Recent advances in single-cell MALDI mass spectrometry imaging and potential clinical impact

Enhancement of Lipid Signals in Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry with Ammonium Fluoride as a Matrix Additive

Lipids are essential macromolecules that play a crucial role in numerous biological events. Lipids are structurally diverse which allows them to fulfill multiple functional roles. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is a powerful tool to understand the spatial localization of lipids within biological systems. Herein, we report the use of ammonium fluoride (NH4F) as a comatrix additive to enhance lipid detection in biological samples, with a signal increase of up to 200%. Emphasis was placed on anionic lipid enhancement with negative polarity measurements, with some preliminary work on cationic lipids detailed. We observed lipid signal enhancement of [M-H]- ions with the addition of NH4F additive attributed to a proton transfer reaction in several different lipid classes. Overall, our study demonstrates that the use of the NH4F comatrix additive substantially improves sensitivity for lipid detection in a MALDI system and is capable of being applied to a variety of different applications.

Advances in Mass Spectrometry-Based Single Cell Analysis

Technological developments and improvements in single-cell isolation and analytical platforms allow for advanced molecular profiling at the single-cell level, which reveals cell-to-cell variation within the admixture cells in complex biological or clinical systems. This helps to understand the cellular heterogeneity of normal or diseased tissues and organs. However, most studies focused on the analysis of nucleic acids (e.g., DNA and RNA) and mass spectrometry (MS)-based analysis for proteins and metabolites of a single cell lagged until recently. Undoubtedly, MS-based single-cell analysis will provide a deeper insight into cellular mechanisms related to health and disease. This review summarizes recent advances in MS-based single-cell analysis methods and their applications in biology and medicine.

Recent advances in mass spectrometry analysis of neuropeptides

Due to their involvement in numerous biochemical pathways, neuropeptides have been the focus of many recent research studies. Unfortunately, classic analytical methods, such as western blots and enzyme-linked immunosorbent assays, are extremely limited in terms of global investigations, leading researchers to search for more advanced techniques capable of probing the entire neuropeptidome of an organism. With recent technological advances, mass spectrometry (MS) has provided methodology to gain global knowledge of a neuropeptidome on a spatial, temporal, and quantitative level. This review will cover key considerations for the analysis of neuropeptides by MS, including sample preparation strategies, instrumental advances for identification, structural characterization, and imaging; insightful functional studies; and newly developed absolute and relative quantitation strategies. While many discoveries have been made with MS, the methodology is still in its infancy. Many of the current challenges and areas that need development will also be highlighted in this review.

Mass spectrometry-based strategies for single-cell metabolomics

Single cell analysis has drawn increasing interest from the research community due to its capability to interrogate cellular heterogeneity, allowing refined tissue classification and facilitating novel biomarker discovery. With the advancement of relevant instruments and techniques, it is now possible to perform multiple omics including genomics, transcriptomics, metabolomics or even proteomics at single cell level. In comparison with other omics studies, single-cell metabolomics (SCM) represents a significant challenge since it involves many types of dynamically changing compounds with a wide range of concentrations. In addition, metabolites cannot be amplified. Although difficult, considerable progress has been made over the past decade in mass spectrometry (MS)-based SCM in terms of processing technologies and biochemical applications. In this review, we will summarize recent progress in the development of promising MS platforms, sample preparation methods and SCM analysis of various cell types (including plant cell, cancer cell, neuron, embryo cell, and yeast cell). Current limitations and future research directions in the field of SCM will also be discussed.

Single-Cell Mass Spectrometry Enables Insight into Heterogeneity in Infectious Disease

Cellular heterogeneity is generally overlooked in infectious diseases. In this study, we investigated host cell heterogeneity during infection with Trypanosoma cruzi (T. cruzi) parasites, causative agents of Chagas disease (CD). In chronic-stage CD, only a few host cells are infected with a large load of parasites and symptoms may appear at sites distal to parasite colonization. Furthermore, recent work has revealed T. cruzi heterogeneity with regard to replication rates and drug susceptibility. However, the role of cellular-level metabolic heterogeneity in these processes has yet to be assessed. To fill this knowledge gap, we developed a Single-probe SCMS (single-cell mass spectrometry) method compatible with biosafety protocols, to acquire metabolomics data from individual cells during T. cruzi infection. This study revealed heterogeneity in the metabolic response of the host cells to T. cruzi infection in vitro. Our results showed that parasite-infected cells possessed divergent metabolism compared to control cells. Strikingly, some uninfected cells adjacent to infected cells showed metabolic impacts as well. Specific metabolic changes include increases in glycerophospholipids with infection. These results provide novel insight into the pathogenesis of CD. Furthermore, they represent the first application of bioanalytical SCMS to the study of mammalian-infectious agents, with the potential for broad applications to study infectious diseases.

