Charge Distribution between Different Classes of Glycerophospolipids in MALDI-MS Imaging

Enhanced MALDI-2 Sensitivity with Reflecting Post-Ionization Laser for High-Resolution MS Imaging Combined with Real-Time Microscope Imaging

Laser-induced matrix-assisted laser desorption/ionization post-ionization (MALDI-2) could improve the MALDI sensitivity of biological metabolites by over 1 order of magnitude. Herein, we demonstrate that MALDI-2 sensitivity can be further enhanced with reflecting post-ionization laser that multiplies the intersection times between laser and MALDI plume. This method, which we named MALDI-2+, typically brought over 2 times sensitivity improvement from conventional MALDI-2. Advancing in sensitivity thereby prompted us to pursue higher mass spectrometry imaging (MSI) spatial resolution. A dedicated T-shaped ion guide was designed to allow perpendicular incidence of ablation laser in reflection geometry MALDI. Although 8-10 μm pixel was used in MALDI imaging due to the limited precision of the motorized stage, the laser spot diameter could be down to 2.5 μm for potentially higher spatial resolution. In addition, this ion source enabled real-time and high-quality microscope imaging from backward of the sample plate. Beneficially, we were able to monitor the actual laser spot condition in real time as well as obtain high-resolution microscopic sample images that inherently register with MSI images. All of these benefits have been demonstrated by analyzing standard samples and imaging of cells. We believe that the enhancement in sensitivity, spatial resolution, and microscope capacity of our design could facilitate spatial omics studies.

Assessing earthworm exposure to a multi-pharmaceutical mixture in soil: unveiling insights through LC-MS and MALDI-MS analyses, and impact of biochar on pharmaceutical bioavailability

In the European circular economy, agricultural practices introduce pharmaceutical (PhAC) residues into the terrestrial environment, posing a potential risk to earthworms. This study aimed to assess earthworm bioaccumulation factors (BAFs), the ecotoxicological effects of PhACs, the impact of biochar on PhAC bioavailability to earthworms, and their persistence in soil and investigate earthworm uptake mechanisms along with the spatial distribution of PhACs. Therefore, earthworms were exposed to contaminated soil for 21 days. The results revealed that BAFs ranged from 0.0216 to 0.329, with no significant ecotoxicological effects on earthworm weight or mortality (p > 0.05). Biochar significantly influenced the uptake of 14 PhACs on the first day (p < 0.05), with diminishing effects over time, and affected significantly the soil-degradation kinetics of 16 PhACs. Moreover, MALDI-MS analysis revealed that PhAC uptake occurs through both the dermal and oral pathways, as pharmaceuticals were distributed throughout the entire earthworm tissue without specific localization. In conclusion, this study suggests ineffective PhAC accumulation in earthworms, highlights the influence of biochar on PhAC degradation rates in soil, and suggests that uptake can occur through both earthworm skin and oral ingestion.

Large-Scale Screening of Pharmaceutical Compounds to Explore the Application Space of On-Tissue MALDI and MALDI-2 Mass Spectrometry

The successful application of matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) in pharmaceutical research is strongly dependent on the detection of the drug of interest at physiologically relevant concentrations. Here we explored how insufficient sensitivity due to low ionization efficiency and/or the interaction of the drug molecule with the local biochemical environment of the tissue can be mitigated for many compound classes using the recently introduced MALDI-MSI coupled with laser-induced postionization, known as MALDI-2-MSI. Leveraging a MALDI-MSI screen of about 1,200 medicines/drug-like compounds from a broad range of medicinal application areas, we demonstrate a significant improvement in drug detection and the degree of sensitivity uplift by using MALDI-2 versus traditional MALDI. Our evaluation was made under simulated imaging conditions using liver homogenate sections as substrate, onto which the compounds were spotted to mimic biological conditions to the first order. To enable an evaluable detection by both MALDI and MALDI-2 for the majority of employed compounds, we spotted 1 μL of a 10 mM solution using a spotting robot and performed our experiments with a Bruker timsTOF fleX MALDI-2 instrument in both positive and negative ion modes. Specifically, we demonstrate using a large cohort of drug-like compounds that ∼60% of the tested compounds showed a more than 10-fold increase in signal intensity and ∼16% showed a more than 100-fold increase upon use of MALDI-2 postionization. Such increases in sensitivity could help advance pharmaceutical MALDI-MSI applications toward the single-cell level.

Advances in mass spectrometry-enabled multiomics at single-cell resolution

Biological organisms are multifaceted, intricate systems where slight perturbations can result in extensive changes in gene expression, protein abundance and/or activity, and metabolic flux. These changes occur at different timescales, spatially across cells of heterogeneous origins, and within single-cells. Hence, multimodal measurements at the smallest biological scales are necessary to capture dynamic changes in heterogeneous biological systems. Of the analytical techniques used to measure biomolecules, mass spectrometry (MS) has proven to be a powerful option due to its sensitivity, robustness, and flexibility with regard to the breadth of biomolecules that can be analyzed. Recently, many studies have coupled MS to other analytical techniques with the goal of measuring multiple modalities from the same single-cell. It is with these concepts in mind that we focus this review on MS-enabled multiomic measurements at single-cell or near-single- cell resolution.

