Contemporary glycomic approaches using ion mobility–mass spectrometry

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTIon Mobility-Mass Spectrometry: Time-Dispersive InstrumentationJody C. May and John A. McLean*View Author Information Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute for Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education , Vanderbilt University, Nashville, Tennessee 37235, United States*E-mail: [email protected]Cite this: Anal. Chem. 2015, 87, 3, 1422–1436Publication Date (Web):December 19, 2014Publication History Published online9 January 2015Published inissue 3 February 2015https://doi.org/10.1021/ac504720mCopyright © 2014 American Chemical SocietyRIGHTS & PERMISSIONSACS AuthorChoiceArticle Views13748Altmetric-Citations286LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (4 MB) Get e-AlertsSUBJECTS:Collisions,Ions,Mass spectrometers,Optimization,Power Get e-Alerts

Chondroitin sulfate (CS) glycosaminoglycans are bioactive sulfated polysaccharides comprising repeating units of uronic acid and N-acetyl galactose sulfated at various positions. The optimal length and sulfation pattern of the CS bioactive sequences remain elusive so that structure-activity relationships cannot be easily established. Development of efficient analytical methods allowing the differentiation of the various sulfation patterns of CS sequences is therefore of particular importance to correlate their biological functions to the sulfation pattern. Discrimination of different oligomers (dp2 to dp6) of synthetic chondroitin sulfate isomers was evaluated by electrospray ionization tandem mass spectrometry (ESI-MS/MS) in the negative-ion mode from deprotonated and alkali adduct species. In addition, ion mobility mass spectrometry (IMS-MS) was used to study the influence of both the degree of polymerization and sulfate group location on the gas-phase conformation of CS oligomers. ESI-MS/MS spectra of chondroitin sulfate isomers show characteristic product ions exclusively from alkali adduct species (Li, Na, K and Cs). Whatever the alkali adducts studied, MS/MS of chondroitin oligosaccharides sulfated at position 6 yields a specific product ion at m/z 139 while CS oligosaccharides sulfated at position 4 show a specific product ion at m/z 154. Being observed for the different CS oligomers di-, tetra- and hexasaccharides, these fragment ions are considered as diagnostic ions for chondroitin 6-O-sulfate and chondroitin 4-O-sulfate, respectively. IMS-MS experiments reveal that collision cross-sections (CCS) of CS oligomers with low charge states evolved linearly with degrees of polymerization indicating a similar gas-phase conformation. This study allows the fast and unambiguous differentiation of CS isomers sulfated at position 6 or 4 for both saturated and unsaturated analogues from MS/MS experiments. In addition, the CCS linear evolution of CS oligomers in function of the degree of polymerization indicates that no folding occurs even for hexasaccharides.

The 1, 2-unsaturated derivatives of (1-4) linked disaccharides serve as versatile building blocks for synthesizing biologically active compounds. Distinguishing between four pairs of stereoisomers in mixtures presents a challenging task. In this study, disaccharide derivatives are analyzed as alkali metal adducts using electrospray ionization tandem mass spectrometry (ESI-MS/MS), both as individual compounds and in mixtures by ion mobility mass spectrometry (IMS). Electrospray ionization (ESI) in combination with tandem mass spectrometry (MS/MS) in positive mode was employed to differentiate lithium adduct ions of hexa-acetyl/hexa-benzyl-D-lactals, and hexa-acetyl/hexa-benzyl-D-maltals, along with their corresponding 2-C-branched malonates. The high resolving power of trapped ion mobility spectrometry (TIMS) with the imeX™ functionality rapidly identified different metal adducts (Li, Na, Cs) as individual isomers and separated mixtures of stereoisomers. The measured collisional cross section (CCS) values were analyzed in relation to predicted CCS values. MS/MS spectra of the [M + Li]+ ions of glycal disaccharide analogues exhibited typical cross-ring and glycosidic bond cleavages. Collision-induced dissociation (CID) spectra provided insights into their fragmentation behavior, allowing differentiation of (1-4) linked disaccharides. TIMS technology delivered adjustable ion mobility resolution for suitable separation of the four sets of stereo isomeric compounds. However, accurately predicting CCS values to differentiate between respective isomeric pairs using the SigmaCCS program for sodium adducts is only partially achievable. ESI CID spectra of [M + Li]+ adduct ions for individual glycal disaccharide analogues facilitate the discrimination between alpha and beta (1-4) linked unsaturated disaccharides and their 2-C-branched analogues. Through optimized experimental conditions, complete baseline ion mobility separation of stereoisomer pairs of the Cs adducts is achieved.

