Laser desorption ionization of red phosphorus clusters and their use for mass calibration in time-of-flight mass spectrometry

Matrix-assisted laser desorption/ionization matrix incorporation evaluation algorithm for improved peak coverage and signal-to-noise ratio in mass spectrometry imaging

RATIONALE

Despite decades of implementation, the selection of optimal sample preparation conditions for matrix-assisted laser desorption/ionization (MALDI) imaging is still ambiguous due to the lack of a universal and comprehensive evaluation methodology. Thus, numerous experiments with different matrix application conditions accompany a translation of the method to novel sample types and matrices.

METHODS

Mouse brain tissues were covered with 9-aminoacridine through sublimation, followed by recrystallization in vapors of 5% (v/v) methanol solution in water. The samples were analyzed by MALDI time-of-flight mass spectrometry, and the efficiency of lipid and small-molecule ionization was evaluated with different metrics.

RESULTS

We first investigate the dependency of matrix density and recrystallization conditions on the thickness of an analyte-empty matrix layer to roughly evaluate the laser shot number required to obtain an intense signal with minimal noise. Then, we introduce metrics for the analysis of small imaging datasets (small sample regions) of model samples based on median quantity of peaks in spectra (medQP) and weighted median signal-to-noise ratio (wmSNR). The evaluation of small regions and taking median values for metrics help overcome the sample heterogeneity and allow for the simultaneous comparison of different acquisition parameters.

CONCLUSIONS

Here, we propose a methodology based on gradual laser ablation of small regions of sample and further implementation of weighted signal-to-noise ratio to assess various matrix application conditions. The proposed approach helps reduce the number of test samples required to determine optimal sample preparation conditions and improve the overall quality of images.

Pulsed laser ablation synthesis of fresh Te nanoparticles for matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS) applications

This work aims to demonstrate the potential of pulsed laser ablation synthesis (PLA) of tellurium nanoparticles (Te NPs) for use in matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS) applications. An experimental laboratory setup for PLA synthesis of fresh Te NPs was designed to prevent unwanted aggregation of uncoated Te NPs and avoid the need to use additional modifiers. Performing pulsed laser ablation synthesis in liquid (PLAL) using acetone was found to be the optimal way of preparing Te NPs. Another possibility is to use commercially available laser ablation devices for laser ablation - inductively coupled plasma mass spectrometry (LA-ICP-MS) to perform PLA in a helium atmosphere, but this approach is less efficient and results in the formation of unwanted larger particles. The prepared Te NPs were studied using the transmission electron microscopy (TEM) and dynamic light scattering (DLS) methods. TEM images showed the formation of Te NP nanochains composed of many crystallized Te NPs with sizes ranging from 8 to 15 nm. The various size distributions of the synthesized Te NPs identified using the DLS method correspond to the size distributions of aggregations rather than individual Te NPs. The synthesized Te NPs were used for a pilot study of their possible use with the MALDI-MS technique. An important effect was observed when Te NPs were used to perform a MALDI-MS analysis of the α-cyclodextrin (α-CD) and cucurbit[7]uril (CB7) macrocycles, which consisted in a decline in the formation of matrix adducts. Furthermore, several changes in MALDI-MS mass spectra of intact cells and a positive effect of Te NPs on the crystallization of the MALDI-MS matrix were observed.

In Vivo Simvastatin and Brain Radiation in a Model of HER2 + Inflammatory Breast Cancer Brain Metastasis

Purpose

Inhibiting HMG-CoA reductase with simvastatin prevents breast cancer metastases in preclinical models and radiosensitizes monolayer and stem-like IBC cell lines in vitro . Given the extensive use of simvastatin worldwide and its expected penetration into the brain, we examined whether regulating cholesterol with simvastatin affected IBC3 HER2+ brain metastases.

Methods and Materials

Breast cancer cell lines KPL4 and MDA-IBC3 were examined in vitro for DNA repair after radiation with or without statin treatment. Brain metastasis endpoints were examined in the MDA-IBC3 brain metastasis model after ex vivo exposure to lipoproteins and after tail vein injections with and without whole-brain radiotherapy (WBR) and oral statin exposure.

Results

Ex vivo preculture of MDA-IBC3 cells with very low-density lipoprotein (vLDL) enhanced the growth of colonized lesions in the brain in vivo compared with control or high-density lipoprotein (HDL), and concurrent oral simvastatin/ WBR reduced the incidence of micrometastatic lesions evaluated 10 days after WBR. However, statin, with or without WBR, did not reduce the incidence, burden, or number of macrometastatic brain lesions evaluated 5 weeks after WBR.

Conclusions

Although a role for cholesterol biosynthesis is demonstrated in DNA repair and response to whole brain radiation in this model, durable in vivo efficacy of concurrent whole brain irradiation and oral statin was not demonstrated.

Robust and versatile assembly for emitter positioning, observation, and heating in atmospheric pressure field desorption mass spectrometry

Atmospheric pressure field desorption (APFD) mass spectrometry (MS) has recently been introduced as a new variant of field desorption (FD) mass spectrometry. The development aimed at providing the basic characteristics of FD-MS in combination with instruments equipped with an atmospheric pressure (AP) interface. Hitherto, APFD has been demonstrated to yield both positive and negative even electron ions of highly polar or ionic compounds as well as to enable the generation of positive molecular ions, M+•, of polycyclic aromatic compounds. The prototype setup for APFD was based on a nano-electrospray ionization (nanoESI) source slightly modified to allow for emitter positioning in front of the AP interface of a Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometer. The entrance electrode of the interface was set to negative or positive high voltage with respect to the emitter at ground potential, thereby permitting the formation of positive or negative ions, respectively. This work describes a custom-built device for quicker and more reproducible sample loading on and positioning of field emitters at the entrance electrode of the atmospheric pressure interface of a mass spectrometer. In addition, the device provides means for observation of the emitter during operation and for resistive emitter heating as employed in traditional FD-MS. Emitter heating both speeds up the desorption of the analytes and allows for the desorption/ionization of analytes of higher molecular weight than without emitter heating. In some cases, the signal-to-noise ratio of APFD mass spectra is improved due to higher ion currents effected by compressing the entire process into shorter periods of spectral acquisition. The new setup enables robust and reliable operation in APFD-MS. Moreover, it has been designed as to allow for use on a range of instruments as it can either be used on an FT-ICR mass spectrometer or in combination with a trapped ion mobility-quadrupole-time-of-flight (TIMS-Q-TOF) instrument.

Research progress on nanomaterial-based matrices for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis

Matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a novel soft ionization bio-mass spectrometry technology emerging in the 1980s, which can realize rapid detection of non-volatile, highly polar, and thermally unstable macromolecules. However, the analysis of small molecular compounds has been a major problem for MALDI-TOF MS all the time. In the MALDI analysis process based on traditional matrices, large numbers of interference peaks in the low molecular weight area and "sweet spots" phenomenon are produced, so the detection method needs to be further optimized. The promotion of matrix means the improvement of MALDI performance. In recent years, many new nanomaterial-based matrices have been successfully applied to the analysis of small molecular compounds, which makes MALDI applicable to a wider range of detection and useful in more fields such as pharmacy and environmental science. In this paper, the newly developed MALDI matrix categories in recent years are reviewed initially. Meanwhile, the potential applications, advantages and disadvantages of various matrices are analyzed. Finally, the future development prospects of nanomaterial-based matrices are also prospected.

