High-resolution Ion Mobility Mass Spectrometry Research Articles

Unraveling the Structure and Dynamics of Ac-PHF6-NH2 Tau Segment Oligomers.

The aggregation of the proteins tau and amyloid-β is a salient feature of Alzheimer's disease, the most common form of neurodegenerative disorders. Upon aggregation, proteins transition from their soluble, monomeric, and functional state into insoluble, fibrillar deposits through a complex process involving a variety of intermediate species of different morphologies, including monomers, toxic oligomers, and insoluble fibrils. To control and direct peptide aggregation, a complete characterization of all species present and an understanding of the molecular processes along the aggregation pathway are essential. However, this is extremely challenging due to the transient nature of oligomers and the complexity of the reaction networks. Therefore, we have employed a combined approach that allows us to probe the structure and kinetics of oligomeric species, following them over time as they form fibrillar structures. Targeting the tau protein peptide segment Ac-PHF6-NH2, which is crucial for the aggregation of the full protein, soft nano-electrospray ionization combined with ion mobility mass spectrometry has been employed to study the kinetics of heparin-induced intact oligomer formation. The oligomers are identified and characterized using high-resolution ion mobility mass spectrometry, demonstrating that the addition of heparin does not alter the structure of the oligomeric species. The kinetics of fibril formation is monitored through a Thioflavin T fluorescence assay. Global fitting of the kinetic data indicates that secondary nucleation plays a key role in the aggregation of the Ac-PHF6-NH2 tau segment, while the primary nucleation rate is greatly accelerated by heparin.

Cation induced changes to the structure of cryptophane cages.

Here the monocation complexes of seven anti-cryptophanes are examined with high-resolution ion-mobility mass spectrometry. The relative size of the [cation + cryptophane]+ complexes were compared based on their measured mobilities and derived collisional cross sections. A paradoxical trend of structural contraction was observed for complexes of increasing cation size. Density functional theory confirmed encapsulation occurs for cation = Na+, K+, Rb+, Cs+ and NH4+. However, cation = Li+ preferred oxygen coordination at a linker over encapsulation within the cavity, leading to a slightly larger gas phase structure overall. Protonated cryptophanes yielded much larger collision cross sections via imploded cryptophane structures. Thus, competing physical effects led to the observed non-periodic size trend of the complexes. Trends in complexation from isothermal titration calorimetry and other condensed phase techniques were borne out by the gas phase studies. Further, predicted cavity sizes compared with the gas phase experimental findings reveal more about the encapsulation mechanisms themselves.

Improved separation of fentanyl isomers using metal cation adducts and high-resolution ion mobility-mass spectrometry.

Fentanyl is a potent synthetic opioid that has attracted significant attention due to its illegal production and distribution, resulting in misuse, overdose, and fatalities. Because numerous fentanyl analogs, including structural isomers, with different potency have been discovered in the field, there is a critical need to continue developing analytical methodologies capable of accurate identification in forensic and clinical laboratories. This study aimed to develop a rapid method for detecting and separating fentanyl isomers based on ion mobility-mass spectrometry (IM-MS), where IM separates gas-phase ions based on differences in their size, shape, and charge. Several strategies for improved differentiation were implemented, including using unconventional cation adducts (e.g., alkali and transition metals) and data post-processing by high-resolution demultiplexing. A collection of collision cross section (CCS) values for the various metal ion adducts was gathered, which can be used to improve confidence of identification in future samples. Notable examples, such as [M + Cu]+ and [M + Ag]+ adducts, contributed to significant improvement of resolution between isomers. Furthermore, the addition of high-resolution post-processing provided resolving power of >150, which constitutes a significant increase in comparison with the normal 50-60 obtained with low-resolution drift tube instruments. Collectively, these improved separation strategies allowed for confident detection and subsequent quantitative analysis. The optimized IM-MS method resulted in quantification of fentanyl in human urine with limits of detection and quantification of 13 pg/mL and 40 pg/mL, respectively.

Abstract P078: Cancer cell derived extracellular vesicles convey protein signatures of small cell lung carcinoma