Metabolomics studies of cell-cell interactions using single cell mass spectrometry combined with fluorescence microscopy

Cell-cell interactions are critical for transmitting signals among cells and maintaining their normal functions from the single-cell level to tissues. In cancer studies, interactions between drug-resistant and drug-sensitive cells play an important role in the development of chemotherapy resistance of tumors. As metabolites directly reflect the cell status, metabolomics studies provide insight into cell-cell communication. Mass spectrometry (MS) is a powerful tool for metabolomics studies, and single cell MS (SCMS) analysis can provide unique information for understanding interactions among heterogeneous cells. In the current study, we utilized a direct co-culture system (with cell-cell contact) to study metabolomics of single cells affected by cell-cell interactions in their living status. A fluorescence microscope was utilized to distinguish these two types of cells for SCMS metabolomics studies using the Single-probe SCMS technique under ambient conditions. Our results show that through interactions with drug-resistant cells, drug-sensitive cancer cells acquired significantly increased drug resistance and exhibited drastically altered metabolites. Further investigation found that the increased drug resistance was associated with multiple metabolism regulations in drug-sensitive cells through co-culture such as the upregulation of sphingomyelins lipids and lactic acid and the downregulation of TCA cycle intermediates. The method allows for direct MS metabolomics studies of individual cells labeled with fluorescent proteins or dyes among heterogeneous populations.

Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging of Glycogen In Situ

Histopathological detection and quantitation of glycogen in situ are important for the assessment of glycogen storage diseases and different types of cancer. The current standard method for defining the regionality of glycogen rely almost exclusively on Periodic Acid-Schiff (PAS) staining, a workflow that lacks specificity and sensitivity. Herein, we describe a new and much improved workflow to detect microenvironmental glycogen in situ using enzyme-assisted matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI). This method provides superior sensitivity and can elucidate the molecular features of glycogen structure, with 50 μm spatial resolution for a next-generation histopathological assessment of glycogen.

Data parsing in mass spectrometry imaging using R Studio and Cardinal: A tutorial

Mass spectrometry imaging (MSI) has emerged as a rapidly expanding field in the MS community. The analysis of large spectral data is further complicated by the added spatial dimension of MSI. A plethora of resources exist for expert users to begin parsing MSI data in R, but there is a critical lack of guidance for absolute beginners. This tutorial is designed to serve as a one-stop guide to start using R with MSI data and describe the possibilities that data science can bring to MSI analysis.

Automatic Registration of the Mass Spectrometry Imaging Data of Sagittal Brain Slices to the Reference Atlas

The registration of the mass spectrometry imaging (MSI) data with mouse brain tissue slices from the atlases could perform automatic anatomical interpretation, and the comparison of MSI data in particular brain regions from different mice could be accelerated. However, the current registration of MSI data with mouse brain tissue slices is mainly focused on the coronal. Although the sagittal plane is able to provide more information about brain regions on a single histological slice than the coronal, it is difficult to directly register the complete sagittal brain slices of a mouse as a result of the more significant individualized differences and more positional shifts of brain regions. Herein, by adding the auxiliary line on the two brain regions of central canal (CC) and cerebral peduncle (CP), the registration accuracy of the MSI data with sagittal brain slices has been improved (∼2-5-folds for different brain regions). Moreover, the histological sections with different degrees deformation and different dyeing effects have been used to verify that this pipeline has a certain universality. Our method facilitates the rapid comparison of sagittal plane MSI data from different animals and accelerates the application in the discovery of disease markers.

