Recommendations for reporting ion mobility mass spectrometry measurements

© 2019 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc. Here we present a guide to ion mobility mass spectrometry experiments, which covers both linear and nonlinear methods: what is measured, how the measurements are done, and how to report the results, including the uncertainties of mobility and collision cross section values. The guide aims to clarify some possibly confusing concepts, and the reporting recommendations should help researchers, authors and reviewers to contribute comprehensive reports, so that the ion mobility data can be reused more confidently. Starting from the concept of the definition of the measurand, we emphasize that (i) mobility values (K0) depend intrinsically on ion structure, the nature of the bath gas, temperature, and E/N; (ii) ion mobility does not measure molecular surfaces directly, but collision cross section (CCS) values are derived from mobility values using a physical model; (iii) methods relying on calibration are empirical (and thus may provide method-dependent results) only if the gas nature, temperature or E/N cannot match those of the primary method. Our analysis highlights the urgency of a community effort toward establishing primary standards and reference materials for ion mobility, and provides recommendations to do so. © 2019 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc

Oversampling Selective Accumulation Trapped Ion Mobility Spectrometry Coupled to FT-ICR MS: Fundamentals and Applications

In the present paper, we describe the fundamentals and analytical advantages of Oversampling Selective Accumulation Trapped Ion Mobility Spectrometry (OSA-TIMS) when coupled to ultrahigh resolution mass analyzers (e.g., FT-ICR MS). During TIMS analysis, ion packages are spatially resolved based on their mobilities along the TIMS analyzer axis and multiple strategies can be utilized during the trapping and elution of the ion population of interest. In the case of OSA-TIMS-FT-ICR MS, the TIMS operation sequence, trapping conditions, and operations are optimized to increase the signal-to-noise and the number of points across the mobility domain, which leads to more accurate mobility and mass measurements. Experimental results show that accurate ion-neutral collision cross sections (<1%) can be measured using OSA-TIMS-FT-ICR MS with high mobility resolving powers (<i>R</i>_IMS up to 250), high mass accuracy (<1 ppm), and ultrahigh mass resolution (<i>R</i>_MS up to 600–1200k at <i>m</i>/<i>z</i> 400) in a single analysis. The analytical advantages of OSA-TIMS over SA-TIMS were illustrated for the analysis of structural peptide isomers (SDGRG and GRGDS [M + H]⁺), conformational isomers (AT-hook peptide 3 KRGRGRPRK [M + 2H]⁺²), and a complex mixture of polyaromatic hydrocarbons (PAH) from coal tar. Baseline separation of the structural peptide isomers SDGRG and GRGDS, [M + H]⁺, was observed, and three conformations were identified for the AT-hook peptide 3 KRGRGRPRK [M + 2H]⁺² during OSA-TIMS-FT-ICR MS. A 2-fold increase in the number of molecular features and a 2–6-fold signal-to-noise increase was observed for OSA-TIMS when compared with SA-TIMS during the PAH analysis. This work provides the proof-of-principle for further application of OSA-TIMS-FT-ICR MS for the unsupervised analysis of complex mixtures based on the characterization of the conformational space and the assignment of chemical formulas in a single analysis

Structural Characterization of Human Histone H4.1 by Tandem Nonlinear and Linear Ion Mobility Spectrometry Complemented with Molecular Dynamics Simulations

Extracellular histone H4 is an attractive drug target owing to its roles in organ failure in sepsis and other diseases. To identify inhibitors using in silico methods, information on histone H4 structural dynamics and three-dimensional (3D) structural coordinates is required. Here, DNA-free histone H4 type 1 (H4.1) was characterized by utilizing tandem nonlinear and linear ion mobility spectrometry (FAIMS-TIMS) coupled to mass spectrometry (MS) complemented with molecular dynamics (MD) simulations. The gas-phase structures of H4.1 are dependent on the starting solution conditions, evidenced by differences in charge state distributions, mobility distributions, and collision-induced unfolding (CIU) pathways. The experimental results show that H4.1 adopts diverse conformational types from compact (C) to partially folded (P) and subsequently elongated (E) structures. Molecular dynamics simulations provided candidate structures for the histone H4.1 monomer in solution and for the gas-phase structures observed using FAIMS-IMS-TOF MS as a function of the charge state and mobility distribution. A combination of the FAIMS-TIMS experimental results with theoretical dipole calculations reveals the important role of charge distribution in the dipole alignment of H4.1 elongated structures at high electric fields. A comparison of the secondary and primary structures of DNA-free H2A.1 and H4.1 is made based on the experimental IMS-MS and MD findings

Integration of Trapped Ion Mobility Spectrometry and Ultraviolet Photodissociation in a Quadrupolar Ion Trap Mass Spectrometer