Abstract Extracellular vesicles (EVs) are known effectors of cell signaling and exchange implicated in cancer development and progression, as well as remodeling and immunomodulation of the tumor microenvironment. EVs are detected in various biofluids and are considered to convey signature features of the cells from which they originate. Clinical assessment of plasma-derived EV molecular contents therefore offers promise of “liquid biopsies” for detection or subtyping of cancers as well as dynamic reporting of tumor status during and after treatment. To date, there have been no comprehensive analyses aimed at interrogating the diverse repertoire of EV protein cargoes in small cell lung carcinoma (SCLC). Using plasmas from a cohort of 18 SCLC cases, 16 lung adenocarcinoma (LUAD) cases and 34 controls matched based on smoking status, age, and sex, EVs were enriched via affinity capture using magnetic beads functionalized with phosphatidyl serine binding protein TIM4 in addition to single-step density flotation ultracentrifugation to deplete abundant protein background. In-depth proteomic profiling was performed on enriched EVs via nano liquid chromatography / high-resolution ion-mobility mass spectrometry. Profiles were intersected with proteomic profiles generated from intratumor EVs dissociated from 12 SCLC patient-derived xenograft (PDX) mouse models as well as EVs isolated from cell-conditioned medias of a panel of 17 SCLC cell lines. A total of 496 proteins were quantified in TIM4pos EVs. Unsupervised hierarchical clustering and principal component analyses showed that TIM4pos EV protein cargoes differentiate SCLC from LUAD and matched controls. Differential analyses identified 117 proteins that were elevated (AUC> 0.60) in TIM4pos SCLC EVs compared to controls. Of these 117 features, 101 (86%) were also elevated (AUC> 0.60) in TIM4pos SCLC EVs compared to TIM4pos LUAD EVs. Intersection of proteins elevated in TIM4pos SCLC EVs with proteomic profiles of intratumor EVs from SCLC PDX models and conditioned media-derived EVs from SCLC cell lines yielded 67 and 92 overlapping proteins, respectively. Overlapping proteins were characterized by YAP1-associated signatures of cytoskeletal re-arrangement and epithelial-to-mesenchymal transition and included a prevalence of neuronal tubulin and actin family members, YWHA family members, and annexins. We developed and applied an optimized EV isolation and proteomics workflow to profile EV protein cargoes and establish circulating EV-associated protein signatures of SCLC with biomarker potential. Our integrated analyses identified novel EV-associated proteins for detection of SCLC that are associated with oncogenic drivers. These studies demonstrate that EVs harbor cancer cell disseminated signatures and that continued efforts to query the EV proteome towards discovery of novel SCLC biomarkers are warranted. Citation Format: Jody Vykoukal, Taketo Kato, Hiroyuki Katayama, Allison Stewart, Ehsan Irajizad, Yining Cai, Fu-Chung Hsiao, Jennifer B. Dennison, Edwin J. Ostrin, Hai T. Tran, Carl M. Gay, Lauren A. Byers, Johannes F. Fahrmann, Samir M. Hanash. Cancer cell derived extracellular vesicles convey protein signatures of small cell lung carcinoma. [abstract]. In: Proceedings of the AACR Special Conference: Precision Prevention, Early Detection, and Interception of Cancer; 2022 Nov 17-19; Austin, TX. Philadelphia (PA): AACR; Can Prev Res 2023;16(1 Suppl): Abstract nr P078.

Mapping Isomeric Peptides Derived from Biopharmaceuticals Using High-Resolution Ion Mobility Mass Spectrometry

The identification and localization of isomeric peptide modifications is a critical requirement of the biopharmaceutical industry. Despite the ability of liquid chromatography-mass spectrometry to identify many of the common post translational modifications, the identification of isobaric or racemized peptides is confounded by modern mass spectrometry-based techniques. Here, we present a novel approach combining liquid chromatography with a high-resolution ion mobility mass spectrometry system to differentiate peptide and peptide fragments based upon their mobility and mass.

Pushing the Proteomics Envelope: More sensitive technology spurs proteomic and metabolomic biomarker identification, clinical use

Pushing the Proteomics Envelope: More sensitive technology spurs proteomic and metabolomic biomarker identification, clinical use

Linear Size Contraction of Ligand Protected Ag29 Clusters by Substituting Ag with Cu

There are only a few examples of atomically precise, ligand protected, bimetallic coinage metal clusters in which molecular structure remains essentially unchanged over a wide composition range starting from the corresponding homometallic species. Such model systems are particularly useful to study the dynamics of alloy formation on the nanoscale. Here we demonstrate the unusual reactivity of solvated metalloid-superatom Ag29(BDT)12(PPh3)4 (BDT = 1,3 benzenedithiol) clusters toward semiconducting Cu12S6(DPPPT)4 (DPPPT = bis(diphenylphosphino)pentane) clusters as an efficient way to exchange multiple copper atoms into the atomically precise silver clusters without changing overall the structure type. Concentration-dependent UV-vis absorption and online mass spectrometry shows that 14 Cu atoms can be exchanged into the silver cluster. Beyond the 14 Cu atom exchange, the cluster degrades to smaller thiolates. Information on cluster structures is obtained from high-resolution ion mobility mass spectrometry, which shows a linear decrease in collision cross section (CCS) with each Ag/Cu exchanged. Several isomeric structures are calculated by density functional theory (DFT), and their calculated collision cross sections are used to identify the most stable isomers for each Ag/Cu exchange product. Ag/Cu exchange is essentially limited to the cluster surface/shell. The core appears not to be involved.