Clinical Insights into Mitochondrial Neurodevelopmental and Neurodegenerative Disorders: Their Biosignatures from Mass Spectrometry-Based Metabolomics

Mitochondria are dynamic multitask organelles that function as hubs for many metabolic pathways. They produce most ATP via the oxidative phosphorylation pathway, a critical pathway that the brain relies on its energy need associated with its numerous functions, such as synaptic homeostasis and plasticity. Therefore, mitochondrial dysfunction is a prevalent pathological hallmark of many neurodevelopmental and neurodegenerative disorders resulting in altered neurometabolic coupling. With the advent of mass spectrometry (MS) technology, MS-based metabolomics provides an emerging mechanistic understanding of their global and dynamic metabolic signatures. In this review, we discuss the pathogenetic causes of mitochondrial metabolic disorders and the recent MS-based metabolomic advances on their metabolomic remodeling. We conclude by exploring the MS-based metabolomic functional insights into their biosignatures to improve diagnostic platforms, stratify patients, and design novel targeted therapeutic strategies.

A Drastic Shift in Lipid Adducts in Colon Cancer Detected by MALDI-IMS Exposes Alterations in Specific K+ Channels

Even though colorectal cancer (CRC) is one of the most preventable cancers, it is one of the deadliest, and recent data show that the incidence in people <50 years has unexpectedly increased. While new techniques for CRC molecular classification are emerging, no molecular feature is as yet firmly associated with prognosis. Imaging mass spectrometry (IMS) lipidomic analyses have demonstrated the specificity of the lipid fingerprint in differentiating pathological from healthy tissues. During IMS lipidomic analysis, the formation of ionic adducts is common. Of particular interest is the [Na⁺]/[K⁺] adduct ratio, which already functions as a biomarker for homeostatic alterations. Herein, we show a drastic shift of the [Na⁺]/[K⁺] adduct ratio in adenomatous colon mucosa compared to healthy mucosa, suggesting a robust increase in K⁺ levels. Interrogating public databases, a strong association was found between poor diagnosis and voltage-gated potassium channel subunit beta-2 (KCNAB2) overexpression. We found this overexpression in three CRC molecular subtypes defined by the CRC Subtyping Consortium, making KCNAB2 an interesting pharmacological target. Consistently, its pharmacological inhibition resulted in a dramatic halt in commercial CRC cell proliferation. Identification of potential pharmacologic targets using lipid adduct information emphasizes the great potential of IMS lipidomic techniques in the clinical field.

Transmission-Mode MALDI Mass Spectrometry Imaging of Single Cells: Optimizing Sample Preparation Protocols

Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) makes it possible to simultaneously visualize the spatial distribution of dozens to hundreds of different biomolecules (e.g., phospho- and glycolipids) in tissue sections and in cell cultures. The implementation of novel desorption and (post-)ionization techniques has recently pushed the pixel size of this imaging technique to the low micrometer scale and below and thus to a cellular and potentially sub-cellular level. However, to fully exploit this potential for cell biology and biomedicine, sample preparation becomes highly demanding. Here, we investigated the effect of several key parameters on the quality of the sample preparation and achievable spatial resolution, that include the washing, drying, chemical fixation, and matrix coating steps. The incubation of cells with formalin for about 5 min in combination with isotonic washing and mild drying produced a robust protocol that largely preserved not only cell morphologies, but also the molecular integrities of amine group-containing cell membrane phospholipids (phosphatidylethanolamines and -serines). A disadvantage of the chemical fixation is an increased permeabilization of cell membranes, resulting in leakage of cytosolic compounds. We demonstrate the pros and cons of the protocols with four model cell lines, cultured directly on indium tin oxide (ITO)-coated glass slides. Transmission (t-)mode MALDI-2-MSI enabled on a Q Exactive plus Orbitrap mass spectrometer was used to analyze the cultures at a pixel size of 2 μm. Phase contrast light microscopy and scanning electron microscopy were used as complementary methods. The protocols described could prove to be an important contribution to the advancement of single-cell MALDI imaging, especially for the characterization of cell-to-cell heterogeneities at a molecular level.

