Chemometric data analysis for deconvolution of overlapped ion mobility profiles

Separation of triacylglycerol (TAG) isomers by cyclic ion mobility mass spectrometry

Triacylglycerols (TAGs), a major lipid class in foods and the human body, consist of three fatty acids esterified to a glycerol backbone. They can occur in various isomeric forms, including sn-positional, cis/trans configurational, acyl chain length, double bond positional, and mixed type isomers. Separating isomeric mixtures is of great interest as different isomers can have distinct influence on mechanisms, such as digestibility, oxidative stability, or lipid metabolism. However, TAG isomer separation remains challenging with established analytical methodologies such as liquid-chromatography coupled to mass spectrometry (LC-MS). In this study, we developed a method with cyclic ion mobility mass spectrometry (cIMS-MS) for the separation and identification of all types of TAG isomers. First, the influence of different adducts (Li+, NH4+, Na+, and K+) on the separation was studied. Overall, it was concluded that the sodium adduct is the best choice to efficiently separate all types of TAG isomers. In addition, trends were found in the influence of specific structural features on the drift time order. An order of relative influence (from high to low) was established; (1) degree of unsaturation of the fatty acid(s) on an exterior position (if the total degree of unsaturation(s) is equal in both TAGs), (2) acyl chain length on the exterior positions, (3) cis/trans configuration, and (4) double bond (DB)-position. Finally, various cIMS-MS strategies were developed for the separation of mixtures containing four, five, and six isomers. To conclude, the developed methods can be used for separation of complex mixtures of TAG isomers and have great potential to be expanded to isomers of similar types of lipids such as di- and monoacylglycerols. This study also shows the potential of cIMS-MS to be used for the application on real TAG samples.

Prediction of Structures of Compounds Encountered in Complex Organic Matter with Highly Flexible Alkyl Chains Using Ion Mobility-Mass Spectrometry

The chemical structure of an organic molecule has a direct influence on its three-dimensional conformation. One way to obtain information on this conformation is to use ion mobility spectrometry. This technique allows the separation of different isomers according to their collision cross section (CCS) with an inert gas. Smaller or more compact molecules will have lower collision cross section values than larger molecules. The CCS is an intrinsic ion parameter for a specific gas and is thus predictable. Today, calculations of rigid molecules are commonly performed to obtain additional structural information on an ion. However, calculations are more complex with very flexible molecules. In particular, molecules presenting long alkyl chains can yield a high number of conformers. Each conformer is then associated with a CCS value that is specific to it. We report, here, a methodology to predict CCS of flexible molecules. The used approach is based on automatic conformers research followed by geometry optimization and CCS calculations. Determination of theoretical and experimental CCS values for a rigid polycyclic aromatic hydrocarbons (PAHs) standard was used to calibrate the Mobcal software. Then, 13 standard molecules ranging from 4 to 19 carbon alkyl chains, including three long alkyl chain isomers of C₂₂H₃₈, were analyzed on a TWIMS-ToF and calculated using our methodology. CCS deviations between experimental and theoretical values were found to be less than 1.5% over the whole studied CCS range. This method was finally applied for structural analysis of petroleum compounds refractory to the hydro-denitrogenation process.

Challenges and emergent solutions for LC-MS/MS based untargeted metabolomics in diseases

In the past decade, advances in liquid chromatography-mass spectrometry (LC-MS) have revolutionized untargeted metabolomics analyses. By mining metabolomes more deeply, researchers are now primed to uncover key metabolites and their associations with diseases. The employment of untargeted metabolomics has led to new biomarker discoveries and a better mechanistic understanding of diseases with applications in precision medicine. However, many major pertinent challenges remain. First, compound identification has been poor, and left an overwhelming number of unidentified peaks. Second, partial, incomplete metabolomes persist due to factors such as limitations in mass spectrometry data acquisition speeds, wide-range of metabolites concentrations, and cellular/tissue/temporal-specific expression changes that confound our understanding of metabolite perturbations. Third, to contextualize metabolites in pathways and biology is difficult because many metabolites partake in multiple pathways, have yet to be described species specificity, or possess unannotated or more-complex functions that are not easily characterized through metabolomics analyses. From a translational perspective, information related to novel metabolite biomarkers, metabolic pathways, and drug targets might be sparser than they should be. Thankfully, significant progress has been made and novel solutions are emerging, achieved through sustained academic and industrial community efforts in terms of hardware, computational, and experimental approaches. Given the rapidly growing utility of metabolomics, this review will offer new perspectives, increase awareness of the major challenges in LC-MS metabolomics that will significantly benefit the metabolomics community and also the broader the biomedical community metabolomics aspire to serve.