Development of Transmission Ambient Pressure Laser Desorption Ionization/Postphotoionization Mass Spectrometry Imaging

Laser-based high-resolution mass spectrometry imaging at ambient conditions has promising applications in life science. However, the ion yield during laser desorption/ablation is poor. Here, transmission atmospheric pressure laser desorption ionization combined with a compact postphotoionization (t-AP-LDI/PI) assembly with a krypton discharge lamp was developed for the untargeted imaging of various biomolecules. The spatial distributions of numerous lipid classes, fatty acids, neurotransmitters, and amino acids in the subregions of mouse cerebellum tissue were obtained. Compared with single laser ablation, the sensitivities for most analytes were increased by 1 to 3 orders of magnitude by dopant-assisted postphotoionization. After careful optimization, a spatial resolution of 4 μm could be achieved for the metabolites in mouse hippocampus tissue. Finally, the melanoma tissue slices were analyzed using t-AP-LDI/PI MSI, which revealed the metabolic heterogeneity of the melanoma microenvironment and exhibited the phenomenon of abnormal proliferation and invasion trends in tumor cells.

A Machine Learning-Driven Comparison of Ion Images Obtained by MALDI and MALDI-2 Mass Spectrometry Imaging

Matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) enables label-free imaging of biomolecules in biological tissues. However, many species remain undetected due to their poor ionization efficiencies. MALDI-2 (laser-induced post-ionization) is the most widely used post-ionization method for improving analyte ionization efficiencies. Mass spectra acquired using MALDI-2 constitute a combination of ions generated by both MALDI and MALDI-2 processes. Until now, no studies have focused on a detailed comparison between the ion images (as opposed to the generated m/z values) produced by MALDI and MALDI-2 for mass spectrometry imaging (MSI) experiments. Herein, we investigated the ion images produced by both MALDI and MALDI-2 on the same tissue section using correlation analysis (to explore similarities in ion images for ions common to both MALDI and MALDI-2) and a deep learning approach. For the latter, we used an analytical workflow based on the Xception convolutional neural network, which was originally trained for human-like natural image classification but which we adapted to elucidate similarities and differences in ion images obtained using the two MSI techniques. Correlation analysis demonstrated that common ions yielded similar spatial distributions with low-correlation species explained by either poor signal intensity in MALDI or the generation of additional unresolved signals using MALDI-2. Using the Xception-based method, we identified many regions in the t-SNE space of spatially similar ion images containing MALDI and MALDI-2-related signals. More notably, the method revealed distinct regions containing only MALDI-2 ion images with unique spatial distributions that were not observed using MALDI. These data explicitly demonstrate the ability of MALDI-2 to reveal molecular features and patterns as well as histological regions of interest that are not visible when using conventional MALDI.

Lipid-related ion suppression on the herbicide atrazine in earthworm samples in ToF-SIMS and matrix-assisted laser desorption ionization mass spectrometry imaging and the role of gas-phase basicity

In mass spectrometry imaging (MSI), ion suppression can lead to a misinterpretation of results. Particularly phospholipids, most of which exhibit high gas-phase basicity (GB), are known to suppress the detection of metabolites and drugs. This study was initiated by the observation that the signal of an herbicide, i.e., atrazine, was suppressed in MSI investigations of earthworm tissue sections. Herbicide accumulation in earthworms was investigated by time-of-flight secondary ion mass spectrometry and matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). Additionally, earthworm tissue sections without accumulation of atrazine but with a homogeneous spray deposition of the herbicide were analyzed to highlight region-specific ion suppression. Furthermore, the relationship of signal intensity and GB in binary mixtures of lipids, amino acids, and atrazine was investigated in both MSI techniques. The GB of atrazine was determined experimentally through a linear plot of the obtained intensity ratios of the binary amino acid mixtures, as well as theoretically. The GBs values for atrazine of 896 and 906 kJ/mol in ToF-SIMS and 933 and 987 kJ/mol in MALDI-MSI were determined experimentally and that of 913 kJ/mol by quantum mechanical calculations. Compared with the GB of a major lipid component, phosphatidylcholine (GBPC = 1044.7 kJ/mol), atrazine's experimentally and computationally determined GBs in this work are significantly lower, making it prone to ion suppression in biological samples containing polar lipids.

Sodium doping and trapped ion mobility spectrometry improve lipid detection for novel MALDI-MSI analysis of oats

Oat (Avena sativa L.) is an important cereal grain with a unique nutritional profile including a high proportion of lipids. Understanding lipid composition and distribution in oats is valuable for plant, food and nutritional research, and can be achieved using MALDI mass spectrometry imaging (MALDI-MSI). However, this approach presents several challenges for sample preparation (hardness of grains) and analysis (isobaric and isomeric properties of lipids). Here, oat sections were successfully mounted onto gelatin-coated indium tin oxide slides with minimal tearing. Poor detection of triacylglycerols was resolved by applying sodium chloride during mounting, increasing signal intensity. In combination with trapped ion mobility spectrometry (TIMS), lipid identification significantly improved, and we report the separation of several isobaric and isomeric lipids with visualisation of their "true" spatial distributions. This study describes a novel MALDI-TIMS-MSI analytical technique for oat lipids, which may be used to improve the discovery of biomarkers for grain quality.