Adaptive Pixel Mass Recalibration for Mass Spectrometry Imaging Based on Locally Endogenous Biological Signals

Mass spectrometry imaging (MSI) is a powerful and convenient method for revealing the spatial chemical composition of different biological samples. Molecular annotation of the detected signals is only possible if a high mass accuracy is maintained over the entire image and the m/z range. However, the change in the number of ions from pixel-to-pixel of the biological samples could lead to small fluctuations in the detected m/z-values, called mass shift. The use of internal calibration is known to offer the best solution to avoid, or at least to reduce, mass shifts. Their "a priori" selection for a global MSI acquisition is prone to false positive detection and therefore to poor recalibration. To fill this gap, this work describes an algorithm that recalibrates each spectrum individually by estimating its mass shift with the help of a list of pixel-specific internal calibrating ions, automatically generated in a data-adaptive manner (https://github.com/LaRoccaRaphael/MSI_recalibration). Through a practical example, we applied the methodology to a zebrafish whole-body section acquired at a high mass resolution to demonstrate the impact of mass shift on data analysis and the capability of our algorithm to recalibrate MSI data. In addition, we illustrate the broad applicability of the method by recalibrating 31 different public MSI data sets from METASPACE from various samples and types of MSI and show that our recalibration significantly increases the numbers of METASPACE annotations (gaining from 20 up to 400 additional annotations), particularly the high-confidence annotations with a low false discovery rate.

Molecular oxygen as a signaling component in plant development

While traditionally hypoxia has been studied as a detrimental component of flooding stress, the last decade has flourished with studies reporting the involvement of molecular oxygen availability in plant developmental processes. Moreover, proliferating and undifferentiated cells from different plant tissues were found to reside in endogenously generated hypoxic niches. Thus, stress-associated acute hypoxia may be distinguished from constitutively generated chronic hypoxia. The Cys/Arg branch of the N-degron pathway assumes a central role in integrating oxygen levels resulting in proteolysis of transcriptional regulators that control different aspects of plant growth and development. As a target of this pathway, group VII of the Ethylene Response Factor (ERF-VII) family has emerged as a hub for the integration of oxygen dynamics in root development and during seedling establishment. Additionally, vegetative shoot meristem activity and reproductive transition were recently associated with oxygen availability via two novel substrates of the N-degron pathways: VERNALISATION 2 (VRN2) and LITTLE ZIPPER 2 (ZPR2). Together, these observations support roles for molecular oxygen as a signalling molecule in plant development, as well as in essential metabolic reactions. Here, we review recent findings regarding oxygen-regulated development, and discuss outstanding questions that spring from these discoveries.

Cell-Type-Specific Metabolic Profiling Achieved by Combining Desorption Electrospray Ionization Mass Spectrometry Imaging and Immunofluorescence Staining

Cell-type-specific metabolic profiling in tissue with heterogeneous composition has been of great interest across all mass spectrometry imaging (MSI) technologies. We report here a powerful new chemical imaging capability in desorption electrospray ionization (DESI) MSI, which enables cell-type-specific and in situ metabolic profiling in complex tissue samples. We accomplish this by combining DESI-MSI with immunofluorescence staining using specific cell-type markers. We take advantage of the variable frequency of each distinct cell type in the lateral septal nucleus (LSN) region of mouse forebrain. This allows computational deconvolution of the cell-type-specific metabolic profile in neurons and astrocytes by convex optimization-a machine learning method. Based on our approach, we observed 107 metabolites that show different distributions and intensities between astrocytes and neurons. We subsequently identified 23 metabolites using high-resolution mass spectrometry (MS) and tandem MS, which include small metabolites such as adenosine and N-acetylaspartate previously associated with astrocytes and neurons, respectively, as well as accumulation of several phospholipid species in neurons which have not been studied before. Overall, this method overcomes the relatively low spatial resolution of DESI-MSI and provides a new platform for in situ metabolic investigation at the cell-type level in complex tissue samples with heterogeneous cell-type composition.

Single-cell protein analysis by mass spectrometry

Human physiology and pathology arise from the coordinated interactions of diverse single cells. However, analyzing single cells has been limited by the low sensitivity and throughput of analytical methods. DNA sequencing has recently made such analysis feasible for nucleic acids but single-cell protein analysis remains limited. Mass spectrometry is the most powerful method for protein analysis, but its application to single cells faces three major challenges: efficiently delivering proteins/peptides to mass spectrometry detectors, identifying their sequences, and scaling the analysis to many thousands of single cells. These challenges have motivated corresponding solutions, including SCoPE design multiplexing and clean, automated, and miniaturized sample preparation. Synergistically applied, these solutions enable quantifying thousands of proteins across many single cells and establish a solid foundation for further advances. Building upon this foundation, the SCoPE concept will enable analyzing subcellular organelles and posttranslational modifications, while increases in multiplexing capabilities will increase the throughput and decrease cost.

