Remodeling nanoDESI Platform with Ion Mobility Spectrometry to Expand Protein Coverage in Cancerous Tissue.

Nanospray desorption electrospray ionization mass spectrometry is an ambient ionization technique that is capable of mapping proteins in tissue sections. However, high-abundant molecules or isobaric interference in biological samples hampers its broad applications in probing low-abundant proteins. To address this challenge, herein we demonstrated an integrated module that coupled pneumatic-assisted nanospray desorption electrospray ionization mass spectrometry with high-field asymmetric ion mobility spectrometry. Using this module to analyze mouse brain sections, the protein coverage was significantly increased. This improvement allowed the mapping of low-abundant proteins in tissue sections with a 5 µm spatial resolution enabled by computationally assisted fusion with optical microscopic images. Moreover, the module was successfully applied to characterize melanoma in skin tissues based on the enhanced protein profiles. The results suggested that this integrating module will be potentially applied to discover novel proteins in cancers.

Distinguishing between long-term-stored and fresh chili pepper powder through fingerprinting of volatiles by headspace capillary-gas chromatography-ion mobility spectrometry.

Long-term storage of chili pepper powder results in physicochemical and microbiological changes that decrease its commercial value; these changes occur owing to fungal growth and production of off-flavor compounds. Herein, long-term-stored chili pepper powder (LSCPP) and fresh chili pepper powder (FCPP) were analyzed using internal transcribed spacer sequencing and volatile organic compound fingerprinting by headspace capillary-gas chromatography-ion mobility spectrometry. Fungal analysis detected only Xeromyces bisporus with high accuracy in all the analyzed LSCPP samples. However, the proliferation of X. bisporus on nonspecific spots complicated the distinguishing process between the two groups based solely on fungal analysis. Therefore, nine compounds (three ketones, one alcohol, two aldehydes, one ester, one furan, and one sulfur compound) obtained by autoxidation and fungal metabolism were selected as potential markers for distinguishing LSCPP and FCPP. These above-mentioned substances, which were confirmed as off-flavor species owing to "stale" odor, emitted lipid fragrance and were used to successfully distinguish LSCPP from FCPP using principal component analysis and linear discriminant analysis. PRACTICAL APPLICATION: According to the research results, it was possible to discriminate between long-term stored and fresh chili pepper powders using nine VOC markers for quality control in industry. In addition, the fungus generated from long-term storage of chili pepper powder was Xeromyces bisporus, which was confirmed to be safe for intake because it does not form secondary toxic metabolites.

Assessing Collision Cross Section Calibration Strategies for Traveling Wave-Based Ion Mobility Separations in Structures for Lossless Ion Manipulations.

The collision cross section (CCS) is an important property that aids in the structural characterization of molecules. Here, we investigated the CCS calibration accuracy with traveling wave ion mobility spectrometry (TWIMS) separations in structures for lossless ion manipulations (SLIM) using three sets of calibrants. A series of singly negatively charged phospholipids and bile acids were calibrated in nitrogen buffer gas using two different TW waveform profiles (square and sine) and amplitudes (20, 25, and 30 V0-p). The calibration errors for the three calibrant sets (Agilent tuning mixture, polyalanine, and one assembled in-house) showed negligible differences using a sine-shaped TW waveform. Calibration errors were all within 1-2% of the drift tube ion mobility spectrometry (DTIMS) measurements, with lower errors for sine waveforms, presumably due to the lower average and maximum fields experienced by ions. Finally, ultrahigh-resolution multipass (long path length) SLIM TWIMS separations demonstrated improved CCS calibration for phospholipid and bile acid isomers.

Rapid determination of intraoperative blood propofol concentration in operating theatre by dopant-enhanced neutral release and negative photoionization ion mobility spectrometry.