Toward Omics-Scale Quantitative Mass Spectrometry Imaging of Lipids in Brain Tissue Using a Multiclass Internal Standard Mixture

Mass spectrometry imaging (MSI) has accelerated our understanding of lipid metabolism and spatial distribution in tissues and cells. However, few MSI studies have approached lipid imaging quantitatively and those that have focused on a single lipid class. We overcome this limitation by using a multiclass internal standard (IS) mixture sprayed homogeneously over the tissue surface with concentrations that reflect those of endogenous lipids. This enabled quantitative MSI (Q-MSI) of 13 lipid classes and subclasses representing almost 200 sum-composition lipid species using both MALDI (negative ion mode) and MALDI-2 (positive ion mode) and pixel-wise normalization of each lipid species in a manner analogous to that widely used in shotgun lipidomics. The Q-MSI approach covered 3 orders of magnitude in dynamic range (lipid concentrations reported in pmol/mm2) and revealed subtle changes in distribution compared to data without normalization. The robustness of the method was evaluated by repeating experiments in two laboratories using both timsTOF and Orbitrap mass spectrometers with an ∼4-fold difference in mass resolution power. There was a strong overall correlation in the Q-MSI results obtained by using the two approaches. Outliers were mostly rationalized by isobaric interferences or the higher sensitivity of one instrument for a particular lipid species. These data provide insight into how the mass resolving power can affect Q-MSI data. This approach opens up the possibility of performing large-scale Q-MSI studies across numerous lipid classes and subclasses and revealing how absolute lipid concentrations vary throughout and between biological tissues.

MALDI-2 Mass Spectrometry for Synthetic Polymer Analysis

Synthetic polymers are ubiquitous in daily life, and their properties offer diverse benefits in numerous applications. However, synthetic polymers also present an increasing environmental burden through their improper disposal and subsequent degradation into secondary micro- and nanoparticles (MNPs). These MNPs accumulate in soil and water environments and can ultimately end up in the food chain, resulting in potential health risks. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) has the potential to study localized biological or toxicological changes in organisms exposed to MNPs. Here, we investigate whether MALDI-2 postionization can provide a sensitivity enhancement in polymer analysis that could contribute to the study of MNPs. We evaluated the effect of MALDI-2 by comparing MALDI and MALDI-2 ion yields from polyethyleneglycol (PEG), polypropylene glycol (PPG), polytetrahydrofuran (PTHF), nylon-6, and polystyrene (PS). MALDI-2 caused a signal enhancement of the protonated species for PEG, PPG, PTHF, and nylon-6. PS, by contrast, preferentially formed radical ions, which we attribute to direct resonance-enhanced multiphoton ionization (REMPI). REMPI of PS led to an improvement in sensitivity by several orders of magnitude, even without cationizing salts. The improved sensitivity demonstrated by MALDI-2 for all polymers tested highlights its potential for studying the distribution of certain classes of polymers in biological systems.

Matrix-Enhanced SIMS: The Influence of Primary Ion Species and Cluster Size on Ion Yield and Ion Yield Enhancement of Lipids

Time-of-flight secondary ion mass spectrometry is one of the most promising techniques for label-free analysis of biomolecules with nanoscale spatial resolution. However, high-resolution imaging of larger biomolecules such as phospholipids and peptides is often hampered by low yields of molecular ions. Matrix-enhanced SIMS (ME-SIMS), in which an organic matrix is added to the sample, is one promising approach to enhancing the ion yield for biomolecules. Optimizing this approach has, however, been challenging because the processes involved in increasing the ion yield in ME-SIMS are not yet fully understood. In this work, the matrix α-cyano-4-hydroxycinnamic acid (HCCA) has been combined with cluster primary ion analysis to better understand the roles of proton donation and reduced fragmentation on lipid molecule ion yield. A model system consisting of 1:100 mol ratio dipalmitoylphosphatidylcholine (DPPC) in HCCA as well as an HCCA-coated mouse brain cryosection have been studied using a range of Bi and Ar cluster ions. Although the molecular ion yield increased with an increase in cluster ion size, the enhancement of the signals from intact lipid molecules decreased with an increase in cluster ion size for both the model system and the mouse brain. Additionally, in both systems, protonated molecular ions were significantly more enhanced than sodium and potassium cationized molecules for all of the primary ions utilized. For the model system, the DPPC molecular ion yield was increased by more than an order of magnitude for all of the primary ions studied, and fragmentation of DPPC was dramatically reduced. However, on the brain sample, even though the HCCA matrix reduced DPPC fragmentation for all of the primary ions studied, the matrix coating suppressed the ion yield for some lipids when the larger cluster primary ions were employed. This indicated insufficient migration of the lipids into the matrix coating, so that dilution by the matrix overpowered the enhancement effect. This study provides strong evidence that the HCCA matrix both enhances protonation and reduces fragmentation. For imaging applications, the ability of the analytes to migrate to the surface of the matrix coating is also a critical factor for useful signal enhancement. This work demonstrates that the HCCA matrix provides a softer desorption environment when using Bi cluster ions than that obtained using the large gas cluster ions studied alone, indicating the potential for improved high spatial resolution imaging with ME-SIMS.

rMSIfragment: improving MALDI-MSI lipidomics through automated in-source fragment annotation

Matrix-Assisted Laser Desorption Ionization Mass Spectrometry Imaging (MALDI-MSI) spatially resolves the chemical composition of tissues. Lipids are of particular interest, as they influence important biological processes in health and disease. However, the identification of lipids in MALDI-MSI remains a challenge due to the lack of chromatographic separation or untargeted tandem mass spectrometry. Recent studies have proposed the use of MALDI in-source fragmentation to infer structural information and aid identification. Here we present rMSIfragment, an open-source R package that exploits known adducts and fragmentation pathways to confidently annotate lipids in MALDI-MSI. The annotations are ranked using a novel score that demonstrates an area under the curve of 0.7 in ROC analyses using HPLC-MS and Target-Decoy validations. rMSIfragment applies to multiple MALDI-MSI sample types and experimental setups. Finally, we demonstrate that overlooking in-source fragments increases the number of incorrect annotations. Annotation workflows should consider in-source fragmentation tools such as rMSIfragment to increase annotation confidence and reduce the number of false positives.