Polymers have a wide range of applications depending on their composition, size, and architecture. Varying any of these three characteristics can greatly impact the resulting chemical, physical, and mechanical properties. While many techniques are available to determine polymer composition and size, determining the exact polymer architecture is more challenging. Herein, tandem mass spectrometry (MS/MS) and ion mobility mass spectrometry (IM-MS) methods are utilized to derive crucial architectural information about dithiol-yne comb polymers. Based on their unique fragmentation products and IM drift times, dithiol-yne oligomers with distinct architectures were successfully differentiated and characterized. Additionally, experimental collision cross-sections (Ω) derived via IM-MS were compared to theoretically extracted Ω values from molecular dynamics simulated structures to deduce the architectural motif of these comb oligomers. Overall, this work demonstrates the benefits of combining various mass spectrometry techniques in order to gain a complete understanding of a complex polymer mixture.

Rationale Saponins are natural compounds presenting a high structural diversity whose structural characterization remains extremely challenging. Ideally, saponin structures are best established using nuclear magnetic resonance experiments conducted on isolated molecules. However, saponins are also increasingly characterized using tandem mass spectrometry (MS/MS) coupled with liquid chromatography, even if collision‐induced dissociation (CID) experiments are often quite limited in accurately determining the saponin structure. Methods We consider here ion mobility mass spectrometry (IMMS) as an orthogonal tool for the structural characterization of saponin isomers by comparing the experimental collisional cross sections (CCSs) of saponin ions with theoretical CCSs for candidate ion structures. Indeed, state‐of‐the‐art theoretical calculations perfectly complement the experimental results, allowing the ion structures to be deciphered at the molecular level. Results We demonstrate that ion mobility can contribute to the structural characterization of saponins because different saponin ions present significantly distinct CCSs. Depending on the nature of the cation (in the positive ion mode), the differences in CCSs can also be exacerbated, optimizing the gas‐phase separation. When associated with molecular dynamics simulations, the CCS data can be used to describe the interactions between the cations, i.e. H + , Na + and K + , and the saponin molecules at a molecular level. Conclusions Our work contributes to resolve the relationship between the primary and secondary structures of saponin ions. However, it is obvious that the structural diversity and complexity of the saponins cannot be definitively unraveled by measuring a single numerical value, here the CCS. Consequently, the structural characterization of unknown saponins will be difficult to achieve based on IMMS alone. Nevertheless, we demonstrated that monodesmosidic and bidesmosidic saponins can be distinguished via IMMS.

Tandem mass spectrometry is a tool to dissect noncovalent protein complexes into smaller substructures for quaternary structure analysis. The commonly used activation method, collision induced dissociation (CID), often provides limited structural information from the typical dissociation pattern where unfolded monomers are ejected from the protein complex. In contrast, surface-induced dissociation (SID) has been shown to be very effective at dissociating protein complexes with less unfolding than CID. We present here SID of a large noncovalent tetradecamer protein, GroEL (801 kDa). A wide variety of products, including heptamers representative of the native topology, are released from the precursor upon SID, significantly different from the ubiquitous monomer ejection in CID. Enhanced dissociation into heptamers is observed when the charge states of the GroEL precursor are reduced by adding triethylammonium acetate into the spraying buffer. Ion mobility is utilized after SID to separate products overlapping in m/z to simplify the SID spectra. Compact heptamers from the charge-reduced tetradecamer are clearly distinguished from other overlapping species. SID can be very useful for quaternary structure studies of large noncovalent protein complexes, as manifested by the GroEL data where the tetradecamer dissociates into heptamers, reflecting the native topology of the complex.

Heparin is a linear sulfated polysaccharide widely used in medicine because of its anticoagulant properties. The various sulfation and/or acetylation patterns on heparin impart different degrees of conformational change around the glycosidic bonds and subsequently alter its function as an anticoagulant, anticancer, or antiviral drug. Characterization of these structures is important for eventual elucidation of its function but presents itself as an analytical challenge due to the inherent heterogeneity of the carbohydrates. Heparin octasaccharide structural isomers of various sulfation patterns were investigated using ion mobility mass spectrometry (IMMS). In addition to distinguishing the isomers, we report the preparation and tandem mass spectrometry analysis for multiple sulfated or acetylated oligosaccharides. Herein, our data indicate that heparin octasaccharide isomers were separated on the basis of their structural conformations in the ion mobility cell. Subsequent to this separation, isomers were further distinguished using product ions resulting from tandem mass spectrometry. Overall, IMMS analysis was used to successfully characterize and separate individual isomers and subsequently measure their conformations.

