Advances of Ion Mobility Platform for Plant Metabolomics

Metabolomics aims to profile the extensive array of metabolites that exists in different types of matrices using modern analytical techniques. These techniques help to separate, identify, and quantify the plethora of chemical compounds at various analytical platforms. Hence, ion mobility spectrometry (IMS) has emerged as an advanced analytical approach, exclusively owing to the 3D separation of metabolites and their isomers. Furthermore, separated metabolites are identified based on their mass fragmentation pattern and CCS (collision cross-section) values. The IMS provides an advanced alternative dimension to separate the isomeric metabolites with enhanced throughput with lesser chemical noise. Thus, the present review highlights the types, factors affecting the resolution, and applications of IMMS (Ion mobility mass spectrometry) for isomeric separations, and ionic contaminants in the plant samples. Furthermore, an overview of IMS-based applications for the identification of plant metabolites (volatile and non-volatile) over the last few decades has been discussed, followed by future assumptions for creating IM-based databases. Such approaches could be significant to accelerate and improve our knowledge of the vast chemical diversity found in plants.

A structural similarity networking assisted collision cross-section prediction interval filtering strategy for multi-compound identification of complex matrix by ion-mobility mass spectrometry

Ion mobility coupled with mass spectrometry (IM-MS), an emerging technology for analysis of complex matrix, has been facing challenges due to the complexities of chemical structures and original data, as well as low-efficiency and error-proneness of manual operations. In this study, we developed a structural similarity networking assisted collision cross-section prediction interval filtering (SSN-CCSPIF) strategy. We first carried out a structural similarity networking (SSN) based on Tanimoto similarities among Morgan fingerprints to classify the authentic compounds potentially existing in complex matrix. By performing automatic regressive prediction statistics on mass-to-charge ratios (m/z) and collision cross-sections (CCS) with a self-built Python software, we explored the IM-MS feature trendlines, established filtering intervals and filtered potential compounds for each SSN classification. Chemical structures of all filtered compounds were further characterized by interpreting their multidimensional IM-MS data. To evaluate the applicability of SSN-CCSPIF, we selected Ginkgo biloba extract and dripping pills. The SSN-CCSPIF subtracted more background interferences (43.24%∼43.92%) than other similar strategies with conventional ClassyFire criteria (10.71%∼12.13%) or without compound classification (35.73%∼36.63%). Totally, 229 compounds, including eight potential new compounds, were characterized. Among them, seven isomeric pairs were discriminated with the integration of IM-separation. Using SSN-CCSPIF, we can achieve high-efficient analysis of complex IM-MS data and comprehensive chemical profiling of complex matrix to reveal their material basis.

Surveying the mugineic acid family: Ion mobility - quadrupole time-of-flight mass spectrometry (IM-QTOFMS) characterization and tandem mass spectrometry (LC-ESI-MS/MS) quantification of all eight naturally occurring phytosiderophores

Phytosiderophores (PS) are root exudates released by grass species (Poaceae) that play a pivotal role in iron (Fe) plant nutrition. A direct determination of PS in biological samples is of paramount importance in understanding micronutrient acquisition mediated by PS. To date, eight plant-born PS have been identified; however, no analytical procedure is currently available to quantify all eight PS simultaneously with high analytical confidence. With access to the full set of PS standards for the first time, we report comprehensive methods to both fully characterize (IM-QTOFMS) and quantify (LC-ESI-MS/MS) all eight naturally occurring PS belonging to the mugineic acid family. The quantitative method was fully validated, yielding linear results for all eight analytes, and no unwanted interferences with soil and plant matrices were observed. LOD and LOQ values determined for each PS were below 11 and 35 nmol L-1, respectively. The method's precision under reproducibility conditions (intra- and inter-day) of measurement was less than 2.5% RSD for all analytes. Additionally, all PS were annotated with high-resolution mass spectrometric fragment spectra and further characterized via drift tube ion mobility-mass spectrometry. The collision cross-sections obtained for primary ion species yielded a valuable database for future research focused on in-depth PS studies. The new quantitative method was applied to analyse root exudates from Fe-controlled and deficient barley, oat, rye, and sorghum plants. All eight PS, including mugineic acid (MA), 3"-hydroxymugineic acid (HMA), 3"-epi-hydroxymugineic acid (epi-HMA), hydroxyavenic acid (HAVA), deoxymugineic acid (DMA), 3"-hydroxydeoxymugineic acid (HDMA), 3"-epi-hydroxydeoxymugineic acid (epi-HDMA) and avenic acid (AVA) were for the first time successfully identified and quantified in root exudates of various graminaceous plants using a single analytical procedure. These newly developed methods can be applied to studies aimed at improving crop yield and micronutrient grain content for food consumption via plant-based biofortification.