Visualization of Differential Cardiolipin Profiles in Murine Retinal Cell Layers by High-Resolution MALDI Mass Spectrometry Imaging

The precise fatty acyl chain configuration of cardiolipin (CL), a tetrameric mitochondrial-specific membrane lipid, exhibits dependence on cell and tissue types. A powerful method to map CL profiles in tissue sections in a spatially resolved manner is matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI). To build on and explore this potential, we employed a quadrupole time-of-flight mass spectrometer along with optimized sample preparation protocols. We imaged the CL profiles of individual murine retinal cell layers at a pixel size of 10 μm. In combination with tandem MS, we obtained detailed insights into the CL composition of individual retinal cell layers. In particular, we found differential expression of the polyunsaturated fatty acids (PUFA) linoleic, arachidonic, and docosahexaenoic acids. PUFAs are prone to peroxidation and hence regarded as critical factors in development and progression of retinal pathologies, such as age-related macular degeneration (AMD). The ability of MALDI-MSI to provide cues on the CL composition in neuronal tissue with close to single-cell resolution can provide important insights into retinal physiology in health and disease.

Mass Spectrometry Imaging of Lipids Using MALDI Coupled with Plasma-Based Post-Ionization on a Trapped Ion Mobility Mass Spectrometer

Here we report the development and optimization of a mass spectrometry imaging (MSI) platform that combines an atmospheric-pressure matrix-assisted laser desorption/ionization platform with plasma postionization (AP-MALDI-PPI) and trapped ion mobility spectrometry (TIMS). We discuss optimal parameters for operating the source, characterize the behavior of a variety of lipid classes in positive- and negative-ion modes, and explore the capabilities for lipid imaging using murine brain tissue. The instrument generates high signal-to-noise for numerous lipid species, with mass spectra sharing many similarities to those obtained using laser postionization (MALDI-2). The system is especially well suited for detecting lipids such as phosphatidylethanolamine (PE), as well as numerous sphingolipid classes and glycerolipids. For the first time, the coupling of plasma-based postionization with ion mobility is presented, and we show the value of ion mobility for the resolution and identification of species within rich spectra that contain numerous isobaric/isomeric signals that are not resolved in the m/z dimension alone, including isomeric PE and demethylated phosphatidylcholine lipids produced by in-source fragmentation. The reported instrument provides a powerful and user-friendly approach for MSI of lipids.

Mass Spectrometry Imaging technology in metabolomics: a systematic review

Mass spectrometry imaging (MSI) is a powerful label-free analysis technique that can provide simultaneous spatial distribution of multiple compounds in a single experiment. By combining the sensitive and rapid screening of high-throughput mass spectrometry with spatial chemical information, metabolite analysis and morphological characteristics are presented in a single image. MSI can be used for qualitative and quantitative analysis of metabolic profiles and it can provide visual analysis of spatial distribution information of complex biological and microbial systems. Matrix assisted laser desorption ionization, laser ablation electrospray ionization and desorption electrospray ionization are commonly used in MSI. Here, we summarize and compare these three technologies, as well as the applications and prospects of MSI in metabolomics.

Single‐Photon‐Induced Post‐Ionization to Boost Ion Yields in MALDI Mass Spectrometry Imaging**

Matrix‐assisted laser desorption/ionization mass spectrometry imaging (MALDI‐MSI) is a rapidly growing method in the life sciences. However, for many analyte classes, its sensitivity is limited due to poor ionization efficiencies. To mitigate this problem, we here introduce a novel post‐ionization scheme based on single‐photon induced chemical ionization using pulsed RF‐Kr lamps. The fine‐vacuum conditions of a dual ion‐funnel ion source effectively thermalize the evolving MALDI plume and enable ample gas‐phase reactions. Injected chemical dopants crucially support fragment‐less ionization to [M+H]⁺/[M−H]⁻ species. Based on this interplay, numerous glycerophospho‐, sphingo‐, and further lipids, registered from mammalian tissue sections, were boosted by up to three orders of magnitude, similar to results obtained with laser‐based post‐ionization (MALDI‐2). Experiments with deuterated matrix and dopant, however, indicated complex chemical ionization pathways different from MALDI‐2.

Mass spectrometry imaging to explore molecular heterogeneity in cell culture

Molecular analysis on the single-cell level represents a rapidly growing field in the life sciences. While bulk analysis from a pool of cells provides a general molecular profile, it is blind to heterogeneities between individual cells. This heterogeneity, however, is an inherent property of every cell population. Its analysis is fundamental to understanding the development, function, and role of specific cells of the same genotype that display different phenotypical properties. Single-cell mass spectrometry (MS) aims to provide broad molecular information for a significantly large number of cells to help decipher cellular heterogeneity using statistical analysis. Here, we present a sensitive approach to single-cell MS based on high-resolution MALDI-2-MS imaging in combination with MALDI-compatible staining and use of optical microscopy. Our approach allowed analyzing large amounts of unperturbed cells directly from the growth chamber. Confident coregistration of both modalities enabled a reliable compilation of single-cell mass spectra and a straightforward inclusion of optical as well as mass spectrometric features in the interpretation of data. The resulting multimodal datasets permit the use of various statistical methods like machine learning-driven classification and multivariate analysis based on molecular profile and establish a direct connection of MS data with microscopy information of individual cells. Displaying data in the form of histograms for individual signal intensities helps to investigate heterogeneous expression of specific lipids within the cell culture and to identify subpopulations intuitively. Ultimately, t-MALDI-2-MSI measurements at 2-µm pixel sizes deliver a glimpse of intracellular lipid distributions and reveal molecular profiles for subcellular domains.