Single-Probe Mass Spectrometry Analysis of Metabolites in Single Cells

Mass spectrometry (MS) is an indispensable analytical technique for bioanalysis. Based on the measurement of mass/charge ratios (m/z) of ions, MS can be used for sensitive detection and accurate identification of species of interest. In traditional studies, MS is utilized to measure analytes in prepared solutions or gas-phase samples. Benefited from recent development of sampling and ionization approaches, MS has been extensively applied to the analysis of broad ranges of biological samples. We have developed a new device, the Single-probe, that can be used for in situ, real-time MS analysis of metabolites inside individual living cells. The Single-probe is a miniaturized multifunctional sampling and ionization device that is directly coupled to the mass spectrometer. With a sampling tip size smaller than 10 μm, we can insert the Single-probe tip into single cells to extract intracellular compounds, which are analyzed using MS in real-time. We have successfully used the Single-probe MS technique to detect a variety of endogenous and exogenous cellular metabolites in individual eukaryotic cells. Single cell mass spectrometry (SCMS) is a new scientific technology that has the potential to reshape approaches in biological and pharmaceutical bioanalytical research.

Quantification of Drug Molecules in Live Single Cells Using the Single-Probe Mass Spectrometry Technique

Analyzing cellular constituents on the single-cell level through mass spectrometry (MS) allows for a wide range of compounds to be studied simultaneously. However, there is a need for quantitative single-cell mass spectrometry (qSCMS) methods to fully characterize drug efficacy from individual cells within cell populations. In this study, qSCMS experiments were carried out using the Single-probe MS technique. The method was successfully used to perform rapid absolute quantifications of the anticancer drug irinotecan in individual mammalian cancer cells under ambient conditions in real time. Traditional liquid chromatography/mass spectrometry (LC/MS) quantifications of irinotecan in cell lysate samples were used to compare the results from Single-probe qSCMS. This technique showcases heterogeneity of drug efficacy on the single-cell level.

Exploring the Fundamental Structures of Life: Non-Targeted, Chemical Analysis of Single Cells and Subcellular Structures

Cells are a basic functional and structural unit of living organisms. Both unicellular communities and multicellular species produce an astonishing chemical diversity, enabling a wide range of divergent functions, yet each cell shares numerous aspects that are common to all living organisms. While there are many approaches for studying this chemical diversity, only a few are non-targeted and capable of analyzing hundreds of different chemicals at cellular resolution. Here, we review the non-targeted approaches used to perform comprehensive chemical analyses, provide chemical imaging information, or obtain high-throughput single-cell profiling data. Single-cell measurement capabilities are rapidly increasing in terms of throughput, limits of detection, and completeness of the chemical analyses; these improvements enable their application to understand ever more complex physiological phenomena, such as learning, memory, and behavior.

Lipid Analysis of 30 000 Individual Rodent Cerebellar Cells Using High-Resolution Mass Spectrometry

Single-cell measurements aid our understanding of chemically heterogeneous systems such as the brain. Lipids are one of the least studied chemical classes, and their cell-to-cell heterogeneity remains largely unexplored. We adapted microscopy-guided single-cell profiling using matrix-assisted laser desorption/ionization ion cyclotron resonance mass spectrometry to profile the lipid composition of over 30 000 individual rat cerebellar cells. We detected 520 lipid features, many of which were found in subsets of cells; Louvain clustering identified 101 distinct groups that can be correlated to neuronal and astrocytic classifications and lipid classes. Overall, the two most common lipids found were [PC(32:0)+H]⁺ and [PC(34:1)+H]⁺, which were present within 98.9 and 89.5% of cells, respectively; lipid signals present in <1% of cells were also detected, including [PC(34:1)+K]⁺ and [PG(40:2(OH))+Na]⁺. These results illustrate the vast lipid heterogeneity found within rodent cerebellar cells and hint at the distinct functional consequences of this heterogeneity.

