Mass Spectrometry Imaging Research Articles

Absolute Quantification of Glutathione Using Top-Hat Optics for IR-MALDESI Mass Spectrometry Imaging.

Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) uses an infrared laser to desorb neutral biomolecules with postionization via ESI at atmospheric pressure. The Gaussian profile of the laser with conventional optics results in the heating of adjacent nonablated tissue due to the energy profile being circular. A diffractive optical element (DOE) was incorporated into the optical train to correct for this disadvantage. The DOE produces a top-hat beam profile and square ablation spots, which have uniform energy distributions. Although beneficial to mass spectrometry imaging (MSI), it is unknown how the DOE affects the ability to perform quantitative MSI (qMSI). In this work, we evaluate the performance of the DOE optical train against our conventional optics to define the potential advantages of the top-hat beam profile. Absolute quantification of glutathione (GSH) was achieved by normalizing the analyte of interest to homoglutathione (hGSH), spotting a dilution series of stable isotope labeled glutathione (SIL-GSH), and analyzing by IR-MALDESI MSI with either the conventional optical train or with the DOE incorporated. Statistical comparison indicates that there was no significant difference between the quantification of GSH by the two optical trains as evidenced by similar calibration curves. Results support that both optical trains can be used for qMSI without a change in the ability to carry out absolute quantification but providing the benefits of the top-hat optical train (i.e., flat energy profile and square ablation spots)-for future qMSI studies.

Co-existence of two antibiotic-producing marine bacteria: Pseudoalteromonas piscicida reduce gene expression and production of the antibacterial compound, tropodithietic acid, in Phaeobacter sp.

Many bacteria co-exist and produce antibiotics, yet we know little about how they cope and occupy the same niche. The purpose of the present study was to determine if and how two potent antibiotic-producing marine bacteria influence the secondary metabolome of each other. We established an agar- and broth-based system allowing co-existence of a Phaeobacter species and Pseudoalteromonas piscicida that, respectively, produce tropodithietic acid (TDA) and bromoalterochromides (BACs). Co-culturing of Phaeobacter sp. strain A36a-5a on Marine Agar with P. piscicida strain B39bio caused a reduction of TDA production in the Phaeobacter colony. We constructed a transcriptional gene reporter fusion in the tdaC gene in the TDA biosynthetic pathway in Phaeobacter and demonstrated that the reduction of TDA by P. piscicida was due to the suppression of the TDA biosynthesis. A stable liquid co-cultivation system was developed, and the expression of tdaC in Phaeobacter was reduced eightfold lower (per cell) in the co-culture compared to the monoculture. Mass spectrometry imaging of co-cultured colonies revealed a reduction of TDA and indicated that BACs diffused into the Phaeobacter colony. BACs were purified from Pseudoalteromonas; however, when added as pure compounds or a mixture they did not influence TDA production. In co-culture, the metabolome was dominated by Pseudoalteromonas features indicating that production of other Phaeobacter compounds besides TDA was reduced. In conclusion, co-existence of two antibiotic-producing bacteria may be allowed by one causing reduction in the antagonistic potential of the other. The reduction (here of TDA) was not caused by degradation but by a yet uncharacterized mechanism allowing Pseudoalteromonas to reduce expression of the TDA biosynthetic pathway.IMPORTANCEThe drug potential of antimicrobial secondary metabolites has been the main driver of research into these compounds. However, in recent years, their natural role in microbial systems and microbiomes has become important to determine the assembly and development of microbiomes. Herein, we demonstrate that two potent antibiotic-producing bacteria can co-exist, and one mechanism allowing the co-existence is the specific reduction of antibiotic production in one bacterium by the other. Understanding the molecular mechanisms in complex interactions provides insights for applied uses, such as when developing TDA-producing bacteria for use as biocontrol in aquaculture.

Nanoscale imaging of DNA-RNA identifies transcriptional plasticity at heterochromatin.