Unraveling the drug distribution in brain enabled by MALDI MS imaging with laser-assisted chemical transfer

Accurate localization of central nervous system (CNS) drug distribution in the brain is quite challenging to matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI), owing to the ionization competition/suppression of highly abundant endogenous biomolecules and MALDI matrix. Herein, we developed a highly efficient sample preparation technique, laser-assisted chemical transfer (LACT), to enhance the detection sensitivity of CNS drugs in brain tissues. A focused diode laser source transilluminated the tissue slide coated with α-cyano-4-hydroxycinnamic acid, an optimal matrix to highly absorb the laser radiation at 405 nm, and a very thin-layer chemical film mainly containing drug molecule was transferred to the acceptor glass slide. Subsequently, MALDI MSI was performed on the chemical film without additional sample treatment. One major advantage of LACT is to minimize ionization competition/suppression from the tissue itself by removing abundant endogenous lipid and protein components. The superior performance of LACT led to the successful visualization of regional distribution patterns of 16 CNS drugs in the mouse brain. Furthermore, the dynamic spatial changes of risperidone and its metabolite were visualized over a 24-h period. Also, the brain-to-plasma (B/P) ratio could be obtained according to MALDI MSI results, providing an alternative means to assess brain penetration in drug discovery.

Reduced Hemoglobin Signal and Improved Detection of Endogenous Proteins in Blood-Rich Tissues for MALDI Mass Spectrometry Imaging

Mass spectrometry imaging provides a powerful approach for the direct analysis and spatial visualization of molecules in tissue sections. Using matrix-assisted laser desorption/ionization mass spectrometry, intact protein imaging has been widely investigated for biomarker analysis and diagnosis in a variety of tissue types and diseases. However, blood-rich or highly vascular tissues present a challenge in molecular imaging due to the high ionization efficiency of hemoglobin, which leads to ion suppression of endogenous proteins. Here, we describe a protocol to selectively reduce hemoglobin signal in blood-rich tissues that can easily be integrated into mass spectrometry imaging workflows.

Effect of the Laser Pulse Width in MALDI-2: A Comparative Study of Picosecond versus Nanosecond Wide Pulses for Laser Postionization

MALDI-2 is a recently introduced technique for postionization (PI) in matrix-assisted laser desorption/ionization (MALDI). It is based on an initial photoionization of neutrally desorbed matrix molecules and subsequent charge-transfer reactions in a fine vacuum or atmospheric pressure ion source. MALDI-2 significantly increases the ion yields for numerous classes of analytes, including lipids, glycans, and a range of pharmaceuticals. To obtain insights into the ionization mechanisms underlying the primary step of PI in MALDI-2, we here conducted a set of experiments with two lasers at 266 nm wavelength and pulse durations of 28 ps and 6 ns, respectively, on a modified orthogonal-extracting time-of-flight mass spectrometer (QTOF, Synapt). 2,5-Dihydroxybenzoic acid (DHB) and 2,5-dihydroxyacetophenone (DHAP) were investigated as MALDI matrices in the positive-ion mode with standardized lipid samples. Analyte- and matrix-derived ion signals were recorded as a function of PI laser pulse energies. The ion signal intensity displays a quadratic dependency on PI-laser pulse energy for low to moderate intensities of up to ∼10⁷ W/cm². This behavior suggests the involvement of resonance enhanced two-photon ionization (REMPI) of neutral matrix molecules in the ionization pathways. Comparing nanosecond and picosecond pulses at the same PI laser pulse energy, higher photon density produced by the shorter pulses generally produced sizably higher ion signal intensities, also corroborating an involvement of REMPI-like processes. Based on a theoretical description of the MALDI-2 process derived from prevalent REMPI theory, comparative measurements allow us to determine the lifetime of the excited states of the employed matrices. Resulting values for both matrices are in good agreement with the literature and corroborate the REMPI-based approach.

MALDI-2 and t-MALDI-2 Mass Spectrometry Imaging

Matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) combined with laser-induced postionization for MALDI-2 enables the simultaneous registration of numerous classes of small molecules (e.g., secondary metabolites including sterols) as well as phospholipids, glycolipids, and glycans from tissue sections and from cell cultures with strongly boosted ion yields. Here, we describe methodological aspects that are key for optimizing the analytical sensitivity and spatial resolution of a MALDI-2 imaging experiment. We will include both top-illumination MALDI-2 as well as the recently introduced transmission (t-) mode MALDI-2 approach.