Genetically Encoded Fluorescent Proteins Enable High-Throughput Assignment of Cell Cohorts Directly from MALDI-MS Images

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) provides a unique in situ chemical profile that can include drugs, nucleic acids, metabolites, lipids, and proteins. MSI of individual cells (of a known cell type) affords a unique insight into normal and disease-related processes and is a prerequisite for combining the results of MSI and other single-cell modalities (e.g. mass cytometry and next-generation sequencing). Technological barriers have prevented the high-throughput assignment of MSI spectra from solid tissue preparations to their cell type. These barriers include obtaining a suitable cell-identifying image (e.g. immunohistochemistry) and obtaining sufficiently accurate registration of the cell-identifying and MALDI-MS images. This study introduces a technique that overcame these barriers by assigning cell type directly from mass spectra. We hypothesized that, in MSI from mice with a defined fluorescent protein expression pattern, the fluorescent protein's molecular ion could be used to identify cell cohorts. A method was developed for the purification of enhanced yellow fluorescent protein (EYFP) from mice. To determine EYFP's molecular mass for MSI studies, we performed intact mass analysis and characterized the protein's primary structure and post-translational modifications through various techniques. MALDI-MSI methods were developed to enhance the detection of EYFP in situ, and by extraction of EYFP's molecular ion from MALDI-MS images, automated, whole-image assignment of cell cohorts was achieved. This method was validated using a well-characterized mouse line that expresses EYFP in motor and sensory neurons and should be applicable to hundreds of commercially available mice (and other animal) strains comprising a multitude of cell-specific fluorescent labels.

Mass Spectrometry Measurement of Single Suspended Cells Using a Combined Cell Manipulation System and a Single-Probe Device

Existing single cell mass spectrometry (SCMS) sampling platforms are largely designed to work only with immobilized cells and not the suspended cells isolated from patient samples. Here, we present a novel method that integrates a commercially available cell manipulation system commonly used for in vitro fertilization with the Single-probe SCMS sampling technology. The combined Single-probe SCMS/cell manipulating platform is capable of rapidly analyzing intracellular species in real time from a suspension leukemia cell line. A broad range of molecular species was detected, and species of interest were verified using tandem MS (MS/MS). Experimental results were analyzed utilizing statistical analyses such as principle component analysis (PCA) and  t-tests. The developed SCMS/cell manipulation system is a versatile tool to provide rapid single cell analysis of broad types of patient cell samples.

Quantitative imaging of lipid droplets in single cells

The combination of next generation sequencing (NGS) and automated liquid handling platforms has led to a revolution in single-cell genomic studies. However, many molecules that are critical to understanding the functional roles of cells in a complex tissue or organs, are not directly encoded in the genome, and therefore cannot be profiled with NGS. Lipids, for example, play a critical role in many metabolic processes but cannot be detected by sequencing. Recent developments in quantitative imaging, particularly coherent Raman scattering (CRS) techniques, have produced a suite of tools for studying lipid content in single cells. This article reviews CRS imaging and computational image processing techniques for non-destructive profiling of dynamic changes in lipid composition and spatial distribution at the single-cell level. As quantitative CRS imaging progresses synergistically with microfluidic and microscopic platforms for single-cell genomic analysis, we anticipate that these techniques will bring researchers closer towards combined lipidomic and genomic analysis.

Why geneticists stole cancer research even though cancer is primarily a signaling disease

Genetic approaches to cancer research have dramatically advanced our understanding of the pathophysiology of this disease, leading to similar genetics-based approaches for precision therapy, which have been less successful. Reconfiguring and adapting the types of technologies that underlie genetic research to dissect tumor cell signaling in clinical samples may offer an alternative road forward.

Functional Genomics via CRISPR-Cas

RNA-guided CRISPR (clustered regularly interspaced short palindromic repeat)-associated Cas proteins have recently emerged as versatile tools to investigate and engineer the genome. The programmability of CRISPR-Cas has proven especially useful for probing genomic function in high-throughput. Facile single-guide RNA library synthesis allows CRISPR-Cas screening to rapidly investigate the functional consequences of genomic, transcriptomic, and epigenomic perturbations. Furthermore, by combining CRISPR-Cas perturbations with downstream single-cell analyses (flow cytometry, expression profiling, etc.), forward screens can generate robust data sets linking genotypes to complex cellular phenotypes. In the following review, we highlight recent advances in CRISPR-Cas genomic screening while outlining protocols and pitfalls associated with screen implementation. Finally, we describe current challenges limiting the utility of CRISPR-Cas screening as well as future research needed to resolve these impediments. As CRISPR-Cas technologies develop, so too will their clinical applications. Looking ahead, patient centric functional screening in primary cells will likely play a greater role in disease management and therapeutic development.