An integrated two-step filtering strategy of collision cross-section interval predicting and mass defect filtering for targeted identification of analogues in herbal medicines using liquid chromatography-ion mobility-mass spectrometry

Rapid identification of chemical analogues in herbal medicines using liquid chromatography-mass spectrometry was an efficient tool for discoveries of potentially active ingredients. Multi-dimensional combination of various separation technologies could significantly enhance the capacities for detection of trace components and discrimination of multiple isomers. In this study, an integrated two-step filtering strategy on liquid chromatography-ion mobility tandem with quadrupole-time-of-flight mass spectrometry (LC-IM-QTOF MS) was developed for identification of analogues in complex matrixes. The extracted raw data were preliminarily filtered by a collision-cross section (CCS) interval generated from power regression with confidence level at 99% for prediction of analogues. Then, the remained ions were further screened using a mass defect filtering (MDF) window based on m/z and decimal m/z of potential skeletons and substituents. By applying this strategy, 86, 102, 73, and 57 isoquinoline alkaloids were identified in herbal materials of Coptis chinensis Franch (CC), C. deltoidea C.Y.Cheng et Hsiao (CD), C. teeta Wall (CT), and Corydalis yanhusuo W.T.Wang (CY). The integrated two-step filtering presented higher efficiencies on exclusion of the background interference and reducing the false-positive rates than previously reported approaches. This study facilitated the application of LC-IM-MS on small molecular analysis and promoted the discoveries of bioactive components of herbal medicines for further pharmacological researches and quality control.

Identification of Metabolites in Single Cells by Ion Mobility Separation and Mass Spectrometry

Non-targeted metabolic analysis of single cells by mass spectrometry (MS) is important for understanding individual cell functions and characterizing cell-to-cell heterogeneity. However, identifying biomolecules in single cells presents significant challenges due to the low picoliter volume samples and the structural diversity of metabolites. Capillary microsampling electrospray ionization (ESI) MS with ion mobility separation (IMS) enables the analysis of single cells under ambient conditions with minimum sample pretreatment and improved specificity. Here, we describe a protocol for the analysis of the metabolic makeup, and the identification of ions produced from single cells by capillary microsampling ESI-IMS-MS.

Structural analysis of glutathionyl hemoglobin using native mass spectrometry

Glutathionylation is an example of reversible post-translation modification of proteins where free and accessible cysteine residues of proteins undergo thiol-disulfide exchange with oxidized glutathione (GSSG). In general, glutathionylation occurs under the condition of elevated oxidative stress in vivo. In human hemoglobin, Cys93 residue of β globin chain was found to undergo this oxidative modification. Glutathionyl hemoglobin (GSHb) was reported to act as a biomarker of oxidative stress under several clinical conditions such as chronic renal failure, iron deficiency anemia, hyperlipidemia, diabetes mellitus, Friedreich's ataxia, atherosclerosis. Previously we showed that the functional abnormality associated with six-fold tighter oxygen binding of GSHb supposedly attributed to the conformational transition of the deoxy state of GSHb towards oxy hemoglobin like conformation. In the present study, we investigated the structural integrity and overall architecture of the quaternary structure of GSHb using native mass spectrometry and ion mobility mass spectrometry platforms. The dissociation equilibrium constants of both tetramer/dimer (K_d1) and dimer/monomer equilibrium (K_d2) was observed to increase by 1.91 folds and 3.64 folds respectively. However, the collision cross-section area of the tetrameric hemoglobin molecule remained unchanged upon glutathionylation. The molecular dynamics simulation data of normal human hemoglobin and GSHb was employed to support our experimental findings.

Quantitative Collision Cross-Sections from FTICR Linewidth Measurements: Improvements in Theory and Experiment

Two corrections to the equation used in the cross-sectional areas by Fourier transform ion cyclotron resonance ("CRAFTI") technique are identified. In CRAFTI, ion collision cross-sections are obtained from the pressure-dependent ion linewidths in Fourier transform mass spectra. The effects of these corrections on the accuracy of the cross-sections obtained using the CRAFTI technique are evaluated experimentally using the 20 biogenic amino acids and several crown ether complexes with protonated alkyl monoamines. Good absolute agreement is obtained between the CRAFTI cross-sections and the corresponding cross-sections obtained using both static drift ion mobility spectrometry and computational simulations. These results indicate that the CRAFTI cross-sections obtained using the updated equation presented here are quantitatively descriptive of the size and shape of the gas-phase ions. Cross-sections that differ by less than 3% are measured for the isobaric isomers n-butylamine and tert-butylamine complexed with the crown ethers. This level of precision is similar to what has been achieved previously using traveling wave ion mobility devices. These results indicate that CRAFTI can be used to probe subtle structural differences between ions with approximately the same precision as that achieved in traveling wave ion mobility devices. Graphical Abstract ᅟ.