The three-dimensional structure of DNA is a biophysical determinant of transcription. The density of chromatin condensation is one determinant of transcriptional output. Chromatin condensation is generally viewed as enforcing transcriptional suppression, and therefore, transcriptional output should be inversely proportional to DNA compaction. We coupled stable isotope tracers with multi-isotope imaging mass spectrometry to quantify and image nanovolumetric relationships between DNA density and newly made RNA within individual nuclei. Proliferative cell lines and cycling cells in the murine small intestine unexpectedly demonstrated no consistent relationship between DNA density and newly made RNA, even though localized examples of this phenomenon were detected at nuclear-cytoplasmic transitions. In contrast, non-dividing hepatocytes demonstrated global reduction in newly made RNA and an inverse relationship between DNA density and transcription, driven by DNA condensates at the nuclear periphery devoid of newly made RNA. Collectively, these data support an evolving model of transcriptional plasticity that extends at least to a subset of chromatin at the extreme of condensation as expected of heterochromatin.

Effects of Heat Treatment on Anodic Porous Alumina Membranes for Mass Spectrometry

Abstract Desorption ionization using through-hole alumina membrane (DIUTHAME) method is a mass spectrometry imaging (MSI) method that uses an anodic porous alumina membrane (APAM) with an array of submicron-sized through-holes as a surface-assisted laser desorption/ionization (SALDI) substrate. The DIUTHAME method is particularly promising for MSI because it does not generate interfering peaks in the low-molecular-weight region. However, the SALDI effect cannot be obtained if the nanostructures of the substrate are destroyed owing to laser irradiation before sample vaporization. APAMs that maintain their structures after irradiation with a high-intensity laser must be fabricated to realize highly sensitive measurements. In this study, we investigated the role of heat treatment suppressing the laser irradiation induced fracture of APAMs. We found that heat treatment at higher temperatures more effectively suppressed APAM fracture associated with laser irradiation. This result was attributed to the reduction of anion-derived impurities in APAMs upon heat treatment. The resulting heat-treated APAM is expected to serve as a substrate for highly sensitive and robust MSI.

Abstract B045: Sensitizing the PDAC tumor microenvironment to immune checkpoint therapies: characterization of a PDAC 3D model to decipher immune infiltration

Abstract Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal solid tumor with an unfavorable prognosis, often resistant to conventional treatments due to its dense stroma rich in Cancer- Associated Fibroblasts (CAFs). Limited T cell infiltration and prevalence of immunosuppressive cells within the tumor hinder the efficacy of immune checkpoint inhibitors (ICIs). The objective of our project is to modify immune landscape of PDAC tumor microenvironment (TME) to induce ICIs sensitization. We thus develop novel therapeutic strategies combining an immunomodulatory cytokine Interleukine-15 (IL15), with conventional chemotherapies (Gemcitabine or Folfirinox). To accurately replicate the complex cancer-stroma interactions within the pancreatic tumor microenvironment, we constructed a three-dimensional in vitro heterospheroid model composed of xenograft-derived tumor cells from PDAC patients, both primary or immortalized CAFs, and peripheral blood mononuclear cells (PBMCs) from healthy donors. Human 3D models were first set up and characterized by cytometry, imaging mass spectrometry and immunohistochemistry. We showed that, CAFs produce components of the extracellular matrix, promote tumor cell growth, improve resistance to chemotherapy and are able to down-regulate immune cell infiltration and modulate the nature of infiltrated immune cells. Spatial analysis of spheroids using imaging mass cytometry show that CAF influences the distribution of immune cells in our models. Interestingly, Interleukine 15 treatment prompted robust infiltration of PBMCs into heterospheroids. Immunophenotyping experiments revealed a substantial shift in the nature of immune infiltration, marked by a pronounced increase in CD4+ and CD8+ T lymphocytes, gDelta T cell and NK cell populations. When combined with Gemcitabine and IL15, immune effector cell infiltration is remarkably increased, resulting in antitumoral effects and control of tumor cell growth. Moreover, therapeutic combinations induce activation of infiltrated immune effector cells with an increase of activation, degranulation and cytotoxic markers, such as IFNγ, CD107a, and Granzyme B respectively. Thus, the heterotypic spheroids described in our study are a suitable in vitro model to both characterize the influence of CAF on therapeutic effects and the mechanisms that drives immune suppressive microenvironment. Moving forward, the next steps will consist to conduct in vivo experiments using a syngeneic PDAC orthotopic model to assess whether this combined therapeutic approach sensitize the PDAC microenvironment to anti-PD1 therapies. Citation Format: Thomas Bessede, Clara Freixinos, Jennifer Barrat, Véronique Garambois, Nadia Vie, Henri-Alexandre Michaud, Julien Faget, Nathalie Bonnefoy, Céline Gongora, Bruno Robert, Laurent Gros, Christel Larbouret. Sensitizing the PDAC tumor microenvironment to immune checkpoint therapies: characterization of a PDAC 3D model to decipher immune infiltration [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr B045.