Applications of Ion Mobility-Mass Spectrometry in Carbohydrate Chemistry and Glycobiology

Carbohydrate analyses are often challenging due to the structural complexity of these molecules, as well as the lack of suitable analytical tools for distinguishing the vast number of possible isomers. The coupled technique, ion mobility-mass spectrometry (IM-MS), has been in use for two decades for the analysis of complex biomolecules, and in recent years it has emerged as a powerful technique for the analysis of carbohydrates. For carbohydrates, most studies have focused on the separation and characterization of isomers in biological samples. IM-MS is capable of separating isomeric ions by drift time, and further characterizing them by mass analysis. Applications of IM-MS in carbohydrate analysis are extremely useful and important for understanding many biological mechanisms and for the determination of disease states, although efforts are still needed for higher sensitivity and resolution.

Characterization of Isomeric Glycans by Reversed Phase Liquid Chromatography-Electronic Excitation Dissociation Tandem Mass Spectrometry

The occurrence of numerous structural isomers in glycans from biological sources presents a severe challenge for structural glycomics. The subtle differences among isomeric structures demand analytical methods that can provide structural details while working efficiently with on-line glycan separation methods. Although liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a powerful tool for mixture analysis, the commonly utilized collision-induced dissociation (CID) method often does not generate a sufficient number of fragments at the MS2 level for comprehensive structural characterization. Here, we studied the electronic excitation dissociation (EED) behaviors of metal-adducted, permethylated glycans, and identified key spectral features that could facilitate both topology and linkage determinations. We developed an EED-based, nanoscale, reversed phase (RP)LC-MS/MS platform, and demonstrated its ability to achieve complete structural elucidation of up to five structural isomers in a single LC-MS/MS analysis. Graphical Abstract.

Broadband ion mobility deconvolution for rapid analysis of complex mixtures

Broadband IM-MS deconvolution allows generation of IM and MS data for species that are UPLC-IM-MS unresolved.

Effective Ion Mobility Peak Width as a New Isomeric Descriptor for the Untargeted Analysis of Complex Mixtures Using Ion Mobility-Mass Spectrometry

Ion mobility coupled with mass spectrometry was proven to be an efficient way to characterize complex mixtures such as petroleum samples. However, the identification of isomeric species is difficult owing to the molecular complexity of petroleum and no availability of standard molecules. This paper proposes a new simple indicator to estimate the isomeric content of highly complex mixtures. This indicator is based on the full width at half maximum (FWHM) of the extracted ion mobility peak measured in millisecond or square angstrom that is corrected for instrumental factors such as ion diffusion. This value can be easily obtained without precisely identifying the number of isomeric species under the ion mobility peaks. Considering the Boduszynski model, the ion mobility profile for a particular elemental composition is expected to be a continuum of various isomeric species. The drift time-dependent fragmentation profile was studied and confirmed this hypothesis, a continuous evolution of the fragmentation profile showing that the larger alkyl chain species were detected at higher drift time values. This new indicator was proven to be a fast and efficient method to compare vacuum gas oils for which no difference was found using other analytical techniques. Graphical Abstract ᅟ.