Lysolipids are prominent in subretinal drusenoid deposits, a high-risk phenotype in age-related macular degeneration

Introduction

Age related macular degeneration (AMD) causes legal blindness worldwide, with few therapeutic targets in early disease and no treatments for 80% of cases. Extracellular deposits, including drusen and subretinal drusenoid deposits (SDD; also called reticular pseudodrusen), disrupt cone and rod photoreceptor functions and strongly confer risk for advanced disease. Due to the differential cholesterol composition of drusen and SDD, lipid transfer and cycling between photoreceptors and support cells are candidate dysregulated pathways leading to deposit formation. The current study explores this hypothesis through a comprehensive lipid compositional analysis of SDD.

Methods

Histology and transmission electron microscopy were used to characterize the morphology of SDD. Highly sensitive tools of imaging mass spectrometry (IMS) and nano liquid chromatography tandem mass spectrometry (nLC-MS/MS) in positive and negative ion modes were used to spatially map and identify SDD lipids, respectively. An interpretable supervised machine learning approach was utilized to compare the lipid composition of SDD to regions of uninvolved retina across 1873 IMS features and to automatically discern candidate markers for SDD. Immunohistochemistry (IHC) was used to localize secretory phospholipase A2 group 5 (PLA2G5).

Results

Among the 1873 detected features in IMS data, three lipid classes, including lysophosphatidylcholine (LysoPC), lysophosphatidylethanolamine (LysoPE) and lysophosphatidic acid (LysoPA) were observed nearly exclusively in SDD while presumed precursors, including phosphatidylcholine (PC), phosphatidylethanolamine (PE) and phosphatidic acid (PA) lipids were detected in SDD and adjacent photoreceptor outer segments. Molecular signals specific to SDD were found in central retina and elsewhere. IHC results indicated abundant PLA2G5 in photoreceptors and retinal pigment epithelium (RPE).

Discussion

The abundance of lysolipids in SDD implicates lipid remodeling or degradation in deposit formation, consistent with ultrastructural evidence of electron dense lipid-containing structures distinct from photoreceptor outer segment disks and immunolocalization of secretory PLA2G5 in photoreceptors and RPE. Further studies are required to understand the role of lipid signals observed in and around SDD.

Visualization of metabolites and microbes at high spatial resolution using MALDI mass spectrometry imaging and in situ fluorescence labeling

Label-free molecular imaging techniques such as matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) enable the direct and simultaneous mapping of hundreds of different metabolites in thin sections of biological tissues. However, in host-microbe interactions it remains challenging to localize microbes and to assign metabolites to the host versus members of the microbiome. We therefore developed a correlative imaging approach combining MALDI-MSI with fluorescence in situ hybridization (FISH) on the same section to identify and localize microbial cells. Here, we detail metaFISH as a robust and easy method for assigning the spatial distribution of metabolites to microbiome members based on imaging of nucleic acid probes, down to single-cell resolution. We describe the steps required for tissue preparation, on-tissue hybridization, fluorescence microscopy, data integration into a correlative image dataset, matrix application and MSI data acquisition. Using metaFISH, we map hundreds of metabolites and several microbial species to the micrometer scale on a single tissue section. For example, intra- and extracellular bacteria, host cells and their associated metabolites can be localized in animal tissues, revealing their complex metabolic interactions. We explain how we identify low-abundance bacterial infection sites as regions of interest for high-resolution MSI analysis, guiding the user to a trade-off between metabolite signal intensities and fluorescence signals. MetaFISH is suitable for a broad range of users from environmental microbiologists to clinical scientists. The protocol requires ~2 work days.

Laser ablation synthesis of tellurium carbides using tellurium with nanodiamond nanocomposite

RATIONALE

Carbides, including tellurium carbides (TeC), play crucial roles in diverse applications, but TeC synthesis has not been described in the literature. Laser ablation synthesis (LAS) coupled with mass spectrometry was used here for in situ TeC clusters synthesis and identification of the reaction products to better understand TeC formation.

METHODS

Laser desorption ionization time-of-flight mass spectrometry (LDI-TOFMS) was used to generate the TeC clusters and determine their stoichiometry via computer modeling of isotopic patterns.

RESULTS

A simple one-pot procedure was developed for Te-nanodiamond nanocomposite preparation. A suspension of fine-powdered Te was mixed with a suspension of nanodiamonds (both in acetonitrile), and the resulting precipitated nanocomposite was suitable for the synthesis of TemC_n clusters using LDI. Various unary and binary clusters were formed. The stoichiometry of the novel TemC_n clusters, determined via computer modeling of isotopic patterns, is reported here for the first time.

CONCLUSIONS

The Te-nanodiamond composite was found to be the most suitable precursor for the generation of TemC_n clusters. In total, 35 binary TemC_n clusters were identified, when several of them were not obtained using commercial TeC material.

Molecular-level degradation pathways of black phosphorus revealed by mass spectrometry fingerprinting

Understanding the molecular mechanism of material transformation raises a great challenge for material characterization techniques. As a promising 2D material, the application potential of black phosphorus (BP) is seriously compromised by its environmental instability. However, until now, the degradation mechanism of BP remains ambiguous. Here we show that by using laser desorption ionization mass spectrometry (LDI-MS) fingerprinting it is possible to unravel the degradation pathways of BP at the molecular level without any chemical labeling. We found that BP-based materials can generate intrinsic phosphorus cluster (Pn+ or Pn-) fingerprint peaks in LDI-MS in both positive-ion and negative-ion modes, which allows the degradation processes of BP materials to be monitored by providing abundant mass information about intermediates and products with the sample-to-sample RSDs in the range of 1.0-28.4%. The stability of BP or cerium-encapsulated BP was monitored under ambient and increased temperature conditions for up to 20 or 180 days. Notably, by using LDI-MS fingerprinting, we reveal an unreported BP degradation pathway, i.e., nitrogen (N2)-addition oxidation, in addition to the direct oxidation pathway. Our results not only enable an in-depth understanding of the chemical instability of BP, but also, importantly, demonstrate a new powerful platform for monitoring and characterization of material transformation.

Nanoliter Scale Parallel Liquid-Liquid Extraction for High-Throughput Purification on a Droplet Microarray

In the current drug discovery process, the synthesis of compound libraries is separated from biological screenings both conceptually and technologically. One of the reasons is that parallel on-chip high-throughput purification of synthesized compounds is still a major challenge. Here, on-chip miniaturized high-throughput liquid-liquid extraction in volumes down to 150 nL with efficiency comparable to or better than large-scale extraction utilizing separation funnels is demonstrated. The method is based on automated and programmable merging of arrays of aqueous nanoliter droplets with organic droplets. Multi-step extraction performed simultaneously or with changing conditions as well as handling of femtomoles of compounds are demonstrated. In addition, the extraction efficiency is analyzed with a fast optical readout as well as matrix-assisted laser desorption ionization-mass spectrometry on-chip detection. The new massively parallel and miniaturized purification method adds another important tool to the chemBIOS concept combining chemical combinatorial synthesis with biological screenings on the same miniaturized droplet microarray platform, which will be essential to accelerate drug discovery.

Spatial Analysis of Nucleotide Metabolism: From CRISPR Knockout Cancer Cells to MALDI Imaging of Tumors

Cancer cells depend on nucleotides for proliferation. Inhibition of nucleotide metabolism by antimetabolites is a well-established anticancer therapy. However, resistance and toxicity to antimetabolite treatments reduce their effectiveness. Here, we focus on the pyrimidine de novo synthesis pathway, which is crucial for cancer cell proliferation, yet its pharmacological targeting in cancer has been without much clinical success so far. Hence, it is important to understand how cancer cells cope with the insufficiency of this pathway. Here, we describe a procedure to prepare subcutaneous tumor model deficient in de novo pyrimidine synthesis. For examination of metabolic responses to de novo synthesis blockade in tumors, we propose application of MALDI imaging that allows spatially resolved examination of metabolic responses to de novo synthesis blockade in tumors.