Abstract B046: Sensitizing the PDAC tumor microenvironment to immune checkpoint therapies: characterization of a PDAC 3D model to decipher immune infiltration

Abstract Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal solid tumor with an unfavorable prognosis, often resistant to conventional treatments due to its dense stroma rich in Cancer- Associated Fibroblasts (CAFs). Limited T cell infiltration and prevalence of immunosuppressive cells within the tumor hinder the efficacy of immune checkpoint inhibitors (ICIs). The objective of our project is to modify immune landscape of PDAC tumor microenvironment (TME) to induce ICIs sensitization. We thus develop novel therapeutic strategies combining an immunomodulatory cytokine Interleukine-15 (IL15), with conventional chemotherapies (Gemcitabine or Folfirinox). To accurately replicate the complex cancer-stroma interactions within the pancreatic tumor microenvironment, we constructed a three-dimensional in vitro heterospheroid model composed of xenograft-derived tumor cells from PDAC patients, both primary or immortalized CAFs, and peripheral blood mononuclear cells (PBMCs) from healthy donors. Human 3D models were first set up and characterized by cytometry, imaging mass spectrometry and immunohistochemistry. We showed that, CAFs produce components of the extracellular matrix, promote tumor cell growth, improve resistance to chemotherapy and are able to down-regulate immune cell infiltration and modulate the nature of infiltrated immune cells. Spatial analysis of spheroids using imaging mass cytometry show that CAF influences the distribution of immune cells in our models. Interestingly, Interleukine 15 treatment prompted robust infiltration of PBMCs into heterospheroids. Immunophenotyping experiments revealed a substantial shift in the nature of immune infiltration, marked by a pronounced increase in CD4+ and CD8+ T lymphocytes, gDelta T cell and NK cell populations. When combined with Gemcitabine and IL15, immune effector cell infiltration is remarkably increased, resulting in antitumoral effects and control of tumor cell growth. Moreover, therapeutic combinations induce activation of infiltrated immune effector cells with an increase of activation, degranulation and cytotoxic markers, such as IFNγ, CD107a, and Granzyme B respectively. Thus, the heterotypic spheroids described in our study are a suitable in vitro model to both characterize the influence of CAF on therapeutic effects and the mechanisms that drives immune suppressive microenvironment. Moving forward, the next steps will consist to conduct in vivo experiments using a syngeneic PDAC orthotopic model to assess whether this combined therapeutic approach sensitize the PDAC microenvironment to anti-PD1 therapies. Citation Format: Thomas Bessede, Clara Freixinos, Jennifer Barrat, Véronique Garambois, Nadia Vie, Henri-Alexandre Michaud, Julien Faget, Nathalie Bonnefoy, Céline Gongora, Bruno Robert, Laurent Gros, Christel Larbouret. Sensitizing the PDAC tumor microenvironment to immune checkpoint therapies: characterization of a PDAC 3D model to decipher immune infiltration [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr B046.