Quantifying the Matrix Metalloproteinase 2 (MMP2) Spatially in Tissues by Probe via MALDI Imaging Mass Spectrometry

As a matrix metalloproteinase, the abnormal expression of MMP2 is associated with multiple biological processes, including tissue remodeling and cancer progression. Therefore, spatial analysis of MMP2 protein in tissues can be used as an important approach to evaluate the expression distribution of MMP2 in complex tissue environments, which will help the diagnosis and treatment of various diseases, including tissue or organ injuries. Moreover, this analysis will also help the evaluation of prognoses. However, MMP2 is difficult to be spatially determined by MALDI TOF mass spectrometry due to its large molecular weight (over 72 KD) and low content. Therefore, a new method should be developed to help this detection. Here, we have designed a specific MMP2 probe that closely binds to MMP2 protein in tissue. This probe has a Cl on Tyr at the terminal, which can provide two isotope peaks to help the accuracy quantitative of MMP2 protein. Based on this, we used the probe to determine the spatial expression of MMP2 in the tissues based on MALDI TOF mass spectrometry. This approach may help to study the influence of multifunctional proteases on the degree of malignancy in vivo.

Enhancement of Tryptic Peptide Signals from Tissue Sections Using MALDI IMS Postionization (MALDI-2)

Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) allows for highly multiplexed, unlabeled mapping of analytes from tissue sections. However, further work is needed to improve the sensitivity and depth of coverage for protein and peptide IMS. We demonstrate signal enhancement of proteolytic peptides from thin tissue sections of human kidney by conventional MALDI (MALDI-1) augmented using a second ionizing laser (termed MALDI-2). Proteins were digested in situ using trypsin prior to IMS analysis. For tentative identification of peptides and proteins, a tissue homogenate from the same organ used for IMS was analyzed by LC-MS/MS, and data are available via ProteomeXchange with identifier PXD023877. These identified proteins were then digested in silico to generate a database of theoretical peptides to then match to MALDI IMS data sets. Peptides were tentatively identified by matching the MALDI peak list to the database peptide list based on mass accuracy (5 ppm mass error). This resulted in 1337 ± 96 (n = 3) peptides and 2076 ± 362 (n = 3) unique peptides matched to IMS peaks from MALDI-1 and MALDI-2, respectively. Protein identifications requiring two or more peptides per protein resulted in 276 ± 20 proteins with MALDI-1 and 401 ± 60 with MALDI-2. These results demonstrate that MALDI-2 provides enhanced sensitivity for the spatial mapping of tryptic peptides and significantly increases the number of proteins identified in IMS experiments.

Imaging lipids in biological samples with surface-assisted laser desorption/ionization mass spectrometry: A concise review of the last decade

Knowing the spatial location of the lipid species present in biological samples is of paramount importance for the elucidation of pathological and physiological processes. In this context, mass spectrometry imaging (MSI) has emerged as a powerful technology allowing the visualization of the spatial distributions of biomolecules, including lipids, in complex biological samples. Among the different ionization methods available, the emerging surface-assisted laser desorption/ionization (SALDI) MSI offers unique capabilities for the study of lipids. This review describes the specific advantages of SALDI-MSI for lipid analysis, including the ability to perform analyses in both ionization modes with the same nanosubstrate, the detection of lipids characterized by low ionization efficiency in MALDI-MS, and the possibilities of surface modification to improve the detection of lipids. The complementarity of SALDI and MALDI-MSI is also discussed. Finally, this review presents data processing strategies applied in SALDI-MSI of lipids, as well as examples of applications of SALDI-MSI in biomedical lipidomics.

Analyzing Mass Spectrometry Imaging Data of 13C-Labeled Phospholipids in Camelina sativa and Thlaspi arvense (Pennycress) Embryos

The combination of ¹³C-isotopic labeling and mass spectrometry imaging (MSI) offers an approach to analyze metabolic flux in situ. However, combining isotopic labeling and MSI presents technical challenges ranging from sample preparation, label incorporation, data collection, and analysis. Isotopic labeling and MSI individually create large, complex data sets, and this is compounded when both methods are combined. Therefore, analyzing isotopically labeled MSI data requires streamlined procedures to support biologically meaningful interpretations. Using currently available software and techniques, here we describe a workflow to analyze ¹³C-labeled isotopologues of the membrane lipid and storage oil lipid intermediate―phosphatidylcholine (PC). Our results with embryos of the oilseed crops, Camelina sativa and Thlaspi arvense (pennycress), demonstrated greater ¹³C-isotopic labeling in the cotyledons of developing embryos compared with the embryonic axis. Greater isotopic enrichment in PC molecular species with more saturated and longer chain fatty acids suggest different flux patterns related to fatty acid desaturation and elongation pathways. The ability to evaluate MSI data of isotopically labeled plant embryos will facilitate the potential to investigate spatial aspects of metabolic flux in situ.

Complementing Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry Imaging with Chromatography Data for Improved Assignment of Isobaric and Isomeric Phospholipids Utilizing Trapped Ion Mobility-Mass Spectrometry

Lipids, such for example the multifaceted category of glycerophospholipids (GP), play a major role in many biological processes. High-resolution mass spectrometry is able to identify these highly diverse lipid species in combination with fragmentation experiments (MS/MS) on the basis of the accurate m/z and fragmentation pattern. However, for the differentiation of isomeric lipids or isobaric interferences, more elaborate separation methods are required. Especially for imaging techniques, such as matrix-assisted laser desorption/ionization (MALDI)-MS imaging, the identification is often exclusively based on the accurate m/z. Fragmentation via MS/MS increases the confidence in lipid annotation in imaging approaches. However, this is sometimes not feasible due to insufficient sensitivity and significantly prolonged analysis time. The use of a separation dimension such as trapped ion mobility spectrometry (TIMS) after ionization strengthens the confidence of the identification based on the collision cross section (CCS). Since CCS libraries are limited, a tissue-specific database was initially generated using hydrophilic interaction liquid chromatography-TIMS-MS. Using this database, the identification of isomeric lipid classes as well as isobaric interferences in a lipid class was performed using a mouse spleen sample in a workflow described in this study. Besides a CCS-based identification as an additional identification criterion for GP in general, the focus was on the distinction of the isomeric GP classes phosphatidylglycerol and bis(monoacylglycero)phosphate, as well as the differentiation of possible isobaric interferences based on the formation of adducts by MALDI-TIMS-MS imaging on a molecular level.