Artificial Neural Networks Coupled with MALDI-TOF MS Serum Fingerprinting To Classify and Diagnose Pathological Pain Subtypes in Preclinical Models

Pathological pain subtypes can be classified as either neuropathic pain, caused by a somatosensory nervous system lesion or disease, or nociplastic pain, which develops without evidence of somatosensory system damage. Since there is no gold standard for the diagnosis of pathological pain subtypes, the proper classification of individual patients is currently an unmet challenge for clinicians. While the determination of specific biomarkers for each condition by current biochemical techniques is a complex task, the use of multimolecular techniques, such as matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), combined with artificial intelligence allows specific fingerprints for pathological pain-subtypes to be obtained, which may be useful for diagnosis. We analyzed whether the information provided by the mass spectra of serum samples of four experimental models of neuropathic and nociplastic pain combined with their functional pain outcomes could enable pathological pain subtype classification by artificial neural networks. As a result, a simple and innovative clinical decision support method has been developed that combines MALDI-TOF MS serum spectra and pain evaluation with its subsequent data analysis by artificial neural networks and allows the identification and classification of pathological pain subtypes in experimental models with a high level of specificity.

MALDI Mass Spectrometry Imaging Highlights Specific Metabolome and Lipidome Profiles in Salivary Gland Tumor Tissues

Salivary gland tumors are relatively uncommon neoplasms that represent less than 5% of head and neck tumors, and about 90% are in the parotid gland. The wide variety of histologies and tumor characteristics makes diagnosis and treatment challenging. In the present study, Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) was used to discriminate the pathological regions of patient-derived biopsies of parotid neoplasms by metabolomic and lipidomic profiles. Fresh frozen parotid tissues were analyzed by MALDI time-of-flight (TOF) MSI, both in positive and negative ionization modes, and additional MALDI-Fourier-transform ion cyclotron resonance (FT-ICR) MSI was carried out for metabolite annotation. MALDI-TOF-MSI spatial segmentation maps with different molecular signatures were compared with the histologic annotation. To maximize the information related to specific alterations between the pathological and healthy tissues, unsupervised (principal component analysis, PCA) and supervised (partial least squares-discriminant analysis, PLS-DA) multivariate analyses were performed presenting a 95.00% accuracy in cross-validation. Glycerophospholipids significantly increased in tumor tissues, while sphingomyelins and triacylglycerols, key players in the signaling pathway and energy production, were sensibly reduced. In addition, a significant increase of amino acids and nucleotide intermediates, consistent with the bioenergetics request of tumor cells, was observed. These results underline the potential of MALDI-MSI as a complementary diagnostic tool to improve the specificity of diagnosis and monitoring of pharmacological therapies.

Characterization of selected organometallic compounds by electrospray ionization- and matrix-assisted laser desorption/ionization-mass spectrometry using different types of instruments: Possibilities and limitations

RATIONALE

Organometallic compounds are becoming increasingly important in their industrial application as catalysts. Mass spectrometry is an essential tool for the structural confirmation of such organometallics. Because the analysis of this class of molecules can be challenging, the ionization behavior and structural confirmation of selected transition metal catalysts are described in this work.

METHODS

The transition metal catalysts investigated were analyzed using classical vacuum MALDI reflectron TOF-MS as well as intermediate pressure matrix-assisted laser desorption/ionization quadrupole time-of-flight mass spectrometry (MALDI QTOF-MS). Obtained mass spectra were compared with electrospray ionization MS (ESI-MS) already established for organometallic compounds, utilizing a QTOF mass spectrometer here. In addition, various sample preparations, including two selected MALDI matrices (trans-2-[3-(4-tert-butylphenyl)-2-methyl-2-propenylidene]malononitrile and 2,2':5',2″-terthiophene) with different solvent combinations for MALDI-MS measurements, were investigated in detail with respect to their correct isotope distribution of the molecular ions observed.

RESULTS

All investigated organometallic compounds were successfully identified by vacuum and intermediate pressure MALDI-MS. Accurate masses of ions related to molecular ion species (e.g., [M-Cl]⁺ , [M]⁺ , and [M + Na]⁺ ) could be determined by MALDI QTOF-MS measurements with a mass error of less than ±5 ppm for all compounds. Both investigated MALDI matrices performed equally on both instruments. The impact of the analyte/matrix solvent mixtures turned out to be crucial for a successful analysis of the investigated compounds. In contrast, ESI QTOF-MS yielded masses of ions related to molecular ion species in favorable cases.

CONCLUSIONS

The use of MALDI-MS for the structural confirmation of organometallic compounds is still not widely used. Nevertheless, this work showed that this analytical technique does have some benefits. The analysis of neutral catalysts proves to be quite useful, concluding that this technique provides a complement and/or an alternative to ESI-MS.

FT-ICR Mass Spectrometry Imaging at Extreme Mass Resolving Power Using a Dynamically Harmonized ICR Cell with 1ω or 2ω Detection

MALDI mass spectrometry imaging (MALDI MSI) is a powerful analytical method for achieving 2D localization of compounds from thin sections of typically but not exclusively biological samples. The dynamically harmonized ICR cell (ParaCell) was recently introduced to achieve extreme spectral resolution capable of providing the isotopic fine structure of ions detected in complex samples. The latest improvement in the ICR technology also includes 2ω detection, which significantly reduces the transient time while preserving the nominal mass resolving power of the ICR cell. High-resolution MS images acquired on FT-ICR instruments equipped with 7T and 9.4T superconducting magnets and the dynamically harmonized ICR cell operating at suboptimal parameters suffered severely from the pixel-to-pixel shifting of m/z peaks due to space-charge effects. The resulting profile average mass spectra have depreciated mass measurement accuracy and mass resolving power under the instrument specifications that affect the confidence level of the identified ions. Here, we propose an analytical workflow based on the monitoring of the total ion current to restrain the pixel-to-pixel m/z shift. Adjustment of the laser parameters is proposed to maintain high spectral resolution and mass accuracy measurement within the instrument specifications during MSI analyses. The optimized method has been successfully employed in replicates to perform high-quality MALDI MS images at resolving power (FWHM) above 1,000,000 in the lipid mass range across the whole image for superconducting magnets of 7T and 9.4T using 1 and 2ω detection. Our data also compare favorably with MALDI MSI experiments performed on higher-magnetic-field superconducting magnets, including the 21T MALDI FT-ICR prototype instrument of the NHMFL group at Tallahassee, Florida.

Matrix enrichment by black phosphorus improves ionization and reproducibility of mass spectrometry of intact cells, peptides, and amino acids

Intact (whole) cell matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS) is an established method for biotyping in clinical microbiology as well as for revealing phenotypic shifts in cultured eukaryotic cells. Intact cell MALDI-TOF MS has recently been introduced as a quality control tool for long-term cultures of pluripotent stem cells. Despite the potential this method holds for revealing minute changes in cells, there is still a need for improving the ionization efficiency or peak reproducibility. Here we report for the first time that supplementation by fine particles of black phosphorus to the standard MALDI matrices, such as sinapinic and α-cyano-4-hydroxycinnamic acids enhance intensities of mass spectra of particular amino acids and peptides, presumably by interactions with aromatic groups within the molecules. In addition, the particles of black phosphorus induce the formation of small and regularly dispersed crystals of sinapinic acid and α-cyano-4-hydroxycinnamic acid with the analyte on a steel MALDI target plate. Patterns of mass spectra recorded from intact cells using black phosphorus-enriched matrix were more reproducible and contained peaks of higher intensities when compared to matrix without black phosphorus supplementation. In summary, enrichment of common organic matrices by black phosphorus can improve discrimination data analysis by enhancing peak intensity and reproducibility of mass spectra acquired from intact cells.