There is a growing demand for lower-cost, benchtop analytical instruments with complementary separation capabilities for the screening and characterization of biological samples. In this study, we report on the custom integration of trapped ion mobility spectrometry and ultraviolet photodissociation capabilities in a commercial Paul quadrupolar ion trap multistage mass spectrometer (TIMS-QIT-MSn UVPD platform). A gated TIMS operation allowed for the accumulation of ion mobility separated ion in the QIT, followed by a mass analysis (MS1 scan) or m/z isolation, followed by selected collision induced dissociation (CID) or ultraviolet photodissociation (UVPD) and a mass analysis (MS2 scan). The analytical potential of this platform for the analysis of complex and labile biological samples is illustrated for the case of positional isomers with varying PTM location of the histone H4 tryptic peptide 4-17 singly and doubly acetylated and the histone H3.1 tail (1-50) singly trimethylated. For all cases, a baseline ion mobility precursor molecular ion preseparation was obtained. The tandem CID and UVPD MS2 allowed for effective sequence confirmation as well as the identification of reporter fragment ions associated with the PTM location; a higher sequence coverage was obtained using UVPD when compared to CID. Different from previous IMS-MS implementation, the novel TIMS-QIT-MSn UVPD platform offers a lower-cost alternative for the structural characterization of biological molecules that can be widely disseminated in clinical laboratories

Characterization of Deasphalted Crude Oils Using Gas Chromatography–Atmospheric Pressure Laser Ionization–Trapped Ion Mobility Spectrometry–Time-of-Flight Mass Spectrometry

In the present work, a novel workflow based on complementary gas-phase separations is applied to the characterization of deasphalted light (Macondo and Calvert), medium (Duri), and heavy (San Ardo) crude oils. The coupling of gas chromatography (GC), atmospheric pressure laser ionization (APLI), and trapped ion mobility spectrometry–mass spectrometry (TIMS–MS) resulted in the effective separation and candidate assignment of polycyclic aromatic hydrocarbons (PAHs) and similar compounds. The analytical power of GC–APLI–TIMS–TOF MS is based on the separation of the isomeric content using the GC and TIMS (R = 50–90 with Sr = 0.18 V/ms) gas-phase separations, followed by the high mass resolution and mass accuracy (<2 ppm) of the TOF MS analyzer. Previously reported PAH-like known compounds (130 compounds) uniquely assigned on the basis of their retention time (RT), collisional cross section (CCS), and mass-to-charge ratio (m/z) showed signature patterns and distinctive diagnostic ratios representative of the thermal maturity, lithology, and microbial contribution to each oil formation. The unsupervised T-Rex 4D analysis of GC–APLI–TIMS–TOF MS generated for the first time an exhaustive list of PAHs and similar unknown components (∼8500), with each component characterized by a RT, CCS, m/z value, and chemical formula and peak areas for each replica analysis (i.e., 12 total, 3× per crude oil). The inspection of the PAHs and similar unknown compounds provided a list of unique identifiers for each crude oil (2–4% of the assigned compounds) as well as molecular components common to all crude oils (∼50% of the assigned compounds). The analytical power of GC–APLI–TIMS–TOF MS is illustrated using unsupervised principal component analysis (PCA), where the four oils can be easily separated in two principal components that account for 70% of the total variance

Characterization of Deasphalted Crude Oils Using Gas Chromatography–Atmospheric Pressure Laser Ionization–Trapped Ion Mobility Spectrometry–Time-of-Flight Mass Spectrometry

In the present work, a novel workflow based on complementary gas-phase separations is applied to the characterization of deasphalted light (Macondo and Calvert), medium (Duri), and heavy (San Ardo) crude oils. The coupling of gas chromatography (GC), atmospheric pressure laser ionization (APLI), and trapped ion mobility spectrometry–mass spectrometry (TIMS–MS) resulted in the effective separation and candidate assignment of polycyclic aromatic hydrocarbons (PAHs) and similar compounds. The analytical power of GC–APLI–TIMS–TOF MS is based on the separation of the isomeric content using the GC and TIMS (R = 50–90 with Sr = 0.18 V/ms) gas-phase separations, followed by the high mass resolution and mass accuracy (<2 ppm) of the TOF MS analyzer. Previously reported PAH-like known compounds (130 compounds) uniquely assigned on the basis of their retention time (RT), collisional cross section (CCS), and mass-to-charge ratio (m/z) showed signature patterns and distinctive diagnostic ratios representative of the thermal maturity, lithology, and microbial contribution to each oil formation. The unsupervised T-Rex 4D analysis of GC–APLI–TIMS–TOF MS generated for the first time an exhaustive list of PAHs and similar unknown components (∼8500), with each component characterized by a RT, CCS, m/z value, and chemical formula and peak areas for each replica analysis (i.e., 12 total, 3× per crude oil). The inspection of the PAHs and similar unknown compounds provided a list of unique identifiers for each crude oil (2–4% of the assigned compounds) as well as molecular components common to all crude oils (∼50% of the assigned compounds). The analytical power of GC–APLI–TIMS–TOF MS is illustrated using unsupervised principal component analysis (PCA), where the four oils can be easily separated in two principal components that account for 70% of the total variance

