions were found to undergo fragmentation over a relatively low but wide range of collision energies compared with the doubly sodiated and hybrid charged ions, and were found to yield both glycan and peptide fragmentation depending on the applied collision energy. By contrast, the various doubly sodiated glycopeptides were found to dissociate over a significantly higher but narrow range of collision energies, and exhibited only glycan cleavages. Interestingly, the hybrid protonated sodium adduct ions were consistently the most stable of the precursor ions studied, and provided fragmentation information spanning both the glycan and the peptide moieties. Taken together, these findings illustrate the influence of charge carrier over the energy-resolved vibrational activation/dissociation characteristics of glycopeptides, and serve to suggest potential strategies that exploit the analytically useful features uniquely afforded by specific charge carriers or combinations thereof.
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Marshall DD, Lei S, Worley B, Huang Y, Garcia-Garcia A, Franco R, Dodds ED, Powers R. Combining DI-ESI-MS and NMR datasets for metabolic profiling. Metabolomics 2015; 11:391-402. [PMID: 25774104 PMCID: PMC4354777 DOI: 10.1007/s11306-014-0704-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Metabolomics datasets are commonly acquired by either mass spectrometry (MS) or nuclear magnetic resonance spectroscopy (NMR), despite their fundamental complementarity. In fact, combining MS and NMR datasets greatly improves the coverage of the metabolome and enhances the accuracy of metabolite identification, providing a detailed and high-throughput analysis of metabolic changes due to disease, drug treatment, or a variety of other environmental stimuli. Ideally, a single metabolomics sample would be simultaneously used for both MS and NMR analyses, minimizing the potential for variability between the two datasets. This necessitates the optimization of sample preparation, data collection and data handling protocols to effectively integrate direct-infusion MS data with one-dimensional (1D) 1H NMR spectra. To achieve this goal, we report for the first time the optimization of (i) metabolomics sample preparation for dual analysis by NMR and MS, (ii) high throughput, positive-ion direct infusion electrospray ionization mass spectrometry (DI-ESI-MS) for the analysis of complex metabolite mixtures, and (iii) data handling protocols to simultaneously analyze DI-ESI-MS and 1D 1H NMR spectral data using multiblock bilinear factorizations, namely multiblock principal component analysis (MB-PCA) and multiblock partial least squares (MB-PLS). Finally, we demonstrate the combined use of backscaled loadings, accurate mass measurements and tandem MS experiments to identify metabolites significantly contributing to class separation in MB-PLS-DA scores. We show that integration of NMR and DI-ESI-MS datasets yields a substantial improvement in the analysis of neurotoxin involvement in dopaminergic cell death.
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