The concentration of propofol in blood is an important indicator for anesthesiologists to monitor and regulate the anesthesia depth of patients during surgery. Herein, a negative photoionization ion mobility spectrometry with acetone as the dopant was developed for rapid and direct determination of intraoperative blood propofol concentration in the operating theatre. High concentration of acetone molecules in the carrier gas was used not only to enhance neutral desorption and release free propofol molecules from the whole blood, but also to increase the intensity of reactant O2- and reduce the amount of non-reactive CO3- ions simultaneously, which allowed to measure trace propofol in less than 2 min without any tedious pretreatment. Under optimized conditions, a linear calibration curve of propofol was obtained with the range of 0.5-20 ng µL-1 and with a limit of detection of 0.14 ng µL-1, which met the clinical requirements and correlated well with standard HPLC methods. Finally, the method was applied to detect intraoperative blood propofol concentration in nearly 100 surgical patients, demonstrating its excellent detection capability and facilitating the study of propofol pharmacokinetics.

Statistical analysis of MCC-IMS data for two group comparisons-an exemplary study on two devices.

The Multi-capillary-column-Ion-mobility-spectrometry (MCC-IMS) technology for measuring breath gas can be used for distinguishing between healthy and diseased subjects or between different types of diseases. The statistical methods for classifying the corresponding breath samples typically neglects potential confounding clinical and technical variables, reducing both accuracy and generalizability of the results. Especially measuring samples on different technical devices can heavily influence the results. We conducted a controlled breath gas study including 49 healthy volunteers to evaluate the effect of the variables sex, smoking habits and technical device. Every person was measured twice, once before and once after consuming a glass of orange juice. The two measurements were obtained on two different devices. The evaluation of the MCC-IMS data regarding metabolite detection was performed once using the software VisualNow, which requires manual interaction, and once using the fully automated algorithm SGLTR-DBSCAN. We present statistical solutions, peak alignment and scaling, to adjust for the different devices. For the other potential confounders sex and smoking, in our study no significant influence was identified.

Rapid characterization of structural and functional similarity for a candidate bevacizumab (Avastin) biosimilar using a multipronged mass-spectrometry-based approach.

The ongoing shift from small molecule drugs to protein therapeutics in the pharmaceuticals industry presents a considerable challenge to generic drug developers who are increasingly required to demonstrate biosimilarity for biological macromolecules, a task that is decidedly more complex than doing the same for small molecule drugs. In this work, we demonstrate a multipronged mass-spectrometry-based workflow that allows rapid and facile molecular characterization of antibody-based protein therapeutics, applied to biosimilars development. Specifically, we use a combination of native mass spectrometry (MS), ion mobility spectrometry (IMS), and global time-resolved hydrogen deuterium exchange (HDX) to provide an unambiguous assessment of the structural, dynamic, and chemical similarity between Avastin (bevacizumab) and a biosimilar in the late stages of pre-clinical development. Minor structural and dynamic differences between the biosimilar and Avastin, and between lots of the biosimilar, were tested for functional relevance using Surface Plasmon Resonance-derived kinetic and equilibrium binding parameters.

A Modified Traveling Wave Ion Mobility Mass Spectrometer as a Versatile Platform for Gas-Phase Ion-Molecule Reactions.

Taken individually, chemical labeling and mass spectrometry are two well-established tools for the structural characterization of biomolecular complexes. A way to combine their respective advantages is to perform gas-phase ion-molecule reactions (IMRs) inside the mass spectrometer. This is, however, not so well developed because of the limited range of usable chemicals and the lack of commercially available IMR devices. Here, we modified a traveling wave ion mobility mass spectrometer to enable IMRs in the trapping region of the instrument. Only one minor hardware modification is needed to allow vapors of a variety of liquid reagents to be leaked into the trap traveling wave ion guide of the instrument. A diverse set of IMRs can then readily be performed without any loss in instrument performance. We demonstrate the advantages of implementing IMR capabilities in general, and to this quadrupole-ion mobility-time-of-flight (Q-IM-TOF) mass spectrometer in particular, by exploiting the full functionality of the instrument, including mass selection, ion mobility separation, and post-mobility fragmentation. The potential to carry out gas-phase IMR kinetics experiments is also illustrated. We demonstrate the versatility of the setup using gas-phase IMRs of established utility for biological mass spectrometry, including hydrogen-deuterium exchange, ion-molecule proton transfer reactions, and covalent modification of DNA anions using trimethylsilyl chloride.