Abstract PR-13: Disruption of sulfatide metabolism by targeting UGT8 is an actionable metabolic vulnerability for pancreatic cancer early interception

Abstract The existence of asymptomatic precursor lesions that are known to predate invasive pancreatic ductal adenocarcinoma (PDAC) by years provides a compelling rationale for cancer interception efforts. One such precursor is intraductal papillary mucinous neoplasm (IPMN). Using Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-MS) imaging of metabolites in tissue sections from resected patient IPMN cases (N=23) and from a KrasG12D/GnasR201C mouse model of IPMN, we have made a discovery of long chain hydroxylated sulfatide species as being selectively enriched in IPMN. Spatial transcriptomics analysis of serial sections from the same IPMN tissues confirmed cognate transcripts, including ceramide galactosyltransferase (CGT, also known as UGT8) and galactose-3-O-sulfotransferase (CST, also known as Gal3St1) enzymes that, respectively, catalyze the addition of galactose from UDP-galactose to ceramide and the O-sulfation of the galactose residue on galactosylceramide (GalCer), to also be highly enriched in IPMN. Functional studies using CRISPR/cas9 UGT8 knockout Kras;Gnas IPMN cells demonstrated that loss of UGT8, the key enzyme that produces the sulfatide precursor GalCer, results in attenuation of sulfatide biosynthesis and impaired mitochondrial function, as evidenced by reduced mitochondrial respiration and ATP production. These changes were met with concomitant decreases in proliferation and invasiveness, and increased susceptibility to intrinsic apoptosis. Targeting of sulfatide metabolism using a selective small molecule inhibitor of UGT8 suppressed sulfatide biosynthesis, induced ceramide-mediated compensatory mitophagy, and subsequent apoptosis in Kras;Gnas IPMN cells. In vivo, UGT8 inhibition suppressed tumor growth in an IPMN allograft model. In conclusion, our work identifies enhanced sulfatide metabolism as an early metabolic alteration in cystic pre-cancerous lesions of the pancreas that persists through invasive neoplasia and represents an actionable vulnerability for PDAC early interception. Citation Format: Riccardo Ballarò, Yihui Chen, Fredrik I Thege, Rongzhang Dou, Jimin Min, Michele Yip-Schneider, Jianjun Zhang, Ranran Wu, Ehsan Irajizad, Yuki Makino, Kimal I Rajapakshe, Mark W Hurd, Ricardo A León-Letelier, Edwin Ostrin, Jody Vykoukal, Jennifer B Dennison, Kim-Anh Do, Samir Hanash, Robert A Wolff, Paola A Guerrero, Michael P Kim, C Max Schmidt, Anirban Maitra, Johannes F Fahrmann. Disruption of sulfatide metabolism by targeting UGT8 is an actionable metabolic vulnerability for pancreatic cancer early interception [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr PR-13.

Mass Spectrometry Imaging for the Characterization of C═C Localization in Unsaturated Lipid Isomers at the Single-Cell Level.

Unsaturated lipids with carbon-carbon double bonds (C═C) have been implicated in the pathogenesis of various diseases. While mass spectrometry imaging (MSI) has been employed to map the distribution of lipid isomers in tissue sections, the identification of lipid C═C positional isomers at the single-cell level using MSI poses a significant challenge. In this study, we developed a novel approach utilizing ToF-SIMS in conjunction with the Paternò-Büchi (P-B) photochemical reaction to characterize the C═C localization in unsaturated lipid isomers at the single-cell level. The P-B reaction was employed to produce adduct products, which were subsequently subjected to collision-induced dissociation by the primary ion beam of ToF-SIMS to generate characteristic ion pairs indicative of the presence of C═C bonds. Utilizing this approach, lipid isomers in brain and skeletal tissues from mice, as well as different cell lines, were visualized at single-cell resolution. Furthermore, distinct variations in the composition of FA 18:1 isomers across different microregions and cell types were revealed. Our P-B ToF-SIMS approach enables the accurate identification and characterization of complex lipid structures with remarkable spatial resolution and can be helpful in understanding the physiological role of these C═C positional isomers.