Accurate Drift Time Determination by Traveling Wave Ion Mobility Spectrometry: The Concept of the Diffusion Calibration

Ion mobility spectrometry (IMS) is a gas phase separation technique, which relies on differences in collision cross section (CCS) of ions. Ionic clouds of unresolved conformers overlap if the CCS difference is below the instrumental resolution expressed as CCS/ΔCCS. The experimental arrival time distribution (ATD) peak is then a superimposition of the various contributions weighted by their relative intensities. This paper introduces a strategy for accurate drift time determination using traveling wave ion mobility spectrometry (TWIMS) of poorly resolved or unresolved conformers. This method implements through a calibration procedure the link between the peak full width at half-maximum (fwhm) and the drift time of model compounds for wide range of settings for wave heights and velocities. We modified a Gaussian equation, which achieves the deconvolution of ATD peaks where the fwhm is fixed according to our calibration procedure. The new fitting Gaussian equation only depends on two parameters: The apex of the peak (A) and the mean drift time value (μ). The standard deviation parameter (correlated to fwhm) becomes a function of the drift time. This correlation function between μ and fwhm is obtained using the TWIMS calibration procedure which determines the maximum instrumental ion beam diffusion under limited and controlled space charge effect using ionic compounds which are detected as single conformers in the gas phase. This deconvolution process has been used to highlight the presence of poorly resolved conformers of crown ether complexes and peptides leading to more accurate CCS determinations in better agreement with quantum chemistry predictions.

Determination of ion mobility collision cross sections for unresolved isomeric mixtures using tandem mass spectrometry and chemometric deconvolution

Ion mobility (IM) is an important analytical technique for determining ion collision cross section (CCS) values in the gas-phase and gaining insight into molecular structures and conformations. However, limited instrument resolving powers for IM may restrict adequate characterization of conformationally similar ions, such as structural isomers, and reduce the accuracy of IM-based CCS calculations. Recently, we introduced an automated technique for extracting "pure" IM and collision-induced dissociation (CID) mass spectra of IM overlapping species using chemometric deconvolution of post-IM/CID mass spectrometry (MS) data [J. Am. Soc. Mass Spectrom., 2014, 25, 1810-1819]. Here we extend those capabilities to demonstrate how extracted IM profiles can be used to calculate accurate CCS values of peptide isomer ions which are not fully resolved by IM. We show that CCS values obtained from deconvoluted IM spectra match with CCS values measured from the individually analyzed corresponding peptides on uniform field IM instrumentation. We introduce an approach that utilizes experimentally determined IM arrival time (AT) "shift factors" to compensate for ion acceleration variations during post-IM/CID and significantly improve the accuracy of the calculated CCS values. Also, we discuss details of this IM deconvolution approach and compare empirical CCS values from traveling wave (TW)IM-MS and drift tube (DT)IM-MS with theoretically calculated CCS values using the projected superposition approximation (PSA). For example, experimentally measured deconvoluted TWIM-MS mean CCS values for doubly-protonated RYGGFM, RMFGYG, MFRYGG, and FRMYGG peptide isomers were 288.8 Å(2), 295.1 Å(2), 296.8 Å(2), and 300.1 Å(2); all four of these CCS values were within 1.5% of independently measured DTIM-MS values.

Chemometrics for ion mobility spectrometry data: recent advances and future prospects

This is the first comprehensive review on chemometric techniques used in ion mobility spectrometry data analysis.

Competing noncovalent host-guest interactions and H/D exchange: reactions of benzyloxycarbonyl-proline glycine dipeptide variants with ND3

A combination of density functional theory calculations, hydrogen/deuterium exchange (HDX) reactions, ion mobility-mass spectrometry, and isotope labeling tandem mass spectrometry was used to study gas-phase "host-guest" type interactions of a benzyloxycarbonyl (Z)-capped proline (P) glycine (G) model dipeptide (i.e., Z-PG) and its various structural analogues with ND3. It is shown that in a solvent-free environment, structural differences between protonated and alkali metal ion (Na(+), K(+), or Cs(+))-complexed species of Z-PG affect ND3 adduct formation. Specifically, [Z-PG + H](+) and [Z-PG-OCH3 + H](+) formed gas-phase ND3 adducts ([Z-PG (or Z-PG-OCH3) + H + ND3](+)) but no ND3 adducts were observed for [Z-PG + alkali metal](+) or [Z-PG + H - CO2](+). Experimentally measured and theoretically calculated collision cross sections (CCSs) of protonated and alkali metal ion-complexed Z-PG species showed similar trends that agreed with the observed structural differences from molecular modeling results. Moreover, results from theoretical ND3 affinity calculations were consistent with experimental HDX observations, indicating a more stable ND3 adduct for [Z-PG + H](+) compared to [Z-PG + alkali metal](+) species. Molecular modeling and experimental MS results for [Z-PG + H](+) and [Z-PG + alkali metal](+) suggest that optimized cation-π and hydrogen bonding interactions of carbonyl groups in final products are important for ND3 adduct formation. Graphical Abstract ᅟ.