Mapping the dark space of chemical reactions with extended nanomole synthesis and MALDI-TOF MS

Understanding the practical limitations of chemical reactions is critically important for efficiently planning the synthesis of compounds in pharmaceutical, agrochemical, and specialty chemical research and development. However, literature reports of the scope of new reactions are often cursory and biased toward successful results, severely limiting the ability to predict reaction outcomes for untested substrates. We herein illustrate strategies for carrying out large-scale surveys of chemical reactivity by using a material-sparing nanomole-scale automated synthesis platform with greatly expanded synthetic scope combined with ultrahigh-throughput matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS).

Mass spectrometry in pathology - Vision for a future workflow

Mass spectrometric (MS) techniques are applied in various areas of medical diagnostics. For the detection of microbiological germs and genetic mutations, MS is a method used in routine. Since MS also allows the analysis of proteins and peptides, it seems an ideal candidate to supplement histopatholological diagnostics. Matrix-assisted laser desorption/ionization time-of-flight Imaging MS links molecular analysis of numerous analytes with morphological information about their spatial distribution in cells or tissues. Herein, we review principle MS techniques as well as potential applications in pathology and discuss our vision for a future workflow.

New techniques, applications and perspectives in neuropeptide research

Neuropeptides are one of the most diverse classes of signaling molecules and have attracted great interest over the years owing to their roles in regulation of a wide range of physiological processes. However, there are unique challenges associated with neuropeptide studies stemming from the highly variable molecular sizes of the peptides, low in vivo concentrations, high degree of structural diversity and large number of isoforms. As a result, much effort has been focused on developing new techniques for studying neuropeptides, as well as novel applications directed towards learning more about these endogenous peptides. The areas of importance for neuropeptide studies include structure, localization within tissues, interaction with their receptors, including ion channels, and physiological function. Here, we discuss these aspects and the associated techniques, focusing on technologies that have demonstrated potential in advancing the field in recent years. Most identification and structural information has been gained by mass spectrometry, either alone or with confirmations from other techniques, such as nuclear magnetic resonance spectroscopy and other spectroscopic tools. While mass spectrometry and bioinformatic tools have proven to be the most powerful for large-scale analyses, they still rely heavily on complementary methods for confirmation. Localization within tissues, for example, can be probed by mass spectrometry imaging, immunohistochemistry and radioimmunoassays. Functional information has been gained primarily from behavioral studies coupled with tissue-specific assays, electrophysiology, mass spectrometry and optogenetic tools. Concerning the receptors for neuropeptides, the discovery of ion channels that are directly gated by neuropeptides opens up the possibility of developing a new generation of tools for neuroscience, which could be used to monitor neuropeptide release or to specifically change the membrane potential of neurons. It is expected that future neuropeptide research will involve the integration of complementary bioanalytical technologies and functional assays.

Metabolic Comparison of Dorsal versus Ventral Cells Directly in the Live 8-cell Frog Embryo by Microprobe Single-cell CE-ESI-MS

Single-cell mass spectrometry (MS) empowers the characterization of metabolomic changes as cells differentiate to different tissues during early embryogenesis. Using whole-cell dissection and capillary electrophoresis electrospray ionization (CE-ESI) MS, we recently uncovered metabolic cell-to-cell differences in the 8- and 16-cell embryo of the South African clawed frog (Xenopus laevis), raising the question whether metabolic cell heterogeneity is also detectable across the dorsal-ventral axis of the 8-cell embryo. Here, we tested this hypothesis directly in the live embryo by quantifying single-cell metabolism between the left dorsal-animal (D1L) and left ventral-animal (V1L) cell pairs in the same embryo using microprobe single-cell CE-ESI-MS in the positive ion mode. After quantifying ~70 molecular features, including 52 identified metabolites, that were reproducibly detected in both cells among n = 5 different embryos, we employed supervised multivariate data analysis based on partial least squares discriminant analysis (PLSDA) to compare metabolism between the cell types. Statistical analysis revealed that asparagine, glycine betaine, and a yet-unidentified molecule were statistically significantly enriched in the D1L cell compared to V1L (p < 0.05 and fold change ≥ 1.5). These results demonstrate that cells derived from the same hemisphere (animal pole) harbor different metabolic activity along the dorsal-ventral axis as early as the 8-cell stage. Apart from providing new evidence of metabolic cell heterogeneity during early embryogenesis, this study demonstrates that microprobe single-cell CE-ESI-MS enables the analysis of multiple single cells in the same live vertebrate embryo.