Analyte regeneration near-infrared fluorescent probe for endogenous formaldehyde detection in living cells and in vivo

Reaction-based fluorescent probes have proved to be promising tools for endogenous formaldehyde (FA) analysis. Among them, analyte regeneration fluorescent probes have attracted much attention due to their ability to maintain FA homeostasis in imaging analysis, but remain to be explored. Herein, we proposed a novel analyte regeneration near-infrared fluorescent probe Cy-MB for endogenous FA detection. Cy-MB was developed on the basis of hemicyanine-based NIR probe CyOH via connecting a 2-(methylamino)benzoate acid. The 2-(methylamino)benzoate in Cy-MB act not only as a fluorescence quenching group, but also a FA regeneration substrate. Such an analyte regeneration NIR probe can be specifically activated by endogenous FA, resulting in a significant fluorescence signal turn on and accompanied by FA regeneration. Probe Cy-MB possesses good analytical performance such as high selectivity and sensitivity toward FA with a detection limit at 0.67 μM. Furthermore, Cy-MB was successfully applied to image endogenous FA in cancer cells and tumor-bearing mice. Additionally, mass spectrometry imaging (MSI) was further performed to qualitatively identified the spatial distribution of the FA activation products of Cy-MB on molecules level in tumor and major organs of mice. We envision that Cy-MB will provide a widespread application in precise imaging of endogenous FA in biosystems.

Imaging the spatial distribution of structurally diverse plant hormones: A comprehensive review.

Plant hormones are essential and structurally diverse molecules that regulate various aspects of plant growth, development, and stress responses. However, the precise analysis of plant hormones in complex biological samples poses a challenge due to their low concentrations, dynamic levels, and intricate spatial distribution. Moreover, the complexity and interconnectedness of hormone signaling networks make it difficult to simultaneously trace multiple hormone distributions. In this review, we provide an overview of the currently recognized small-molecule plant hormones, signal peptide hormones, and plant growth regulators, along with the analytical methods employed for their analysis. We delve into the latest advancements in mass spectrometry imaging and in situ fluorescence techniques, which enable the examination of the spatial distribution of plant hormones. The advantages and disadvantages of these imaging techniques are further discussed. Finally, we propose potential avenues for future research in this field to further enhance our understanding of plant hormone biology.

Utilizing Fisheye Cameras and Mass Spectrometry Imaging to Obtain Probing Coordinates for Histological Samples

Detecting chemical compositions in histological samples using mass spectrometry often requires time-consuming user interaction with a probe to ensure it is positioned as closely as possible to a sampling region. Fisheye cameras can obtain images of samples with a wide field-of-view; however, barrel distortion makes it difficult to analyze them as a flat plane. This research project aimed to develop an application that unwarps live images of histological samples captured with a fisheye camera and calculates the exact image-to-real-world probing coordinates with minor user interaction. Python’s PyQt5 and OpenCV libraries were utilized to create interactive software that removes fisheye distortion, finds image-to-real-world coordinates, and segments images. Connected hardware consisted of a Prusa 3D printer, liquid micro junction-surface sampling probe, fisheye camera, and LED light strips. The printer provided a bed for capturing sample images and control of the camera and probe within 1/100 of a millimetre. The software was outlined to process at least 2 photos of checkerboards for the fisheye undistortion, capture a photo of a sample to be unwarped, and require the user to map 4 points from the image to probe coordinates. Using this approach, real-world coordinates could be found for any image location. The application successfully unwarps live photos and converts image-to-real-world coordinates with sub-millimeter accuracy. Users can take new calibration photos, control lighting, save photos, and check undistortion entirely within the application to ensure all parameters are satisfactory. Coordinates of significant regions are displayed or may be manually selected, making it easier to sample specific areas. The success of unwarping relies on the camera’s focus and height, lighting, and object positioning. Future development plans to improve robustness and coordinate accuracy, and reduce the amount of calibration needed.

The simultaneous inhibition of SLC6A19 and BCRP transporters leads to an increase of indoxyl sulfate (a uremic toxin) in plasma and kidney.