Accurate Quantitative Proteomic Analyses Using Metabolic Labeling and High Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS).

Stable isotope labeling by amino acids in cell culture (SILAC) is routinely used to profile changes in protein and peptide abundance across different experimental paradigms. As with other quantitative proteomic approaches, the detection of peptide isotopomers can be limited by the presence of interference ions that ultimately affect the quality of quantitative measurements. Here, we evaluate high field asymmetric waveform ion mobility spectrometry (FAIMS) to improve the accuracy and dynamic range of quantitative proteomic analyses using SILAC. We compared quantitative measurements for tryptic digests of isotopically labeled protein extracts mixed in different ratios using LC-MS/MS with and without FAIMS. To further reduce sample complexity, we also examined the improvement in quantitative measurements when combining strong cation exchange (SCX) fractionation prior to LC-MS/MS analyses. Using the same amount of sample consumed, analyses performed using FAIMS provided more than 30% and 200% increase in the number of quantifiable peptides compared to LC-MS/MS performed with and without SCX fractionation, respectively. Furthermore, FAIMS reduced the occurrence of interfering isobaric ions and improved the accuracy of quantitative measurements. We leveraged the application of FAIMS in phosphoproteomic analyses to profile dynamic changes in protein phosphorylation in HEK293 cells subjected to heat shock for periods up to 20 min. In addition to the enhanced phosphoproteomic coverage, FAIMS also provided the ability to separate phosphopeptide isomers that often coelute and can be misassigned in conventional LC-MS/MS experiments.

Comprehensive Single-Shot Proteomics with FAIMS on a Hybrid Orbitrap Mass Spectrometer.

Liquid chromatography (LC) prefractionation is often implemented to increase proteomic coverage; however, while effective, this approach is laborious, requires considerable sample amount, and can be cumbersome. We describe how interfacing a recently described high-field asymmetric waveform ion mobility spectrometry (FAIMS) device between a nanoelectrospray ionization (nanoESI) emitter and an Orbitrap hybrid mass spectrometer (MS) enables the collection of single-shot proteomic data with comparable depth to that of conventional two-dimensional LC approaches. This next generation FAIMS device incorporates improved ion sampling at the ESI-FAIMS interface, increased electric field strength, and a helium-free ion transport gas. With fast internal compensation voltage (CV) stepping (25 ms/transition), multiple unique gas-phase fractions may be analyzed simultaneously over the course of an MS analysis. We have comprehensively demonstrated how this device performs for bottom-up proteomics experiments as well as characterized the effects of peptide charge state, mass loading, analysis time, and additional variables. We also offer recommendations for the number of CVs and which CVs to use for different lengths of experiments. Internal CV stepping experiments increase protein identifications from a single-shot experiment to >8000, from over 100 000 peptide identifications in as little as 5 h. In single-shot 4 h label-free quantitation (LFQ) experiments of a human cell line, we quantified 7818 proteins with FAIMS using intra-analysis CV switching compared to 6809 without FAIMS. Single-shot FAIMS results also compare favorably with LC fractionation experiments. A 6 h single-shot FAIMS experiment generates 8007 protein identifications, while four fractions analyzed for 1.5 h each produce 7776 protein identifications.

Identification of terpenes and essential oils by means of static headspace gas chromatography-ion mobility spectrometry.