Separation and identification of ACE inhibitory peptides from defatted walnut meal

The peptide obtained from walnut protein enzymatic hydrolysate had high ACE inhibitory activity. Through centrifugation, ultrafiltration, gel chromatography and high performance liquid chromatography (HPLC), the walnut oligo-peptide, which was denoted as P4-c with high ACE inhibitory activity was obtained. Three novel ACE inhibitory peptides, GVVPHN, EHSLDPLK and KTLLNFGPN, were identified from P4-c by high-resolution ion mobility mass spectrometry (IM-MS). The three novel ACE inhibitory peptides possessed good ACE inhibitory activity and the fraction GVVPHN had high ACE inhibitory activity with 27.3 µmol L−1 of IC50. The molar percentage of hydrophobic amino acids in the peptide GVVPHN was 50% while the hydrophobic amino acid contents of EHSLDPLK and KTLLNFGPN were 37.5% and 44.4%, respectively, which indicates ACE inhibitory activities were hydrophobicity of amino acid-dependent.

Detection of Intermediates in Dual Gold Catalysis Using High-Resolution Ion Mobility Mass Spectrometry

We have probed for reaction intermediates involved in the dual-gold-catalyzed activation of a conjugated 1,5-diyne substrate and its further coupling to benzene in the liquid phase. This was done by sampling the reaction mixture by electrospray ionization followed by high-resolution ion mobility mass spectrometry—under conditions allowing for the resolution of structural isomers differing in their collision cross sections by less than 0.5%. For the cationic mass corresponding to catalyst + diyne (activation stage) we resolve four isomers. At the mass corresponding to catalyst + diyne + benzene, two isomers are observed. By comparing the experimentally obtained cross sections to those inferred for model structures derived from density functional computations, we find our measurements to be consistent with the proposed solution mechanism. This constitutes the first direct observation of intermediates in dual gold catalysis and supports the previous inference that the mechanism involves cooperative interacti...

High resolution-ion mobility mass spectrometry as an additional powerful tool for structural characterization of mycotoxin metabolites

This work was designed as a proof of concept, to demonstrate the successful use of the comparison between theoretical and experimental collision cross section (CCS) values to support the identification of isomeric forms. To this purpose, thirteen mycotoxins were considered and analyzed using drift time ion mobility mass spectrometry. A good linear correlation (r2 = 0.962) between theoretical and experimental CCS was found. The average ΔCCS was 3.2%, fully consistent with the acceptability threshold value commonly set at 5%. The agreement between theoretical and experimental CCS obtained for mycotoxin glucuronides suggested the potential of the CCS matching in supporting the annotation procedure.

An experimental investigation into the reduced mobilities of lanthanide cations using high-resolution ion mobility mass spectrometry

Reduced mobilities for ground-state electronic configurations of the complete lanthanide series of cations, excluding promethium, have been measured. These values were obtained using an ion mobility mass spectrometer that utilizes a 2m drift tube to generate high-resolution ion mobility data. In all cases, lanthanide cations were generated using pulsed-laser vaporization of either a metal rod or foil target. The mobilities of Eu+, Gd+, Yb+, and Lu+ have been previously examined and these data are also included. All other lanthanide cation mobilities, measured in He, are reported here for the first time. A discussion of the observed trends in the mobilities of the lanthanide series is also provided.

Reduced mobilities of lanthanide cations measured using high-resolution ion mobility mass spectrometry with comparisons between experiment and theory

Reduced mobilities for ground-state electronic configurations of Eu+, Gd+, Yb+, and Lu+ have been measured using a high-resolution ion mobility mass spectrometer. The instrument uses a 2m drift tube to generate high-resolution ion mobility data. Lanthanide cations were generated using pulsed-laser vaporization of either a metal rod or foil target. The mobilities of these four lanthanide cations have been previously studied using high-quality ab initio calculations, to determine potential energy curves that described their interactions with the noble gases (He to Xe). A comparison between experimental and theoretical results shows extremely good agreement in three of the four systems.

Characterizing the electronic states of the second-row transition metal cations using high-resolution ion mobility mass spectrometry

Reduced mobilities for ground-state and electronic excited-state configurations of the second-row transition metal cations, excluding Tc+, have been measured. These values were obtained using an ion mobility mass spectrometer that utilizes a 2m drift tube to generate high-resolution ion mobility data. Several of these atomic cations have been previously studied and the results obtained here are compared to reduced mobilities reported in the literature. In all cases, ions were generated using pulsed-laser vaporization of either a metal rod or foil target. Presented here for the first time are the reduced mobilities of Y+, Ru+, and Rh+. A discussion of the observed trends in the mobilities of the second-row transition metal series, relative to those measured for the first-row series, is also provided.