Enhancing isomer specificity in mass spectrometry by combining silver ion adduction and ion mobility

Proteome analysis currently heavily relies on tandem mass spectrometry (MS/MS), which does not fully utilize MS1 features, as many precursors remain unselected for MS/MS fragmentation, especially in the cases of low abundance samples and wide abundance dynamic range samples. Therefore, leveraging MS1 features as a complement to MS/MS has become an attractive option to improve the coverage of feature identification. Herein, we propose MonoMS1, an approach combining deep learning-based retention time, ion mobility, detectability prediction, and logistic regression-based scoring for MS1 feature identification. The approach achieved a significant increase in MS1 feature identification based on an E. coli data set. Application of MonoMS1 to data sets with wide dynamic range, such as human serum proteome samples, and with low sample abundance, such as single-cell proteome samples, enabled substantial complementation of MS/MS-based peptide and protein identification. This method opens a new avenue for proteomic analysis and can boost proteomic research on complex samples.

Ion mobility in the pharmaceutical industry: an established biophysical technique or still niche?

The Paternò-Büchi (PB) reaction is a common organic reaction in which a carbonyl radical formed by exposure to UV radiation reacts with an alkene to form an oxetane ring. Recent analytical applications of this reaction have included the determination of C═C bond position in lipid fatty acyl tails using tandem mass spectrometry. Our group has recently investigated methods for structurally modifying steroid isomers to improve their identification and resolution using ion mobility spectrometry. Herein, we report the first application of the Paternò-Büchi reaction to form steroid oxetanes using a simple, low-cost, and high efficiency method with a low pressure mercury lamp. This methodology is performed on several endogenous steroid isomers, resulting in unique ion mobility spectra that provide a unique fingerprint for each. These fingerprint spectra can add confidence in identification of those compounds, especially in complex biological matrixes. Testosterone and epitestosterone, an epimer pair commonly interrogated in a number of applications such as for their use as performance enhancing drugs, displayed one and three unique ion mobility peaks, respectively. These spectra and their measured collision cross sections (CCS) allow for unambiguous differentiation of these and several other steroid isomer groups analyzed in this work. Finally, multiple anabolic androgenic steroids prohibited by the World Anti-Doping Agency were tested with this method and resulted in unique CCS for their PB reaction products. This approach can offer improved confidence in their identification as well as for many other banned substances.

Peptide and protein aggregation involves the formationof oligomericspecies, but the complex interplay between oligomers of differentconformations and sizes complicates their structural elucidation.Using ion mobility mass spectrometry (IM-MS), we aim to reveal theseearly steps of aggregation for the Ac-PHF6-NH2 peptidesegment from tau protein, thereby distinguishing between differentoligomeric species and gaining an understanding of the aggregationpathway. An important factor that is often neglected, but which canalter the aggregation propensity of peptides, is the terminal cappinggroups. Here, we demonstrate the use of IM-MS to probe the early stagesof aggregate formation of Ac-PHF6-NH2, Ac-PHF6, PHF6-NH2, and uncapped PHF6 peptide segments. The aggregation propensityof the four PHF6 segments is confirmed using thioflavin T fluorescenceassays and transmission electron microscopy. A novel approach basedon post-IM fragmentation and quadrupole selection on the TIMS-Qq-ToF(trapped ion mobility) spectrometer was developed to enhance oligomerassignment, especially for the higher-order aggregates. This approachpushes the limits of IM identification of isobaric species, whosesignatures appear closer to each other with increasing oligomer size,and provides new insights into the interpretation of IM-MS data. Inaddition, TIMS collision cross section values are compared with travelingwave ion mobility (TWIMS) data to evaluate potential instrumentalbias in the trapped ion mobility results. The two IM-MS instrumentalplatforms are based on different ion mobility principles and havedifferent configurations, thereby providing us with valuable insightinto the preservation of weakly bound biomolecular complexes suchas peptide aggregates.