SLC6A19 inhibitors are being studied as therapeutic agents for Phenylketonuria. In this work, a potent SLC6A19 inhibitor (RA836) elevated rat kidney uremic toxin indoxyl sulfate (IDS) levels by intensity (arbitrary unit) of 13.7{plus minus}7.7 compared to vehicle 0.3{plus minus}0.1 (P=0.01) as determined by tissue mass spectrometry imaging (tMSI) analysis. We hypothesized that increased plasma and kidney levels of IDS could be caused by the simultaneous inhibition of both Slc6a19 and a kidney IDS transporter responsible for excretion of IDS into urine. To test this, we first confirmed the formation of IDS through tryptophan metabolism by feeding rats a Trp-free diet. Inhibiting Slc6a19 with RA836 led to increased IDS in these rats. Next, RA836 and its key metabolites were evaluated in vitro for inhibiting kidney transporters OAT1, OAT3 and BCRP. RA836 inhibits BCRP with an IC50 of 0.045 µM but shows no significant inhibition of OAT1 or OAT3. Finally, RA836 analogs with either potent or no inhibition of SLC6A19 and/or BCRP were synthesized and administered to rats fed a normal diet. Plasma and kidney samples were collected to quantify IDS using LC-MS. Neither a SLC6A19 inactive but potent BCRP inhibitor nor a SLC6A19 active but weak BCRP inhibitor raised IDS levels, while compounds inhibiting both transporters caused IDS accumulation in rat plasma and kidney, supporting the hypothesis that rat Bcrp contributes to the excretion of IDS. In summary, we identified that inhibiting Slc6a19 increases IDS formation, while simultaneously inhibiting Bcrp results in IDS accumulation in the kidney and plasma. Significance Statement This is the first publication to decipher the mechanism for accumulation of IDS (a uremic toxin) in rats via inhibition of both Slc6a19 and Bcrp. Specifically, inhibition of Slc6a19 in the GI track increases IDS formation and inhibition of Bcrp in the kidney blocks IDS excretion. Therefore, we should avoid inhibiting both SLC6A19 and BCRP simultaneously in humans to prevent accumulation of IDS, a known risk factor for cardiovascular disease, psychic anxiety, and mortality in chronic kidney disease patients.

Spatial Metabolomic Profiling of Pinelliae Rhizoma from Different Leaf Types Using Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging.

Pinelliae Rhizoma (PR), a highly esteemed traditional Chinese medicinal herb, is widely applied in clinical settings due to its diverse pharmacological effects, including antitussive, expectorant, antiemetic, sedative-hypnotic, and antitumor activities. Pinellia ternata exhibits morphological variation in its leaves, with types resembling peach, bamboo, and willow leaves. However, the chemical composition differences among the corresponding rhizomes of these leaf phenotypes remain unelucidated. This pioneering research employed Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging (MALDI-MSI) to conduct the in situ identification and spatial profiling of 35 PR metabolites in PR, comprising 12 alkaloids, 4 organic acids, 12 amino acids, 5 flavonoids, 1 sterol, and 1 anthraquinone. Our findings revealed distinct spatial distribution patterns of secondary metabolites within the rhizome tissues of varying leaf types. Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA) effectively differentiated between rhizomes associated with different leaf morphologies. Furthermore, this study identified five potential differential biomarkers-methylophiopogonanone B, inosine, cytidine, adenine, and leucine/isoleucine-that elucidate the biochemical distinctions among leaf types. The precise tissue-specific localization of these secondary metabolites offers compelling insights into the specialized accumulation of bioactive compounds in medicinal plants, thereby enhancing our comprehension of PR's therapeutic potential.

Correlative Imaging for Comprehensive Molecular Mapping of Individual Cell Types in Biological Tissues.