Detection of serum phospholipids by microchannel-integrated black phosphorus-assisted laser desorption/ionization mass spectrometry

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been widely applied in the analysis of phospholipids in biological samples. However, it remains a challenge to improve the sensitivity and reproducibility and to control the background noise of matrices. In this study, black phosphorus nanomaterial was used as the matrix of MALDI-MS, and microchannel technique was combined. This microchannel-integrated black phosphorus-assisted laser desorption/ionization (BPALDI) MS approach can effectively detect a variety of lipids with a small amount of sample, and has high sensitivity for phosphatidylcholines (PC) and lysophosphatidylcholines (LPC) with a detection limit of 0.2 μg/mL. Compared with traditional matrices, BPALDI-MS has the advantages of high sensitivity, good reproducibility, and high salt tolerance. This method was successfully applied in the detection of serum PC/LPC ratios in children patients with asthma or bronchopneumonia. This work provides a novel application of black phosphorus matrix and microchannel technique, and gives new insights into method development of rapid screening and identification of disease indicators in biological fluids.

MALDI Mass Spectrometry Imaging of Lipids on Free-Floating Brain Sections and Immunohistochemically Colocalized Markers of Neurodegeneration

In mass spectrometry imaging (MSI), the essential steps in sample preparation include collection and storage. The most widely used preservation procedure for MSI consists in freezing samples and storing them at temperatures below -80 °C. On the other hand, the most common method for preserving biological samples in clinical practice is their fixation in paraformaldehyde. The storage of free-floating sections is a particular type of the preservation of paraformaldehyde-fixed tissues that is used in immunohistochemistry. This chapter describes the approach of the multimodal imaging of free-floating brain sections using the MSI of lipids and the immunohistochemistry of neurodegeneration markers.

Elemental red phosphorus-based photocatalysts for environmental remediation: A review

The low-cost and environmentally benign elemental red phosphorus (RP) is a new class of photocatalysts with tunable bandgaps (ca. 1.5-2.4 eV) and has a strong visible-light response. It has been considered as a promising metal-free photocatalyst for solving the energy crisis and environmental problems. Unfortunately, due to the low-charge carrier mobility, and serve charge trapping effects, its photocatalytic activity is still restricted in comparison with the traditional compound photocatalysts. Considerable efforts, such as morphology modification, cocatalysts addition, heterostructure construction, charge trapping mitigation, have been conducted to improve the photocatalytic activity of the RP photocatalysts. In this review, the physical and chemical properties and the synthetic strategies of the RP photocatalysts were summarized along with the application in environmental remediation accompanied by the photocatalytic reaction mechanism. Finally, an overview and outlook on the problems and future avenues in designing and constructing advanced RP photocatalysts were also proposed.

ANALYSIS OF CARBOHYDRATES AND GLYCOCONJUGATES BY MATRIX-ASSISTED LASER DESORPTION/IONIZATION MASS SPECTROMETRY: AN UPDATE FOR 2015-2016

This review is the ninth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2016. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented over 30 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show no sign of deminishing. © 2020 Wiley Periodicals, Inc.

Quantification and molecular imaging of fatty acid isomers from complex biological samples by mass spectrometry

Elucidating the isomeric structure of free fatty acids (FAs) in biological samples is essential to comprehend their biological functions in various physiological and pathological processes. Herein, we report a novel approach of using peracetic acid (PAA) induced epoxidation coupled with mass spectrometry (MS) for localization of the C[double bond, length as m-dash]C bond in unsaturated FAs, which enables both quantification and spatial visualization of FA isomers from biological samples. Abundant diagnostic fragment ions indicative of the C[double bond, length as m-dash]C positions were produced upon fragmentation of the FA epoxides derived from either in-solution or on-tissue PAA epoxidation of free FAs. The performance of the proposed approach was evaluated by analysis of FAs in human cell lines as well as mapping the FA isomers from cancer tissue samples with MALDI-TOF/TOF-MS. Merits of the newly developed method include high sensitivity, simplicity, high reaction efficiency, and capability of spatial characterization of FA isomers in tissue samples.

Fibrous Phase Red Phosphorene as a New Photocatalyst for Carbon Dioxide Reduction and Hydrogen Evolution

2D photocatalysts are one of the hottest issues in energy and material science. In the field of photocatalysis, a 2D material with an appropriate bandgap of 1.3 to 2.0 eV is desirable. Herein, a new kind of fibrous phase red phosphorene with a bandgap between 1.43 to 1.54 eV is obtained. This is much better than black phosphorus because the bandgap of black P depends of its layer number. The black P needs to be as thin as 1-2 layers for suitable band diagram, which is difficult to control. The fibrous red phosphorene is first used for photocatalytic CO₂ reduction, and its activity is superior to the majority of mainstream photocatalysts and reaches a record-high value among phosphorus. Besides, its activity in hydrogen evolution is higher than most of the phosphorus photocatalysts. The intralayer charge transfer is much easier than interlayer transfer. The mobility of electron and hole along the phosphorene plane is about 20 times higher than that perpendicular to different layers. The activity sites is at region between the two P[21] chains. These regions are easy to be exposed for fibrous phase phosphorene, making it to exhibit high activity.

Comprehensive Lists of Internal Calibrants for Ultrahigh-Resolution Mass Spectrometry Analysis of Crude Oil and Natural Organic Matter and Their Preparation Recipes

In this work, comprehensive lists of internal calibrants for accurate mass determination of molecules in crude oils, natural organic matter, and soil as well as their preparation recipes are presented. The lists include various sets of chemicals for positive- and negative-ion mode electrospray ionization, atmospheric pressure chemical ionization, atmospheric pressure photoionization, and laser desorption ionization. The chemicals were chosen based on their solvent compatibility, ionization efficiency, and accessibility. The sample preparation process was optimized for each ionization method and type of sample. The lists include detailed information on preparation solvent, concentrations, and mixing ratios of sample and calibrants. Internal calibration using the information in the lists results in successful calibration, and all the data presented in this study show root-mean-square errors between the theoretical and obtained m/z numbers of less than 0.4 ppm. The information presented in this study provides an important guideline for researchers working on complex mixtures with ultrahigh-resolution mass spectrometry.

Monitoring the three-dimensional distribution of endogenous species in the lungs by matrix-assisted laser desorption/ionization mass spectrometry imaging

RATIONALE

Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is routinely employed to monitor the distribution of compounds in tissue sections and generate two-dimensional (2D) images. Whilst informative the images do not represent the distribution of the analyte of interest through the entire organ. The generation of 3D images is an exciting field that can provide a deeper view of the analyte of interest throughout an entire organ.

METHODS

Serial sections of mouse and rat lung tissue were obtained at 120 μm depth intervals and imaged individually. Homogenate registration markers were incorporated in order to aid the final 3D image construction. Using freely available software packages, the images were stacked together to generate a 3D image that showed the distribution of endogenous species throughout the lungs.

RESULTS

Preliminary tests were performed on 16 serial tissue sections of mouse lungs. A 3D model showing the distribution of phosphocholine at m/z 184.09 was constructed, which defined the external structure of the lungs and trachea. Later, a second experiment was performed using 24 serial tissue sections of the left lung of a rat. Two molecular markers, identified as [PC (32:1) + K]⁺ at m/z 770.51 and [PC (36:4) + K]⁺ at m/z 820.52, were used to generate 3D models of the parenchyma and airways, respectively.

CONCLUSIONS

A straightforward method to generate 3D MALDI-MS images of selected molecules in lung tissue has been presented. Using freely available imaging software, the 3D distributions of molecules related to different anatomical features were determined.