MALDI-2 at Atmospheric Pressure-Parameter Optimization and First Imaging Experiments

Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is a powerful label-free technique for mapping the spatial distribution of biomolecules directly from tissue. However, like most other MSI techniques, it suffers from low ionization yields and ion suppression effects for biomolecules that might be of interest for a specific application at hand. Recently, a form of laser postionization was introduced (coined MALDI-2) that critically boosts the ion yield for many glyco- and phospholipids by several orders of magnitude and makes the detection of further biomolecular species possible. While the MALDI-2 technique is being increasingly applied by the MSI community, it is still only implemented in fine vacuum ion sources in a pressure range of about 1-10 mbar. Here, we show the first implementation of the technique to a custom-built atmospheric pressure ion source coupled to an Orbitrap Elite system. We present results from parameter optimization of MALDI-2 at atmospheric pressure, compare our findings to previously published fine vacuum data, and show first imaging results from mouse cerebellum with a 20 μm pixel size. Our findings broaden the feasibility of the technique to overall more flexible atmospheric pressure ion sources.

MALDI-2 for the Enhanced Analysis of N-Linked Glycans by Mass Spectrometry Imaging

N-glycans are important players in a variety of pathologies including different types of cancer, (auto)immune diseases, and also viral infections. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is an important tool for high-throughput N-glycan profiling and, upon use of tandem MS, for structure determination. By use of MALDI-MS imaging (MSI) in combination with PNGase F treatment, also spatially correlated N-glycan profiling from tissue sections becomes possible. Here we coupled laser-induced postionization, or MALDI-2, to a trapped ion mobility quadrupole time-of-flight mass spectrometer (timsTOF fleX MALDI-2, Bruker Daltonics). We demonstrate that with MALDI-2 the sensitivity for the detection of molecular [M – H]⁻ species of N-glycans increased by about 3 orders of magnitude. Compared to the current gold standard, the positive ion mode analysis of [M + Na]⁺ adducts, a sensitivity increase by about a factor of 10 is achieved. By exploiting the advantageous fragmentation behavior of [M – H]⁻ ions, exceedingly rich structural information on the composition of complex N-glycans was moreover obtained directly from thin tissue sections of human cerebellum and upon use of low-energy collision-induced dissociation tandem MS. In another set of experiments, in this case by use of a modified Synapt G2-S QTOF mass spectrometer (Waters), we investigated the influence of relevant input parameters, in particular pressure of the N₂ cooling gas in the ion source, delay between the two laser pulses, and that of their pulse energies. In this way, analytical conditions were identified at which molecular ion abundances were maximized and fragmentation reactions minimized. The use of negative ion mode MALDI-2-MSI could constitute a valuable tool in glycobiology research.

Multifunctional Reactive MALDI Matrix Enabling High-Lateral Resolution Dual Polarity MS Imaging and Lipid C═C Position-Resolved MS2 Imaging

Local lipid variations in tissues are readily revealed with mass spectrometry imaging (MSI) methods, and the resulting lipid distributions serve as bioanalytical signatures to reveal cell- or tissue-specific lipids. Comprehensive MSI lipid mapping requires measurements in both ion polarities. Additionally, structural lipid characterization is necessary to link the lipid structure to lipid function. Whereas some structural elements of lipids are readily derived from high-resolution mass spectrometry (MS) and tandem-MS (MSⁿ), the localization of C═C double bonds (DBs) requires specialized fragmentation and/or functionalization methods. In this work, we identify a multifunctional matrix-assisted laser desorption/ionization (MALDI) matrix for spatially resolved lipidomics investigations that reacts with lipids in Paternò-Büchi (PB) reactions during laser irradiation facilitating DB-position assignment and allows dual-polarity high-resolution MALDI-MSI and MALDI MS²I studies. By screening 12 compounds for improved ionization efficiency in positive-/negative-ion mode and the functionalization yield compared to the previously introduced reactive MALDI matrix benzophenone, 2-benzoylpyridine (BzPy) is identified as the best candidate. The new matrix enables DB localization of authentic standards belonging to 12 lipid classes and helps to assign 133/58 lipid features in positive-/negative-ion mode from mouse cerebellum tissue. The analytical capabilities of BzPy as a multifunctional MALDI-MSI matrix are demonstrated by imaging endogenous and PB-functionalized lipids in mouse kidney sections with 7 μm lateral resolution in both ion modes. Tracking diagnostic lipid DB-position fragment ions in mouse pancreatic tissue with down to 10 μm pixel size allows us to identify the islets of Langerhans associated with lipid isomer upregulation and depletion.