Arrival time distributions of product ions reveal isomeric ratio of deprotonated molecules in ion mobility-mass spectrometry of hyaluronan-derived oligosaccharides

Hyaluronic acid is a naturally occurring linear polysaccharide with substantial medical potential. In this work, discrimination of tyramine-based hyaluronan derivatives was accessed by ion mobility-mass spectrometry of deprotonated molecules and nuclear magnetic resonance spectroscopy. As the product ion mass spectra did not allow for direct isomer discrimination in mixture, the reductive labeling of oligosaccharides as well as stable isotope labeling was performed. The ion mobility separation of parent ions together with the characteristic fragmentation for reduced isomers providing unique product ions allowed us to identify isomers present in a mixture and determine their mutual isomeric ratio. The determination used simple recalculation of arrival time distribution areas of unique ions to areas of deprotonated molecules. Mass spectrometry data were confirmed by nuclear magnetic resonance spectroscopy.

Collision-energy resolved ion mobility characterization of isomeric mixtures

Existing instrumental resolving power limitations in ion mobility spectrometry (IMS) often restrict adequate characterization of unresolved or co-eluting chemical isomers.

Automated deconvolution of overlapped ion mobility profiles

Presence of unresolved ion mobility (IM) profiles limits the efficient utilization of IM mass spectrometry (IM-MS) systems for isomer differentiation. Here, we introduce an automated ion mobility deconvolution (AIMD) computer software for streamlined deconvolution of overlapped IM-MS profiles. AIMD is based on a previously reported post-IM/collision-induced dissociation (CID) deconvolution approach [J. Am. Soc. Mass Spectrom. 23, 1873 (2012)] and, unlike the previously reported manual approach, it does not require resampling of post-IM/CID data. A novel data preprocessing approach is utilized to improve the accuracy and efficiency of the deconvolution process. Results from AIMD analysis of overlapped IM profiles of data from (1) Waters Synapt G1 for a binary mixture of isomeric peptides (amino acid sequences: GRGDS and SDGRG) and (2) Waters Synapt G2-S for a binary mixture of isomeric trisaccharides (raffinose and isomaltotriose) are presented.

Loss of internal backbone carbonyls: additional evidence for sequence-scrambling in collision-induced dissociation of y-type ions

It is shown that y-type ions, after losing C-terminal H2O or NH3, can lose an internal backbone carbonyl (CO) from different peptide positions and yield structurally different product fragment ions upon collision-induced dissociation (CID). Such CO losses from internal peptide backbones of y-fragment ions are not unique to a single peptide and were observed in four of five model peptides studied herein. Experimental details on examples of CO losses from y-type fragment ions for an isotopically labeled AAAAHAA-NH2 heptapeptide and des-acetylated-α-melanocyte-stimulating hormone (dα-MSH) (SYSMEHFRWGKPV-NH2) are reported. Results from isotope labeling, tandem mass spectrometry (MS(n)), and ion mobility-mass spectrometry (IM-MS) confirm that CO losses from different amino acids of m/z-isolated y-type ions yield structurally different ions. It is shown that losses of internal backbone carbonyls (as CID products of m/z-isolated y-type ions) are among intermediate steps towards formation of rearranged or permutated product fragment ions. Possible mechanisms for generation of the observed sequence-scrambled a-"like" ions, as intermediates in sequence-scrambling pathways of y-type ions, are proposed and discussed.