Abstract. Measurement techniques that provide molecular-level information are needed to elucidate the multiphase processes that produce secondary organic aerosol (SOA) species in the atmosphere. Here we demonstrate the application of ion mobility spectrometry-mass spectrometry (IMS–MS) to the simultaneous characterization of the elemental composition and molecular structures of organic species in the gas and particulate phases. Molecular ions of gas-phase organic species are measured online with IMS–MS after ionization with a custom-built nitrate chemical ionization (CI) source. This CI–IMS–MS technique is used to obtain time-resolved measurements (5 min) of highly oxidized organic molecules during the 2013 Southern Oxidant and Aerosol Study (SOAS) ambient field campaign in the forested SE US. The ambient IMS–MS signals are consistent with laboratory IMS–MS spectra obtained from single-component carboxylic acids and multicomponent mixtures of isoprene and monoterpene oxidation products. Mass-mobility correlations in the 2-D IMS–MS space provide a means of identifying ions with similar molecular structures within complex mass spectra and are used to separate and identify monoterpene oxidation products in the ambient data that are produced from different chemical pathways. Water-soluble organic carbon (WSOC) constituents of fine aerosol particles that are not resolvable with standard analytical separation methods, such as liquid chromatography (LC), are shown to be separable with IMS–MS coupled to an electrospray ionization (ESI) source. The capability to use ion mobility to differentiate between isomers is demonstrated for organosulfates derived from the reactive uptake of isomers of isoprene epoxydiols (IEPOX) onto wet acidic sulfate aerosol. Controlled fragmentation of precursor ions by collisionally induced dissociation (CID) in the transfer region between the IMS and the MS is used to validate MS peak assignments, elucidate structures of oligomers, and confirm the presence of the organosulfate functional group.

Since the development of electrospray ionization (ESI) for ion mobility spectrometry mass spectrometry (IMMS), IMMS have been extensively applied for characterization of gas-phase bio-molecules. Conventional ion mobility spectrometry (IMS), defined as drift tube IMS (DT-IMS), is typically a stacked ring design that utilizes a low electric field gradient. Field asymmetric ion mobility spectrometry (FAIMS) is a newer version of IMS, however, the geometry of the system is significantly different than DT-IMS and data are collected using a much higher electric field. Here we report construction of a novel ambient pressure dual gate DT-IMS coupled with a FAIMS system and then coupled to a quadrupole ion trap mass spectrometer (QITMS) to form a hybrid three-dimensional separation instrument, DT-IMS-FAIMS-QITMS. The DT-IMS was operated at ~3 Townsend (electric field/number density (E/N) or (Td)) and was coupled in series with a FAIMS, operated at ~80 Td. Ions were mobility-selected by the dual gate DT-IMS into the FAIMS and from the FAIMS the ions were detected by the QITMS for as either MS or MSn. The system was evaluated using cocaine as an analytical standard and tested for the application of separating three isomeric tri-peptides: tyrosine-glycine-tryptophan (YGW), tryptophan-glycine-tyrosine (WGY) and tyrosine-tryptophan-glycine (YWG). All three tri-peptides were separated in the DT-IMS dimension and each had one mobility peak. The samples were partially separated in the FAIMS dimension but two conformation peaks were detected for the YWG sample while YGW and WGY produced only one peak. Ion validation was achieved for all three samples using QITMS.

Polyfluoroalkyl substances (PFASs) and para-phenylenediamines (PPDs) are emerging classes of anthropogenic contaminants that are environmentally persistent (most often found in ground and surface water sources), bioaccumulative, and harmful to human health. These chemicals are currently regulated in the US by the Environmental Protection Agency (EPA), the Food and Drug Administration (FDA), and the Occupational Safety and Health Administration (OSHA). Analysis of these contaminants is currently spearheaded by mass spectrometry (MS) coupled to liquid chromatography (LC) because of their high sensitivity and separation capabilities. Although effective, a major flaw in LC-MS analysis is its large consumption of solvents and the amount of time required for each experiment. Direct analysis in real time mass spectrometry (DART-MS) is a new technique that offers high sensitivity and permits rapid analysis with little to no sample preparation. Herein, we present the qualitative and quantitative analysis of PFASs and PPDs by high-resolution DART-MS, interfaced with ion mobility (IM) and tandem mass spectrometry (MS/MS) characterization, demonstrating the utility of this multidimensional approach for the fast separation and detection of environmental contaminants.