The Influence of Lipid Bilayer Physicochemical Properties on Gramicidin A Conformer Preferences

The conformational preferences adopted by gramicidin A (GA) dimers inserted into phospholipid bilayers are reported as a function of the bilayer cholesterol content, temperature, and incubation time. Through use of vesicle capture-freeze drying methodology, GA dimers were captured in lipid bilayers and the conformational preferences of the complex were analyzed using ion mobility-mass spectrometry. Perturbations that affect the physicochemical interactions in the lipid bilayer such as cholesterol incorporation, temperature, and incubation time directly alter the conformer preferences of the complex. Regardless of bilayer cholesterol concentration, the antiparallel double helix (ADH) conformation was observed to be most abundant for GA dimers in bilayers composed of lipids with 12 to 22 carbon acyl chains. Incorporation of cholesterol into lipid bilayers yields increased bilayer thickness and rigidity, and an increased abundance of parallel double helix (PDH) and single-stranded head-to-head (SSHH) dimers were observed. Bilayers prepared using 1,2-dilauroyl-sn-glycero-3-phosphocholine, a lipid with 12 carbon acyl chains, yielded a nascent conformer that decreased in abundance as a function of bilayer cholesterol content. High resolution ion mobility-mass spectrometry data revealed two peaks in the ADH region suggesting that ADH populations are composed of two distinct conformers. The conformer preferences of GA dimers from 1,2-distearoyl-sn-glycero-3-phosphocholine bilayers were significantly different for samples incubated at 4°C vs. 60°C; increased cholesterol content yielded more PDH and SSHH at 60°C. The addition of cholesterol as well as incubating samples of 1,2-distearoyl-sn-glycero-3-phosphocholine at 60°C for 24–72 h yielded an increase in PDH and SSHH abundance.

High resolution ion mobility-mass spectrometry for separation and identification of isomeric lipids.

Lipidomics is a particularly difficult analytical challenge due to the number and importance of isomeric species that are known or postulated in biological samples. Current separation and identification techniques are too often insufficiently powerful, slow or ambiguous. High resolution, low field ion mobility coupled to mass spectrometry is shown here to have sufficient performance to represent a new alternative for lipidomics. For the first time, drift-tube ion mobility separation of lipid isomers that differ only in position of the acyl chain, position of the double bond or double bond geometry is demonstrated. Differences in collision cross sections of less than 1% are sufficient for baseline separation. The same level of performance is maintained in complex biological mixtures. More than 130 high-precision reduced mobility and collision cross section values were also determined for a range of lipids. Such data can be the basis of a new lipidomics workflow, as the appropriate libraries are developed.

The Periodic Focusing Ion Funnel: Theory, Design, and Experimental Characterization by High-Resolution Ion Mobility-Mass Spectrometry

Simulation-based development and experimental characterization of a DC-only ion funnel is described herein. Radial ion confinement is achieved via periodic focusing whereby a collisionally dampened effective potential is generated in the inertial frame of an ion traversing the device with appreciable velocity. The new device, termed a periodic focusing ion funnel (PF IF), provides an efficient alternative to the rf ion funnel providing high ion transmission with fewer electrodes, simplified electrical circuitry, and reduced power supply requirements. The utility of the PF IF for structural ion mobility-mass spectrometry (IM-MS) studies is demonstrated using model peptide ions (bradykinin, gramicidin S, and trpzip 1).

Metabolic profiling of human blood by high-resolution ion mobility mass spectrometry (IM-MS)

A high-resolution ion mobility time-of-flight mass spectrometer with electrospray ionization source (ESI-IM-MS) was evaluated as an analytical method for rapid analysis of complex biological samples such as human blood metabolome. The hybrid instrument (IM-MS) provided an average ion mobility resolving power of ∼90 and a mass resolution of ∼1500 (at m/ z 100). A few μL of whole blood was extracted with methanol, centrifuged and infused into the IM-MS via an electrospray ionization source. Upon IM-MS profiling of the human blood metabolome approximately 1100 metabolite ions were detected and 300 isomeric metabolites separated in short analyses time (30 min). Estimated concentration of the metabolites ranged from the low micromolar to the low nanomolar level. Various classes of metabolites (amino acids, organic acids, fatty acids, carbohydrates, purines and pyrimidines, etc.) were found to form characteristic mobility-mass correlation curves (MMCCs) that aided in metabolite identification. Peaks corresponding to various sterol derivatives, estrogen derivatives, phosphocholines, prostaglandins, and cholesterol derivatives detected in the blood extract were found to occupy characteristic two-dimensional IM-MS space. Low abundance metabolite peaks that can be lost in MS random noise were resolved from noise peaks by differentiation in mobility space. In addition, the peak capacity of MS increased sixfold by coupling IMS prior to MS analysis.