Inactivation of N-Acetylglucosaminyltransferase I and α1,3-Fucosyltransferase Genes in Nicotiana tabacum BY-2 Cells Results in Glycoproteins With Highly Homogeneous, High-Mannose N-Glycans

Nicotiana tabacum Bright Yellow-2 (BY-2) suspension cells are among the most commonly used plant cell lines for producing biopharmaceutical glycoproteins. Recombinant glycoproteins are usually produced with a mix of high-mannose and complex N-glycans. However, N-glycan heterogeneity is a concern for the production of therapeutic or vaccine glycoproteins because it can alter protein activity and might lead to batch-to-batch variability. In this report, a BY-2 cell line producing glycoproteins devoid of complex N-glycans was obtained using CRISPR/Cas9 edition of two N-acetylglucosaminyltransferase I (GnTI) genes, whose activity is a prerequisite for the formation of all complex N-glycans. The suppression of complex N-glycans in the GnTI-knocked out (KO) cell lines was assessed by Western blotting. Lack of β1,2-xylose residues confirmed the abolition of GnTI activity. Unexpectedly, α1,3-fucose residues were still detected albeit dramatically reduced as compared with wild-type cells. To suppress the remaining α1,3-fucose residues, a second genome editing targeted both GnTI and α1,3-fucosyltransferase (FucT) genes. No β1,2-xylose nor α1,3-fucose residues were detected on the glycoproteins produced by the GnTI/FucT-KO cell lines. Absence of complex N-glycans on secreted glycoproteins of GnTI-KO and GnTI/FucT-KO cell lines was confirmed by mass spectrometry. Both cell lines produced high-mannose N-glycans, mainly Man5 (80 and 86%, respectively) and Man4 (16 and 11%, respectively). The high degree of N-glycan homogeneity and the high-mannose N-glycosylation profile of these BY-2 cell lines is an asset for their use as expression platforms.

Lipid Landscape of the Human Retina and Supporting Tissues Revealed by High-Resolution Imaging Mass Spectrometry

The human retina provides vision at light levels ranging from starlight to sunlight. Its supporting tissues regulate plasma-delivered lipophilic essentials for vision, including retinoids. The macula is an anatomic specialization for high-acuity and color vision that is also vulnerable to prevalent blinding diseases. The retina's exquisite architecture comprises numerous cell types that are aligned horizontally, yielding structurally distinct cell, synaptic, and vascular layers that are visible in histology and in diagnostic clinical imaging. MALDI imaging mass spectrometry (IMS) is now capable of uniting low micrometer spatial resolution with high levels of chemical specificity. In this study, a multimodal imaging approach fortified with accurate multi-image registration was used to localize lipids in human retina tissue at laminar, cellular, and subcellular levels. Multimodal imaging results indicate differences in distributions and abundances of lipid species across and within single cell types. Of note are distinct localizations of signals within specific layers of the macula. For example, phosphatidylethanolamine and phosphatidylinositol lipids were localized to central RPE cells, whereas specific plasmalogen lipids were localized to cells of the perifoveal RPE and Henle fiber layer. Subcellular compartments of photoreceptors were distinguished by PE(20:0_22:5) in the outer nuclear layer, PE(18:0_22:6) in outer and inner segments, and cardiolipin CL(70:5) in the mitochondria-rich inner segments. Several lipids, differing by a single double bond, have markedly different distributions between the central fovea and the ganglion cell and inner nuclear layers. A lipid atlas, initiated in this study, can serve as a reference database for future examination of diseased tissues.

Antigen Retrieval and Its Effect on the MALDI-MSI of Lipids in Formalin-Fixed Paraffin-Embedded Tissue

Formalin-fixed paraffin-embedded (FFPE) tissue represents the primary source of clinical tissue and is routinely used in MALDI-MSI studies. However, it is not particularly suitable for lipidomics imaging given that many species are depleted during tissue processing. Irrespective, a number of solvent-resistant lipids remain, but their extraction may be hindered by the cross-link between proteins. Therefore, an antigen retrieval step could enable the extraction of a greater number of lipids and may provide information that is complementary to that which can be obtained from other biomolecules, such as proteins. In this short communication, we aim to address the effect of performing antigen retrieval prior to MALDI-MSI of lipids in FFPE tissue. As a result, an increased number of lipid signals could be detected and may have derived from lipid species that are known to be implicated in the lipid-protein cross-linking that is formed as a result of formalin fixation. Human renal cancer tissue was used as a proof of concept to determine whether using these detected lipid signals were also able to highlight the histopathological regions that were present. These preliminary findings may highlight the potential to enhance the clinical relevance of the lipidomic information obtained from FFPE tissue.

Spatial Localization of Vitamin D Metabolites in Mouse Kidney by Mass Spectrometry Imaging

Vitamin D plays a key role in the maintenance of calcium/phosphate homeostasis and elicits biological effects that are relevant to immune function and metabolism. It is predominantly formed through UV exposure in the skin by conversion of 7-dehydrocholsterol (vitamin D3). The clinical biomarker, 25-hydroxyvitamin D (25-(OH)-D), is enzymatically generated in the liver with the active hormone 1,25-dihydroxyvitamin D then formed under classical endocrine control in the kidney. Vitamin D metabolites are measured in biomatrices by liquid chromatography-tandem mass spectrometry (LC-MS/MS). In LC-MS/MS, chemical derivatization (CD) approaches have been employed to achieve the desired limit of quantitation. Recently, matrix-assisted laser desorption/ionization (MALDI) has also been reported as an alternative method. However, these quantitative approaches do not offer any spatial information. Mass spectrometry imaging (MSI) has been proven to be a powerful tool to image the spatial distribution of molecules from the surface of biological tissue sections. On-tissue chemical derivatization (OTCD) enables MSI to image molecules with poor ionization efficiently. In this technical report, several derivatization reagents and OTCD methods were evaluated using different MSI ionization techniques. Here, a method for detection and spatial distribution of vitamin D metabolites in murine kidney tissue sections using an OTCD-MALDI-MSI platform is presented. Moreover, the suitability of using the Bruker ImagePrep for OTCD-based platforms has been demonstrated. Importantly, this method opens the door for expanding the range of other poor ionizable molecules that can be studied by OTCD-MSI by adapting existing CD methods.

HCN emission by a Polydesmid Millipede Detected Remotely by Reactive Adsorption on Gold Nanoparticles Followed by Laser Desorption/Ionization Mass Spectrometry (LDI-MS)

Hydrocyanic acid (HCN) is a well-known defensive allomone in the chemical arsenal of millipedes in the order Polydesmida. The presence of HCN in the headspace vapor of adult Xystocheir dissecta (Wood, 1867), a common millipede from the San Francisco Bay Area, was traced by laser desorption/ionization-mass spectrometry (LDI-MS). To accomplish this, the headspace vapor surrounding caged, live millipedes was allowed to diffuse passively over gold-nanoparticle (AuNP) deposits placed at various distances from the emitting source. The stainless steel plates with AuNP deposits were removed and irradiated by a 355-nm laser. The gaseous ions generated in this way were detected by time-of-flight mass spectrometry. The intensity of the mass spectrometric peak detected at m/z 249 for the Au(CN)₂^- complex anion was compared to that of the residual Au^- signal (m/z 197). Using this procedure, HCN vapors produced by the live millipedes could be detected up to 50 cm away from the source. Furthermore, the addition of H₂O₂, as an internal oxygen source for the gold cyanidation reaction that takes place in the AuNP deposits, significantly increased the detection sensitivity. Using the modified H₂O₂ addition procedure, HCN could now be detected at 80 cm from the source. Moreover, we found a decreasing intensity ratio of the Au(CN)₂^-/Au^- signals as the distance from the emitting source increased, following an exponential-decay distribution as predicted by Fick's law of diffusion. Graphical abstract.