Detailed Characterization of the Postionization Efficiencies in MALDI-2 as a Function of Relevant Input Parameters

A recently introduced technique based on MALDI with laser-induced postionization (PI), also named MALDI-2, increases the ion yields for numerous classes of lipids, metabolites, and carbohydrates in MALDI-MS imaging experiments under certain experimental conditions. Here, we used a semiautomatic LabVIEW-based protocol to investigate and optimize the efficiency of the PI process dependent on four relevant input parameters and a dense parameter grid: pulse energies of the two lasers, delay between the laser pulses, and buffer gas pressure in the ion source. All experiments were conducted with a modified MALDI-2 Synapt G2-S mass spectrometer (Waters) and use of a focal spot size on the sample of 15-17 μm. A wavelength-tunable optical parametric oscillator (OPO) laser served for PI at 260 or 280 nm. The investigated MALDI matrices were: 2,5-dihydroxybenzoic acid (positive ion mode, +), 2,5-dihydroxyacetophenone (+), α-cyano-4-hydroxycinnamic acid (+), norharmane (negative-ion mode, -), and 1,5-diaminonapthalene (-). A porcine brain extract served as lipid standard. In the positive-ion mode, a maximum boost for the generated [M + H]⁺ species was found with a N₂ buffer gas pressure of ∼2 mbar and a delay between the laser emissions of ∼10 μs. Higher optimal delay settings of several 10 μs were registered for the two studied matrices in negative-ion mode. With regard to the laser fluences, best PI efficiencies were reached using maximum available ablation and PI laser pulse energies of up to 25 and 160 μJ, respectively. For analytes not profiting from MALDI-2, best ion signal yields were recorded for ablation laser pulse energies of around 7 μJ, depending on the MALDI matrix. At higher laser pulse energies, sizable fragmentation is observed for these ions. The PI laser pulse energy did not have any influence on the ion signals of these species. For optimal ion yield of all analyte species, best results were obtained with an ablation laser pulse energy of ∼7 μJ and a PI laser pulse energy of ∼160 μJ. Our comprehensive data set provides valuable insight into the mechanisms underlying the MALDI-2 processes and could help to further optimize this emerging technique.

Validation of MALDI-MS imaging data of selected membrane lipids in murine brain with and without laser postionization by quantitative nano-HPLC-MS using laser microdissection

MALDI mass spectrometry imaging (MALDI-MSI) is a widely used technique to map the spatial distribution of molecules in sectioned tissue. The technique is based on the systematic generation and analysis of ions from small sample volumes, each representing a single pixel of the investigated sample surface. Subsequently, mass spectrometric images for any recorded ion species can be generated by displaying the signal intensity at the coordinate of origin for each of these pixels. Although easily equalized, these recorded signal intensities, however, are not necessarily a good measure for the underlying amount of analyte and care has to be taken in the interpretation of MALDI-MSI data. Physical and chemical properties that define the analyte molecules’ adjacencies in the tissue largely influence the local extraction and ionization efficiencies, possibly leading to strong variations in signal intensity response. Here, we inspect the validity of signal intensity distributions recorded from murine cerebellum as a measure for the underlying molar distributions. Based on segmentation derived from MALDI-MSI measurements, laser microdissection (LMD) was used to cut out regions of interest with a homogenous signal intensity. The molar concentration of six exemplary selected membrane lipids from different lipid classes in these tissue regions was determined using quantitative nano-HPLC-ESI-MS. Comparison of molar concentrations and signal intensity revealed strong deviations between underlying concentration and the distribution suggested by MSI data. Determined signal intensity response factors strongly depend on tissue type and lipid species.

MALDI-2 Mass Spectrometry and Immunohistochemistry Imaging of Gb3Cer, Gb4Cer, and Further Glycosphingolipids in Human Colorectal Cancer Tissue

The main cellular receptors of Shiga toxins (Stxs), the neutral glycosphingolipids (GSLs), globotriaosylceramide (Gb3Cer/CD77) and globotetraosylceramide (Gb4Cer), are significantly upregulated in about half of the human colorectal carcinomas (CRC) and in other cancers. Therefore, conjugates exploiting the Gb3Cer/Gb4Cer-binding B subunit of Stx (StxB) have attracted great interest for both diagnostic and adjuvant therapeutic interventions. Moreover, fucosylated GSLs were recognized as potential tumor-associated targets. One obstacle to a broader use of these receptor/ligand systems is that the contribution of specific GSLs to tumorigenesis, in particular, in the context of an altered lipid metabolism, is only poorly understood. A second is that also nondiseased organs (e.g., kidney) and blood vessels can express high levels of certain GSLs, not least Gb3Cer/Gb4Cer. Here, we used, in a proof-of-concept study, matrix-assisted laser desorption/ionization mass spectrometry imaging combined with laser-induced postionization (MALDI-2-MSI) to simultaneously visualize the distribution of several Gb3Cer/Gb4Cer lipoforms and those of related GSLs (e.g., Gb3Cer/Gb4Cer precursors and fucosylated GSLs) in tissue biopsies from three CRC patients. Using MALDI-2 and StxB-based immunofluorescence microscopy, Gb3Cer and Gb4Cer were mainly found in dedifferentiated tumor cell areas, tumor stroma, and tumor-infiltrating blood vessels. Notably, fucosylated GSL such as Fuc-(n)Lc4Cer generally showed a highly localized expression in dysplastic glands and indian file-like cells infiltrating adipose tissue. Our "molecular histology" approach could support stratifying patients for intratumoral GSL expression to identify an optimal therapeutic strategy. The improved chemical coverage by MALDI-2 can also help to improve our understanding of the molecular basis of tumor development and GSL metabolism.