Benchmark Comparison for a Multi-Processing Ion Mobility Calculator in the Free Molecular Regime

A benchmark comparison between two ion mobility and collision cross-section (CCS) calculators, MOBCAL and IMoS, is presented here as a standard to test the efficiency and performance of both programs. Utilizing 47 organic ions, results are in excellent agreement between IMoS and MOBCAL in He and N_2, when both programs use identical input parameters. Due to a more efficiently written algorithm and to its parallelization, IMoS is able to calculate the same CCS (within 1%) with a speed around two orders of magnitude faster than its MOBCAL counterpart when seven cores are used. Due to the high computational cost of MOBCAL in N₂, reaching tens of thousands of seconds even for small ions, the comparison between IMoS and MOBCAL is stopped at 70 atoms. Large biomolecules (>10000 atoms) remain computationally expensive when IMoS is used in N₂ (even when employing 16 cores). Approximations such as diffuse trajectory methods (DHSS, TDHSS) with and without partial charges and projected area approximation corrections can be used to reduce the total computational time by several folds without hurting the accuracy of the solution. These latter methods can in principle be used with coarse-grained model structures and should yield acceptable CCS results. Graphical Abstract ᅟ.

Structural Characterization of Monomers and Oligomers of D-Amino Acid-Containing Peptides Using T-Wave Ion Mobility Mass Spectrometry

The D-residues are crucial to biological function of D-amino acid containing peptides (DAACPs). Previous ion mobility mass spectrometry (IM-MS) studies revealing oligomerization patterns of amyloid cascade demonstrated conversion from native soluble unstructured assembly to fibril ß-sheet oligomers, which has been implicated in amyloid diseases, such as Alzheimer's disease and type 2 diabetes. Although neuropeptides are typically present at very low concentrations in circulation, their local concentrations could be much higher in large dense core vesicles, forming dimers or oligomers. We studied the oligomerization of protonated and metal-adducted achatin I and dermorphin peptide isomers with IM-MS. Our results suggested that dimerization, oligomerization, and metal adduction augment the structural differences between D/L peptide isomers compared to protonated monomers. Dimers and oligomers enhanced the structural differences between D/L peptide isomers in both aqueous and organic solvent system. Furthermore, some oligomer forms were only observed for either D- or L-isomers, indicating the importance of chiral center in oligomerization process. The oligomerization patterns of D/L isomers appear to be similar. Potassium adducts were detected to enlarge the structural differences between D/L isomers. Graphical Abstract ᅟ.

Analysis of diacylglycerols by ultra performance liquid chromatography-quadrupole time-of-flight mass spectrometry: Double bond location and isomers separation

Diacylglycerols (DAGs) are important lipid intermediates and have been implicated in human diseases. Isomerism complicates their mass spectrometric analysis; in particular, it is difficult to identify fatty acid substituents and locate the double bond positions in unsaturated DAGs. We have developed an analytical strategy using ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC/Q-TOF MS) in conjunction with dimethyl disulfide (DMDS) derivatization and collision cross-section (CCS) measurement to characterize DAGs in biological samples. The method employs non-aqueous reversed-phase chromatographic separation and profile collision energy (CE) mode for MS(E) and MS/MS analyses. Three types of fragment ions were produced simultaneously. Hydrocarbon ions (m/z 50-200) obtained at high CE helped to distinguish unsaturated and saturated DAGs rapidly. Neutral loss ions and acylium ions (m/z 300-400) produced at low CE were used to identify fatty acid substituents. Informative methyl thioalkane fragment ions were used to locate the double bonds of unsaturated DAGs. Mono-methylthio derivatives were formed mainly by the reaction of DAGs with DMDS, where methyl thiol underwent addition to the first double bond farthest from the ester terminus of unsaturated fatty acid chains. The addition of CCS values maximized the separation of isomeric DAG species and improved the confidence of DAG identification. Fourteen DAGs were identified in mouse myotube cells based on accurate masses, characteristic fragment ions, DMDS derivatization, and CCS values.