Immersion by rotation-based application of the matrix for fast and reproducible sample preparations and robust results in mass spectrometry imaging

Automated matrix deposition for matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) is crucial for producing reproducible analyte ion signals. Here we report an innovative method employing an automated immersion apparatus, which enables a robust matrix deposition within 5 minutes and with scalable throughput by using MAPS matrix and non-polar solvents. MSI results received from mouse heart and rat brain tissues were qualitatively similar to those from nozzle sprayed samples with respect to peak number and quality of the ion images. Overall, the immersion-method enables a fast and careful matrix deposition and has the future potential for implementation in clinical tissue diagnostics.

Mass spectrometry imaging reveals lipid upregulation and bile acid changes indicating amitriptyline induced steatosis in a rat model

As a consequence of the detoxification process, drugs and drug related metabolites can accumulate in the liver, resulting in drug induced liver injury (DILI), which is the major cause for dose limitation. Amitriptyline, a commonly used tricyclic anti-depressant, is known to cause DILI. The mechanism of Amitriptyline induced liver injury is not yet completely understood. However, as it undergoes extensive hepatic metabolism, unraveling the molecular changes in the liver upon Amitriptyline treatment can help understand Amitriptyline's mode of toxicity. In this study, Amitriptyline treated male rat liver tissue was analyzed using Matrix Assisted Laser Desorption/Ionization-Mass Spectrometry Imaging (MALDI-MSI) to investigate the spatial abundances of Amitriptyline, lipids, and bile acids. The metabolism of Amitriptyline in liver tissue was successfully demonstrated, as the spatial distribution of Amitriptyline and its metabolites localize throughout treatment group liver samples. Several lipids appear upregulated, from which nine were identified as distinct phosphatidylcholine (PC) species. The detected bile acids were found to be lower in Amitriptyline treatment group. The combined results from histological findings, Oil Red O staining, and lipid zonation by MSI revealed lipid upregulation in the periportal area indicating drug induced macrovesicular steatosis (DIS).

Developing a Drug Screening Platform: MALDI-Mass Spectrometry Imaging of Paper-Based Cultures

Many potential chemotherapeutics fail to reach patients. One of the key reasons is that compounds are tested during the drug discovery stage in two-dimensional (2D) cell cultures, which are often unable to accurately model in vivo outcomes. Three-dimensional (3D) in vitro tumor models are more predictive of chemotherapeutic effectiveness than 2D cultures, and thus, their implementation during the drug screening stage has the potential to more accurately evaluate compounds earlier, saving both time and money. Paper-based cultures (PBCs) are an emerging 3D culture platform in which cells suspended in Matrigel are seeded into paper scaffolds and cultured to generate a tissue-like environment. In this study, we demonstrate the potential of matrix-assisted laser desorption/ionization-mass spectrometry imaging with PBCs (MALDI-MSI-PBC) as a drug screening platform. This method discriminated regions of the PBCs with and without cells and/or drugs, indicating that coupling PBCs with MALDI-MSI has the potential to develop rapid, large-scale, and parallel mass spectrometric drug screens.

MALDI-Mass Spectrometry Imaging to Investigate Lipid and Bile Acid Modifications Caused by Lentil Extract Used as a Potential Hypocholesterolemic Treatment

This paper reports matrix-assisted laser desorption/ionization mass spectrometry imaging to investigate systematic effects of a lentil extract treatment to lower cholesterol levels. For this purpose, mass spectrometry imaging was used to spatially investigate modifications in the lipid composition and cholesterol levels in the brain, liver, and intestines as well as bile acids in the liver and intestine of rats treated with lentil extract. Neither the lipid composition nor cholesterol levels in the brain samples were found to be significantly different between the treated and not-treated animal groups. The hypercholesterolemic livers showed signs of steatosis (lipid marker PG 36:4), but no modifications in bile acid, cholesterol, and lipid composition. We found significant differences (AUC > 0.75) in the intestines regarding bile acid and lipid composition after treatment with the lentil extract. The treated rats showed a decreased reabsorption (increased excretion) of ursodeoxycholic acid, deoxycholic acid, and chenodeoxycholic acid and an increased deconjugation of taurine-conjugated bile acids (taurochenodeoxycholic acid, taurodeoxycholic acid, taurocholic acid, and 3-keto-taurocholic acid). This indicates that the lentil extract lowers the total cholesterol level in two synergic ways: (i) it increases the excretion of bile acids; hence, new bile acids are produced in the liver from serum cholesterol and (ii) the prebiotic effect leads to free taurine which upregulates the de novo synthesis of bile acid from cholesterol while activating LDL receptors. We demonstrate here that mass spectrometry imaging is a valuable tool for a better understanding of the effects of treatments such as for the synergistic cholesterol-lowering effect of the lentil extract.

Mass spectrometric investigation of amorphous Ga-Sb-Se thin films

Amorphous chalcogenide thin films are widely studied due to their enhanced properties and extensive applications. Here, we have studied amorphous Ga-Sb-Se chalcogenide thin films prepared by magnetron co-sputtering, via laser ablation quadrupole ion trap time-of-flight mass spectrometry. Furthermore, the stoichiometry of the generated clusters was determined which gives information about individual species present in the plasma plume originating from the interaction of amorphous chalcogenides with high energy laser pulses. Seven different compositions of thin films (Ga content 7.6–31.7 at. %, Sb content 5.2–31.2 at. %, Se content 61.2–63.3 at. %) were studied and in each case about ~50 different clusters were identified in positive and ~20–30 clusters in negative ion mode. Assuming that polymers can influence the laser desorption (laser ablation) process, we have used parafilm as a material to reduce the destruction of the amorphous network structure and/or promote the laser ablation synthesis of heavier species from those of lower mass. In this case, many new and higher mass clusters were identified. The maximum number of (40) new clusters was detected for the Ga-Sb-Se thin film containing the highest amount of antimony (31.2 at. %). This approach opens new possibilities for laser desorption ionization/laser ablation study of other materials. Finally, for selected binary and ternary clusters, their structure was calculated by using density functional theory optimization procedure.

Gold Nanoparticles (AuNPs) as Reactive Matrix for Detection of Trace Levels of HCN in Air by Laser Desorption/Ionization Mass Spectrometry (LDI-MS)

Under direct laser desorption/ionization mass spectrometric conditions, the irradiation of target spots made of gold nanoparticle residues generates a series of peaks at m/z 197, 394, 591… representing Au_n^- ions (n = 1-3). In contrast, spectra recorded from gold nanoparticles directly mixed with an alkali cyanide exhibited an additional peak at m/z 249, indicating an abundant generation of gaseous [Au(CN)₂]^- ions upon irradiation. The relative intensity of the m/z 249 peak surged when the amount of cyanide in the mixture was increased. Most remarkably, a peak at m/z 249 was observed even from neat AuNPs upon irradiation, if a nearby spot, which was not irradiated, happened to bear a cyanide sample. We postulated that traces of HCN emanating from the headspace of aqueous cyanide solution during the sample-plate preparation is sufficient to convert gold to AuCN, which is subsequently detected as [Au(CN)₂]^-. Further experiments demonstrated that the relative intensity of the m/z 249 peak diminishes exponentially as the AuNP spot becomes more distant from the putative HCN source. Eventually, the method was developed as an efficient procedure to detect HCN or alkali cyanides. Using KCN, the detection limits were determined to be below 10 pg of CN^- per spot. The method also demonstrated that, upon crushing, the seeds or roots of certain fruits and vegetables such as apple, peach, radish, and cassava, but not carrot, release HCN in amounts detectable by this method. Graphical Abstract.

Gallium selenide clusters generated via laser desorption ionisation quadrupole ion trap time-of-flight mass spectrometry

RATIONALE

Gallium selenide thin films important for electronics and phase-change materials are prepared via pulsed laser deposition (PLD); however, there are no studies concerning the analysis of gallium selenide clusters formed in the gas phase. Laser desorption ionisation (LDI) combined with time-of-flight mass spectrometry (TOF-MS) has great potential to generate charged Ga_m Se_n clusters, to analyse them and thus to develop new materials.