Differentiating Parallel and Antiparallel DNA Duplexes in the Gas Phase Using Trapped Ion Mobility Spectrometry

Deoxyribonucleic acids can form a wide variety of structural motifs which differ greatly from the typical antiparallel duplex stabilized by Watson–Crick base pairing. Many of these structures are thought to occur in vivo and may have essential roles in the biology of the cell. Among these is the parallel-stranded duplexa structural motif in which DNA strands associate in a head-to-head fashion with the 5′ ends at the same end of the duplexwhich is stabilized by reverse Watson–Crick base pairing. In this study, parallel- and antiparallel-stranded DNA duplexes formed from two different 12-mer oligonucleotides were studied using native electrospray ionization combined with trapped ion mobility spectrometry and mass spectrometry. The DNA duplex charge plays an important role in the gas-phase mobility profile, with a more compact form in negative mode than in positive mode (ΔΩ ≈ 100 Ų between −4 and +4). Despite sequence mismatches, homo- and hetero-DNA duplexes were formed in solution and transfer to the gas phase, where a more compact structure was observed for the parallel compared to the antiparallel duplexes (ΔΩ ≈ 50 Ų), in good agreement with theoretical calculations. Theoretical studies suggest that a reduction (or compaction) along the helical axis of the parallel and antiparallel DNA duplexes is observed upon transfer to the gas phase

A Bifunctional Leader Peptidase/ABC Transporter Protein Is Involved in the Maturation of the Lasso Peptide Cochonodin I from <i>Streptococcus</i> <i>suis</i>

Lasso peptides are members of the natural product superfamily of ribosomally synthesized and post-translationally modified peptides (RiPPs). Here, we describe the first lasso peptide originating from a biosynthetic gene cluster belonging to a unique lasso peptide subclade defined by the presence of a bifunctional protein harboring both a leader peptidase (B2) and an ABC transporter (D) domain. Bioinformatic analysis revealed that these clusters also encode homologues of the NisR/NisK regulatory system and the NisF/NisE/NisG immunity factors, which are usually associated with the clusters of antimicrobial class I lanthipeptides, such as nisin, another distinct RiPP subfamily. The cluster enabling the heterologous production of the lasso peptide cochonodin I in E. coli originated from Streptococcus suis LSS65, and the threaded structure of cochonodin I was evidenced through extensive MS/MS analysis and stability assays. It was shown that the ABC transporter domain from SsuB2/D is not essential for lasso peptide maturation. By extensive genome mining dedicated exclusively to other lasso peptide biosynthetic gene clusters featuring bifunctional B2/D proteins, it was furthermore revealed that many bacteria associated with human or animal microbiota hold the biosynthetic potential to produce cochonodin-like lasso peptides, implying that these natural products might play roles in human and animal health

Description of Dissolved Organic Matter Transformational Networks at the Molecular Level

Dissolved Organic Matter (DOM) is an important component of the global carbon cycle. Unscrambling the structural footprint of DOM is key to understand its biogeochemical transformations at the mechanistic level. Although numerous studies have improved our knowledge of DOM chemical makeup, its three-dimensional picture remains largely unrevealed. In this work, we compare four solid phase extracted (SPE) DOM samples from three different freshwater ecosystems using high resolution mobility and ultrahigh-resolution Fourier transform ion cyclotron resonance tandem mass spectrometry (FT-ICR MS/MS). Structural families were identified based on neutral losses at the level of nominal mass using continuous accumulation of selected ions-collision induced dissociation (CASI-CID)­FT-ICR MS/MS. Comparison of the structural families indicated dissimilarities in the structural footprint of this sample set. The structural family representation using Cytoscape software revealed characteristic clustering patterns among the DOM samples, thus confirming clear differences at the structural level (Only 10% is common across the four samples.). The analysis at the level of neutral loss-based functionalities suggests that hydration and carboxylation are ubiquitous transformational processes across the three ecosystems. In contrast, transformation mechanisms involving methoxy moieties may be constrained in estuarine systems due to extensive upstream lignin biodegradation. The inclusion of the isomeric content (mobility measurements at the level of chemical formula) in the structural family description suggests that additional transformation pathways and/or source variations are possible and account for the dissimilarities observed. While the structural character of more and diverse types of DOM samples needs to be assessed and added to this database, the results presented here demonstrate that Graph-DOM is a powerful tool capable of providing novel information on the DOM chemical footprint, based on structural interconnections of precursor molecules generated by fragmentation pathways and collisional cross sections