Mass spectrometry imaging (MSI) is a powerful technique for label-free spatial mapping of multiple classes of biomolecules in tissue sections. However, differences in desorption and ionization efficiency of different classes of molecules make it challenging to simultaneously map biomolecules at each omics layer in the same tissue sample. Herein, we present a correlative imaging method using nanospray desorption electrospray ionization (nano-DESI) MSI, which enables the spatial mapping of lipids, metabolites, peptides, and proteins with cellular-level spatial resolution in a single tissue section. We demonstrate the molecular profiling of specific cell types and identify truncated peptides in mouse pancreatic tissue. Distinct chemical gradients of peptides and lipids extending from endocrine cells to exocrine cells indicate their different roles in endocrine-exocrine crosstalk and intracellular signaling. The results underscore the power of the developed imaging approach for spatial multi-omics analysis that provides deep insights into cellular diversity and the intricate molecular interactions that occur within heterogenous biological tissues.

Combining Enhanced Resolving Power with Duty Cycle Improvements on a Multi-Reflecting Time-of-Flight Mass Spectrometer.

The combination of enhanced resolving power and improved duty cycle on a multireflecting time-of-flight mass spectrometer is described. Resolving power increases are achieved by extending the effective ion path length from 47 m to greater than 200 m. Path length increases are achieved through containment of ions within the analyzer for up to N = 5 passes using a pulsed deflection electrode. Resolving power was shown to increase from 220,000 to 402,000 (fwhm) at m/z 785 for N = 1 and N = 4 analyzer passes, respectively. Due to the timing of the pulsed deflection electrode, the approach is particularly suited to high resolution analysis over a targeted m/z range. Duty cycle enhancements are achieved for ions of the targeted m/z range via accumulation prior to orthogonal acceleration, providing signal improvements of 2 orders of magnitude. Achieving such high resolving powers at fast scan rates (30 Hz) can yield additional information such as fine isotope structure; when combined with ppb mass measurement accuracy, high confidence in analyte identification can be achieved. The technique is applied for N = 2 analyzer passes, demonstrating fine isotope structure for a typical UHPLC metabolite identification experiment at a 10 Hz acquisition rate. Additionally, mass spectrometry imaging data is acquired using DESI, demonstrating the improved image clarity achieved at >300,000 (fwhm).

Leveraging Supervised Machine Learning Algorithms for System Suitability Testing of Mass Spectrometry Imaging Platforms.

Quality control and system suitability testing are vital protocols implemented to ensure the repeatability and reproducibility of data in mass spectrometry investigations. However, mass spectrometry imaging (MSI) analyses present added complexity since both chemical and spatial information are measured. Herein, we employ various machine learning algorithms and a novel quality control mixture to classify the working conditions of an MSI platform. Each algorithm was evaluated in terms of its performance on unseen data, validated with negative control data sets to rule out confounding variables or chance agreement, and utilized to determine the necessary sample size to achieve a high level of accurate classifications. In this work, a robust machine learning workflow was established where models could accurately classify the instrument condition as clean or compromised based on data metrics extracted from the analyzed quality control sample. This work highlights the power of machine learning to recognize complex patterns in MSI data and use those relationships to perform a system suitability test for MSI platforms.

MSIGen: An Open-Source Python Package for Processing and Visualizing Mass Spectrometry Imaging Data.

Mass spectrometry imaging (MSI) provides information about the spatial localization of molecules in complex samples with high sensitivity and molecular selectivity. Although point-wise data acquisition, in which mass spectra are acquired at predefined points in a grid pattern, is common in MSI, several MSI techniques use line-wise data acquisition. In line-wise mode, the imaged surface is continuously sampled along consecutive parallel lines and MSI data are acquired as a collection of line scans across the sample. Furthermore, aside from the standard imaging mode in which full mass spectra are acquired, other acquisition modes have been developed to enhance molecular specificity, enable separation of isobaric and isomeric species, and improve sensitivity to facilitate the imaging of low abundance species. These methods, including MS/MS-MSI in both MS2 and MS3 modes, multiple-reaction monitoring (MRM)-MSI, and ion mobility spectrometry (IMS)-MSI have all demonstrated their capabilities, but their broader implementation is limited by the existing MSI analysis software. Here, we present MSIGen, an open-source Python package for the visualization of MSI experiments performed in line-wise acquisition mode containing MS1, MS2, MRM, and IMS data, which is available at https://github.com/LabLaskin/MSIGen. The package supports multiple vendor-specific and open-source data formats and contains tools for targeted extraction of ion images, normalization, and exportation as images, arrays, or publication-style images. MSIGen offers multiple interfaces, allowing for accessibility and easy integration with other workflows. Considering its support for a wide variety of MSI imaging modes and vendor formats, MSIGen is a valuable tool for the visualization and analysis of MSI data.