METHODS

LDI of Ga-Se mixtures using a pulsed laser (337 nm nitrogen) was used to generate gallium-selenide clusters. Mass spectra were recorded (in positive and negative ion mode) on a TOF mass spectrometer equipped with a quadrupole ion trap and reflectron mass analyser.

RESULTS

Ga-Se mixtures were found to be suitable for laser ablation synthesis (LAS) of gallium selenide clusters, although their composition was strongly dependent on the laser energy. The effect of laser energy on the stoichiometry of the generated clusters was established. In total, over 100 gallium selenide Ga_m Se_n clusters were generated and identified from Ga-Se mixtures. LDI of Ga₂ Se₃ crystals showed almost the same clusters up to m/z 1000 with lower intensities, whereas no clusters from Ga₂ Se₃ were observed above m/z 1000.

CONCLUSIONS

A family of over 100 gallium selenide clusters, generated and identified for the first time, shows rich and complex chemistry. Some of the clusters represent new compounds that have the potential to be used in the development of advanced materials.

Laser ablation synthesis of carbon-phosphides from graphene/nanodiamond-phosphorus composite precursors: Laser desorption ionisation time-of-flight mass spectrometry

RATIONALE

Carbon-phosphides are new and promising strategic materials with applications e.g. in optoelectronics. However, their chemistry and methods of synthesis are not completely understood, and only a limited number of C-P clusters have been detected up to now. Laser ablation synthesis (LAS) or laser desorption ionisation (LDI) has great potential to generate C_m P_n clusters in the gas phase and to act as the basis for the development of new technology.

METHODS

The LAS of carbon phosphides using mixtures of nano-carbon sources (graphene, nanodiamonds) with phosphorus allotropes (red, black, and phosphorene) was examined. Since phosphorene is not commercially available, it was synthesised. A reflectron time-of-flight mass spectrometer was used to produce and identify the C-P clusters. A transmission electron microscope was used to characterise the prepared composites.

RESULTS

LDI of various carbon-phosphorus composites generated a range of carbon-phosphides. From graphene-red phosphorus, C_m P⁺ (m = 3-47), C_m P₂ ⁺ (m = 2-44), C_m P₃ ⁺ (m = 1-42), C_m P₄ ⁺ (m = 1-39), C_m P₅ ⁺ (m = 1-37), C_m P₆ ⁺ (m = 1-34), C_m P₇ ⁺ (m = 1-31), C_m P₈ ⁺ (m = 1-29), C_m P₉ ⁺ (m = 1-26), C_m P₁₀ ⁺ (m = 1-24), C_m P₁₁ ⁺ (m = 1-21), and C_m P₁₂ ⁺ (m = 1-19) clusters were detected, while nanodiamond composites with red/black phosphorus and with phosphorene yielded C₂₄ P_5 + 2n ⁺ (n = 0-28), C₂₄ P_5 + 2n ⁺ (n = 0-16), and C₂₄ P_5 + 2n ⁺ (n = 0-14) clusters, respectively. In total, over 300 new carbon-phosphide clusters were generated.

CONCLUSIONS

The novel series of carbon-phosphide clusters generated from graphene or nanodiamond composites with red/black phosphorus or with phosphorene demonstrated rich carbon-phosphide chemistry that might inspire the development of novel nano-materials with specific properties.

Detection and fragmentation of doubly charged peptide ions in MALDI-Q-TOF-MS by ion mobility spectrometry for improved protein identification

Today, bottom-up protein identification in MALDI-MS is based on employing singly charged peptide ions, which are predominantly formed in the ionization process. However, peptide mass fingerprinting (PMF) with subsequent tandem MS confirmation using these peptide ions is often hampered due to the lower quality of fragment ion mass spectra caused by the higher collision energy necessary for fragmenting singly protonated peptides. Accordingly, peptide ions of higher charge states would be of high interest for analytical purposes, but they are usually not detected in MALDI-MS experiments as they overlap with singly charged matrix clusters and peptide ions. However, when utilizing ion mobility spectrometry (IMS), doubly charged peptide ions can be actively used by separating them from the singly protonated peptides, visualized, and selectively targeted for tandem MS experiments. The generated peptide fragment ion spectra can be used for a more confident protein identification using PMF with tandem MS confirmation, as most doubly protonated peptide ions yield fragment ion mass spectra of higher quality compared to tandem mass spectra of the corresponding singly protonated precursor ions. Mascot protein scores can be increased by approximately 50% when using tandem mass spectra of doubly charged peptide ions, with ion scores up to six times higher compared with ion scores of tandem mass spectra from singly charged precursors.

Three-Dimensional Mass Spectrometry Imaging Identifies Lipid Markers of Medulloblastoma Metastasis

Treatment for medulloblastoma (MB) — the most common malignant pediatric brain tumor — includes prophylactic radiation administered to the entire brain and spine due to the high incidence of metastasis to the central nervous system. However, the majority of long-term survivors are left with permanent and debilitating neurocognitive impairments as a result of this therapy, while the remaining 30–40% of patients relapse with terminal metastatic disease. Development of more effective targeted therapies has been hindered by our lack of understanding of the underlying mechanisms regulating the metastatic process in this disease. To understand the mechanism by which MB metastasis occurs, three-dimensional matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) experiments were performed on whole brains from a mouse model of human medulloblastoma. Analyzing the tumor and surrounding normal brain in its entirety enabled the detection of low abundance, spatially-heterogeneous lipids associated with tumor development. Boundaries of metastasizing and non-metastasizing primary tumors were readily defined, leading to the identification of lipids associated with medulloblastoma metastasis, including phosphatidic acids, phosphatidylethanolamines, phosphatidylserines, and phosphoinositides. These lipids provide a greater insight into the metastatic process and may ultimately lead to the discovery of biomarkers and novel targets for the diagnosis and treatment of metastasizing MB in humans.

Mass spectrometry imaging of lipids: untargeted consensus spectra reveal spatial distributions in Niemann-Pick disease type C1

Mass spectrometry imaging (MSI) is a tool to rapidly map the spatial location of analytes without the need for tagging or a reporter system. Niemann-Pick disease type C1 (NPC1) is a neurodegenerative, lysosomal storage disorder characterized by accumulation of unesterified cholesterol and sphingolipids in the endo-lysosomal system. Here, we use MSI to visualize lipids including cholesterol in cerebellar brain tissue from the NPC1 symptomatic mouse model and unaffected controls. To complement the imaging studies, a data-processing pipeline was developed to generate consensus mass spectra, thereby using both technical and biological image replicates to assess differences. The consensus spectra are used to determine true differences in lipid relative abundance; lipid distributions can be determined in an unbiased fashion without prior knowledge of location. We show the cerebellar distribution of gangliosides GM1, GM2, and GM3, including variants of lipid chain length. We also performed MALDI-MSI of cholesterol. Further analysis of lobules IV/V and X of the cerebellum gangliosides indicates regional differences. The specificity achieved highlights the power of MSI, and this new workflow demonstrates a universal approach for addressing reproducibility in imaging experiments applied to NPC1.