Energy-resolved ion mobility-mass spectrometry--a concept to improve the separation of isomeric carbohydrates

Recent works using ion mobility-mass spectrometry (IM-MS) have highlighted the power of this instrumental configuration to tackle one of the greatest challenges in glycomics and glycoproteomics: the existence of isobaric isomers. For a successful separation of species with identical mass but different structure via IM-MS, it is crucial to have sufficient IM resolution. In commercially available IM-MS instruments, however, this resolution is limited by the design of the instrument and usually cannot be increased at-will without extensive modifications. Here, we present a systematic approach to improve the resolving capability of IM-MS instruments using so-called energy-resolved ion mobility-mass spectrometry. The technique utilizes the fact that individual components in an isobaric mixture fragment at considerably different energies when activated in the gas phase via collision-induced dissociation (CID). As a result, certain components can be suppressed selectively at increased CID activation energy. Using a mixture of four isobaric carbohydrates, we show that each of the individual sugars can be resolved and unambiguously identified even when their drift times differ by as little as 3%. However, the presented results also indicate that a certain difference in the gas-phase stability of the individual components is crucial for a successful separation via energy-resolved IM-MS.

Evidence for sequence scrambling and divergent H/D exchange reactions of doubly-charged isobaric b-type fragment ions

To date, only a limited number of reports are available on structural variants of multiply-charged b-fragment ions. We report on observed bimodal gas-phase hydrogen/deuterium exchange (HDX) reaction kinetics and patterns for substance P b10(2+) that point to presence of isomeric structures. We also compare HDX reactions, post-ion mobility/collision-induced dissociation (post-IM/CID), and sustained off-resonance irradiation-collision induced dissociation (SORI-CID) of substance P b10(2+) and a cyclic peptide with an identical amino acid (AA) sequence order to substance P b10. The observed HDX patterns and reaction kinetics and SORI-CID pattern for the doubly charged head-to-tail cyclized peptide were different from either of the presumed isomers of substance P b10(2+), suggesting that b10(2+) may not exist exclusively as a head-to-tail cyclized structure. Ultra-high mass measurement accuracy was used to assign identities of the observed SORI-CID fragment ions of substance P b10(2+); over 30% of the observed SORI-CID fragment ions from substance P b10(2+) had rearranged (scrambled) AA sequences. Moreover, post-IM/CID experiments revealed the presence of two conformer types for substance P b10(2+), whereas only one conformer type was observed for the head-to-tail cyclized peptide. We also show that AA sequence scrambling from CID of doubly-charged b-fragment ions is not unique to substance P b10(2+).

Combined use of post-ion mobility/collision-induced dissociation and chemometrics for b fragment ion analysis

Although structural isomers may yield indistinguishable ion mobility (IM) arrival times and similar fragment ions in tandem mass spectrometry (MS), it is demonstrated that post-IM/collision-induced dissociation MS (post-IM/CID MS) combined with chemometrics can enable independent study of the IM-overlapped isomers. The new approach allowed us to investigate the propensity of selected b type fragment ions from AlaAlaAlaHisAlaAlaAla-NH2 (AAA(His)AAA) heptapeptide to form different isomers. Principle component analysis (PCA) of the unresolved post-IM/CID profiles indicated the presence of two different isomer types for b4(+), b5(+), and b6(+) and a single isomer type for b7(+) fragments of AAA(His)AAA. We employed a simple-to-use interactive self-modeling mixture analysis (SIMPLISMA) to calculate the total IM profiles and CID mass spectra of b fragment isomers. The deconvoluted CID mass spectra showed discernible fragmentation patterns for the two isomers of b4(+), b5(+), and b6(+) fragments. Under our experimental conditions, calculated percentages of the "cyclic" isomers (at the 95% confidence level for n = 3) for b4(+), b5(+), and b6(+) were 61 (± 5)%, 36 (± 5)%, and 48 (± 2)%, respectively. Results from the SIMPLISMA deconvolution of b5(+) species resembled the CID MS patterns of fully resolved IM profiles for the two b5(+) isomers. The "cyclic" isomers for each of the two-component b fragment ions were less susceptible to ion fragmentation than their "linear" counterparts.