Spatial Metabolomics Profiling Reveals Curcumin Induces Metabolic Reprogramming in Three-Dimensional Tumor Spheroids.

Curcumin is widely recognized for its diverse antitumor properties, ranging from breast cancer to many other types of cancers. However, its role in the tumor microenvironment remains to be elucidated. In this study, we established a 3D tumor spheroids model that can simulate the growth environment of tumor cells and visualized the antitumor metabolic alteration caused by curcumin using mass spectrometry imaging technology. Our results showed that curcumin not only exerts a profound impact on the growth and proliferation of breast cancer cells but in situ multivariate statistical analysis also reveals the significant effect on the overall metabolic profile of tumor spheroids. Meanwhile, our visualization map characterized curcumin metabolic processes of reduction and glucuronidation in tumor spheroids. More importantly, abnormal metabolic pathways related to lipid metabolism and polyamine metabolism were also remodeled at the metabolite and gene levels after curcumin intervention. These insights deepen our comprehension of the regulatory mechanism of curcumin on the tumor metabolic network, furnishing powerful references for antitumor treatment.

Spatial lipidomic profiles of atherosclerotic plaques: A mass spectrometry imaging study

Lipids contribute to atherosclerotic cardiovascular disease but their roles are not fully understood. Spatial lipid composition of atherosclerotic plaques was compared between species focusing on aortic plaques from New Zealand White rabbits and carotid plaques from humans (n = 3), using matrix-assisted laser desorption/ionization mass spectrometry imaging. Histologically discriminant lipids within plaque features (neointima and media in rabbits, and lipid-necrotic core and fibrous cap/tissue in humans) included sphingomyelins, phosphatidylcholines, and cholesteryl esters. There were 67 differential lipids between rabbit plaque features and 199 differential lipids in human, each with variable importance in projection score ≥1.0 and p < 0.05. The lipid profile of plaques in the rabbit model closely mimicked that of human plaques and two key pathways (impact value ≥ 0.1), sphingolipid and glycerophospholipid metabolism, were disrupted by atherosclerosis in both species. Thus, mass spectrometry imaging of spatial biomarkers offers valuable insights into atherosclerosis.

Profiling of collagen and extracellular matrix deposition from cell culture using in vitro ExtraCellular matrix mass spectrometry imaging (ivECM-MSI)

While numerous approaches have been reported towards understanding single cell regulation, there is limited understanding of single cell production of extracellular matrix phenotypes. Collagens are major proteins of the extracellular microenvironment extensively used in basic cell culture, tissue engineering, and biomedical applications. However, identifying compositional regulation of collagen remains challenging. Here, we report the development of In vitro ExtraCellular Matrix Mass Spectrometry Imaging (ivECM-MSI) as a tool to rapidly and simultaneously define collagen subtypes from coatings and basic cell culture applications. The tool uses the mass spectrometry imaging platform with reference libraries to produce visual and numerical data types. The method is highly integrated with basic in vitro strategies as it may be used with conventional cell chambers on minimal numbers of cells and with minimal changes to biological experiments. Applications tested include semi-quantitation of collagen composition in culture coatings, time course collagen deposition, deposition altered by gene knockout, and changes induced by drug treatment. This approach provides new access to proteomic information on how cell types respond to and change the extracellular microenvironment and provides a holistic understanding of both the cell and extracellular response.