Brimstone chemistry under laser light assists mass spectrometric detection and imaging the distribution of arsenic in minerals

Singly charged As2n+1 ion clusters (n = 2-11) were generated from elemental arsenic by negative-ion laser-ablation mass spectrometry. The overall abundance of the gaseous As ions generated upon laser irradiation was enhanced nearly a hundred times when As-bearing samples were admixed with sulfur. However, sulfur does not act purely as an inert matrix: irradiating arsenic-sulfur mixtures revealed a novel pathway to generate and detect a series of [AsSn]- clusters (n = 2-6). Intriguingly, the spectra recorded from As2O3, NaAsO2, Na3AsO4, cacodylic acid and 3-amino-4-hydroxyphenylarsonic acid together with sulfur as the matrix were remarkably similar to that acquired from an elemental arsenic and sulfur mixture. This result indicated that arsenic sulfide cluster-ions are generated directly from arsenic compounds by a hitherto unknown pathway. The mechanism of elemental sulfur extracting chemically bound arsenic from compounds and forming [AsSn]- clusters is enigmatic; however, this discovery has a practical value as a general detection method for arsenic compounds. For example, the method was employed for the detection of As in its minerals, and for the imaging of arsenic distribution in minerals such as domeykite. LDI-MS data recorded from a latent image imprinted on a piece of paper from a flat mineral surface, and wetting the paper with a solution of sulfur, enabled the localization of arsenic in the mineral. The distribution of As was visualized as false-color images by extracting from acquired data the relative intensities of m/z 139 (AsS2-) and m/z 171 (AsS3-) ions.

Matrix Assisted and/or Laser Desorption Ionization Quadrupole Ion Trap Time-of-Flight Mass Spectrometry of WO3 Clusters Formation in Gas Phase. Nanodiamonds, Fullerene, and Graphene Oxide Matrices

The formation of W _x O _y^+●/-● clusters in the gas phase was studied by laser desorption ionization (LDI) and matrix assisted laser desorption ionization (MALDI) of solid WO₃. LDI produced (WO₃) _n^{+ ●/- ●} (n = 1-7) clusters. In MALDI, when using nano-diamonds (NDs), graphene oxide (GO), or fullerene (C₆₀) matrices, higher mass clusters were generated. In addition to (WO₃) _n^-● clusters, oxygen-rich or -deficient species were found in both LDI and MALDI (with the total number of clusters exceeding one hundred ≈ 137). This is the first time that such matrices have been used for the generation of(WO₃) _n^+●/-● clusters in the gas phase, while new high mass clusters (WO₃) _n^-● (n = 12-19) were also detected. Graphical Abstract.

Miniaturized dispersive liquid-liquid microextraction and MALDI MS using ionic liquid matrices for the detection of bacterial communication molecules and virulence factors

The identification and quantification of molecules involved in bacterial communication are major prerequisites for the understanding of interspecies interactions at the molecular level. We developed a procedure allowing the determination of 2-heptyl-4(1H)-quinolone (HHQ) and 2-heptyl-3-hydroxy-4(1H)-quinolone (PQS) and the virulence factor pyocyanin (PYO) formed by the Gram-negative bacterium Pseudomonas aeruginosa. The method is based on dispersive liquid-liquid microextraction from small supernatant volumes (below 10 μL) followed by quantitative matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS). The use of ionic liquid matrix led to a lowered limit of detection for pyocyanin and, due to suppression of matrix background signals, easy to interpret mass spectra compared to crystalline matrices. Using an isotope-labeled pyocyanin standard synthesized in small-scale synthesis, quantitative analysis spanning approximately one order of magnitude (0.5 to 250 fmol) was feasible. The method was successfully applied to the detection of the signaling molecules PQS and HHQ in cultures of P. aeruginosa strains isolated from sputum of cystic fibrosis patients and allowed a highly sensitive quantification of PYO from these cultures. Hence, the developed method bears the potential to be used for screening purposes in clinical settings and will help to decipher the molecular basis of bacterial communication. Graphical abstract Ionic liquid matrices for the detection and quantification of the toxin pyocyanin and other signaling molecules from P. aeruginosa by MALDI MS.

Bis(monoacylglycero)phosphate lipids in the retinal pigment epithelium implicate lysosomal/endosomal dysfunction in a model of Stargardt disease and human retinas

Stargardt disease is a juvenile onset retinal degeneration, associated with elevated levels of lipofuscin and its bis-retinoid components, such as N-retinylidene-N-retinylethanolamine (A2E). However, the pathogenesis of Stargardt is still poorly understood and targeted treatments are not available. Utilizing high spatial and high mass resolution matrix assisted laser desorption ionization (MALDI) imaging mass spectrometry (IMS), we determined alterations of lipid profiles specifically localized to the retinal pigment epithelium (RPE) in Abca4 -/- Stargardt model mice compared to their relevant background strain. Extensive analysis by LC-MS/MS in both positive and negative ion mode was required to accurately confirm the identity of one highly expressed lipid class, bis(monoacylgylercoro)phosphate (BMP) lipids, and to distinguish them from isobaric species. The same BMP lipids were also detected in the RPE of healthy human retina. BMP lipids have been previously associated with the endosomal/lysosomal storage diseases Niemann-Pick and neuronal ceroid lipofuscinosis and have been reported to regulate cholesterol levels in endosomes. These results suggest that perturbations in lipid metabolism associated with late endosomal/lysosomal dysfunction may play a role in the pathogenesis of Stargardt disease and is evidenced in human retinas.

Laser Desorption Ionization of As2Ch3 (Ch = S, Se, and Te) Chalcogenides Using Quadrupole Ion Trap Time-of-Flight Mass Spectrometry: A Comparative Study

Laser desorption ionization using time-of-flight mass spectrometer afforded with quadrupole ion trap was used to study As₂Ch₃ (Ch = S, Se, and Te) bulk chalcogenide materials. The main goal of the study is the identification of species present in the plasma originating from the interaction of laser pulses with solid state material. The generated clusters in both positive and negative ion mode are identified as 10 unary (S _p^+/- and As _m^+/- ) and 34 binary (As _m S _p^+/- ) species for As₂S₃ glass, 2 unary (Se _q^+/- ) and 26 binary (As _m Se _q^+/- ) species for As₂Se₃ glass, 7 unary (Te _r^+/- ) and 23 binary (As _m Te _r^+/- ) species for As₂Te₃ material. The fragmentation of chalcogenide materials was diminished using some polymers and in this way 45 new, higher mass clusters have been detected. This novel approach opens a new possibility for laser desorption ionization mass spectrometry analysis of chalcogenides as well as other materials. Graphical abstract ᅟ.

Oxygen-Dependent Lipid Profiles of Three-Dimensional Cultured Human Chondrocytes Revealed by MALDI-MSI

Articular cartilage is exposed to a gradient of oxygen levels ranging from 5% at the surface to 1% in the deepest layers. While most cartilage research is performed in supraphysiological oxygen levels (19–21%), culturing chondrocytes under hypoxic oxygen levels (≤8%) promotes the chondrogenic phenotype. Exposure of cells to various oxygen levels alters their lipid metabolism, but detailed studies examining how hypoxia affects lipid metabolism in chondrocytes are lacking. To better understand the chondrocyte’s behavior in response to oxygen, we cultured 3D pellets of human primary chondrocytes in normoxia (20% oxygen) and hypoxia (2.5% oxygen) and employed matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) in order to characterize the lipid profiles and their spatial distribution. In this work we show that chondrocytes cultured in hypoxia and normoxia can be differentiated by their lipid profiles. Among other species, phosphatidylglycerol species were increased in normoxic pellets, whereas phosphatidylinositol species were the most prominent lipids in hypoxic pellets. Moreover, spatial mapping revealed that phospahtidylglyycerol species were less prominent in the center of pellets where the oxygen level is lower. Additional analysis revealed a higher abundance of the mitochondrial-specific lipids, cardiolipins, in normoxic conditions. In conclusion MALDI-MSI described specific lipid profiles that could be used as sensors of oxygen level changes and may especially be relevant for retaining the chondrogenic phenotype, which has important implications for the treatment of bone and cartilage diseases.