Static headspace gas chromatography-ion mobility spectrometry (SHS GC-IMS) is a relatively new analytical technique that has considerable potential for analysis of volatile organic compounds (VOCs). In this study, SHS GC-IMS was used for the identification of the major terpene components of various essential oils (EOs). Based on the data obtained from 25 terpene standards and 50 EOs, a database for fingerprint identification of characteristic terpenes and EOs was generated utilizing SHS GC-IMS for authenticity testing of fragrances in foods, cosmetics, and personal care products. This database contains specific normalized IMS drift times and GC retention indices for 50 terpene components of EOs. Initially, the SHS GC-IMS parameters, e.g., drift gas and carrier gas flow rates, drift tube, and column temperatures, were evaluated to determine suitable operating conditions for terpene separation and identification. Gas chromatography-mass spectrometry (GC-MS) was used as a reference method for the identification of terpenes in EOs. The fingerprint pattern based on the normalized IMS drift times and retention indices of 50 terpenes is presented for 50 EOs. The applicability of the method was proven on examples of ten commercially available food, cosmetic, and personal care product samples. The results confirm the suitability of SHS GC-IMS as a powerful analytical technique for direct identification of terpene components in solid and liquid samples without any pretreatment. Graphical abstract Fingerprint pattern identification of terpenes and essential oils using static headspace gas chromatography-ion mobility spectrometry.

Variables Affecting the Internal Energy of Peptide Ions During Separation by Differential Ion Mobility Spectrometry.

Differential ion mobility spectrometry (DIMS) devices separate ions on the basis of differences in ion mobility in low and high electric fields, and can be used as a stand-alone analytical method or as a separation step before further analysis. As with other ion mobility separation techniques, the ability of DIMS separations to retain the structural characteristics of analytes has been of concern. For DIMS separations, this potential loss of ion structure originates from the fact that the separations occur at atmospheric pressure and the ions, during their transit through the device, undergo repeated collisions with the DIMS carrier gas while being accelerated by the electric field. These collisions have the ability to increase the internal energy distribution of the ions, which can cause isomerization or fragmentation. The increase in internal energy of the ions is based on a number of variables, including the dispersion field and characteristics of the carrier gas such as temperature and composition. The effects of these parameters on the intra-DIMS fragmentation of multiply charged ions of the peptides bradykinin (RPPGFSPFR) and GLISH are discussed herein. Furthermore, similarities and differences in the internal energy deposition that occur during collisional activation in tandem mass spectrometry experiments are discussed, as the fragmentation pathways accessed by both are similar. Graphical Abstract ᅟ.

Compression Ratio Ion Mobility Programming (CRIMP) Accumulation and Compression of Billions of Ions for Ion Mobility-Mass Spectrometry Using Traveling Waves in Structures for Lossless Ion Manipulations (SLIM).

We report on the implementation of a traveling wave (TW) based compression ratio ion mobility programming (CRIMP) approach within structures for lossless ion manipulations (SLIM) that enables both greatly enlarged trapped ion charge capacities and also efficient ion population compression for use in ion mobility (IM) separations. Ion accumulation is conducted in a SLIM serpentine ultralong path with extended routing (SUPER) region after which CRIMP compression allows the large ion populations to be "squeezed". The SLIM SUPER IM module has two regions, one operating with conventional traveling waves (i.e., traveling trap; TT region) and the second having an intermittently pausing or "stuttering" TW (i.e., stuttering trap; ST region). When a stationary voltage profile was used in the ST region, ions are blocked at the TT-ST interface and accumulated in the TT region and then can be released by resuming a conventional TW in the ST region. The population can also be compressed using CRIMP by the repetitive merging of ions distributed over multiple TW bins in the TT region into a single TW bin in the ST region. Ion accumulation followed by CRIMP compression provides the basis for the use of larger ion populations for IM separations. We show that over 109 ions can be accumulated with high efficiency in the present device and that the extent of subsequent compression is only limited by the space charge capacity of the trapping region. Approximately 5 × 109 charges introduced from an electrospray ionization source were trapped for a 40 s accumulation period, more than 2 orders of magnitude greater than the previously reported charge capacity of an ion funnel trap. Importantly, we show that extended ion accumulation in conjunction with CRIMP compression and multiple passes through the serpentine path provides the basis for a highly desirable combination of ultrahigh sensitivity and SLIM SUPER high-resolution IM separations.