Label-free molecular imaging of the kidney

In this review, we will highlight technologies that enable scientists to study the molecular characteristics of tissues and/or cells without the need for antibodies or other labeling techniques. Specifically, we will focus on matrix-assisted laser desorption/ionization imaging mass spectrometry, infrared spectroscopy, and Raman spectroscopy.

Imaging mass spectrometry identifies prognostic ganglioside species in rodent intracranial transplants of glioma and medulloblastoma

Matrix-assisted laser desorption ionization (MALDI) imaging mass spectrometry (MALDI-MSI) allows us to investigate the distribution of lipid molecules within tissues. We used MALDI-MSI to identify prognostic gangliosides in tissue sections of rat intracranial allografts of rat glioma and mouse intracranial xenografts of human medulloblastoma. In the healthy adult rodent brain, GM1 and GD1 were the main types of glycolipids. Both gangliosides were absent in both intracranial transplants. The ganglioside GM3 was not present in the healthy adult brain but was highly expressed in rat glioma allografts. In combination with tandem mass spectrometry GM3 (d18:1/C24:0) was identified as the most abundant ganglioside species in the glioma allotransplant. By contrast, mouse xenografts of human medulloblastoma were characterized by prominent expression of the ganglioside GM2 (d18:0/C18:0). Together, these data demonstrate that tissue-based MALDI-MSI of gangliosides is able to discriminate between different brain tumors and may be a useful clinical tool for their classification and grading.

Segmented flow sampling with push-pull theta pipettes

We report development of a mobile and easy-to-fabricate theta pipette microfluidic device for segmented flow sampling. The theta pipettes were also used as electrospray emitters for analysis of sub-nanoliter segments, which resulted in delivery of analyte to the vacuum inlet of the mass spectrometer without multiple transfer steps. Theta pipette probes enable sample collection with high spatial resolution due to micron or smaller sized probe inlets and can be used to manipulate aqueous segments in the range of 200 pL to tens of nanoliters. Optimized conditions can enable sampling with high spatial and temporal resolution, suitable for chemical monitoring in biological samples and studies of sample heterogeneity. Intercellular heterogeneity among Allium cepa cells was studied by collecting cytoplasm from multiple cells using a single probe. Extracted cytoplasm was analyzed in a fast and high throughput manner by direct electrospray mass spectrometry of segmented sample from the probe tip.

More than Pictures: When MS Imaging Meets Histology

Attaining high-resolution spatial information is a recurrent challenge in biological research, particularly in the case of small-molecule distribution. Mass spectrometry imaging (MSI) is an innovative molecular histology technique that could provide such information. It allows in situ and label-free measurement of both the abundance and distribution of a variety of molecules at the tissue or single cell level. The application of MSI in plant research has received considerable attention; thus, in this review, we describe the current state of MSI in plants. In particular, we present an overview of MSI approaches, highlight the recent technical and methodological developments, and discuss a range of applications contributing to the field of plant science.

Using Dicationic Ion-Pairing Compounds To Enhance the Single Cell Mass Spectrometry Analysis Using the Single-Probe: A Microscale Sampling and Ionization Device

A unique mass spectrometry (MS) method has been developed to determine the negatively charged species in live single cells using the positive ionization mode. The method utilizes dicationic ion-pairing compounds through the miniaturized multifunctional device, the single-probe, for reactive MS analysis of live single cells under ambient conditions. In this study, two dicationic reagents, 1,5-pentanediyl-bis(1-butylpyrrolidinium) difluoride (C5(bpyr)2F2) and 1,3-propanediyl-bis(tripropylphosphonium) difluoride (C3(triprp)2F2), were added in the solvent and introduced into single cells to extract cellular contents for real-time MS analysis. The negatively charged (1- charged) cell metabolites, which form stable ion-pairs (1+ charged) with dicationic compounds (2+ charged), were detected in positive ionization mode with a greatly improved sensitivity. We have tentatively assigned 192 and 70 negatively charged common metabolites as adducts with (C5(bpyr)2F2) and (C3(triprp)2F2), respectively, in three separate SCMS experiments in the positive ion mode. The total number of tentatively assigned metabolites is 285 for C5(bpyr)2F2 and 143 for C3(triprp)2F2. In addition, the selectivity of dicationic compounds in the complex formation allows for the discrimination of overlapped ion peaks with low abundances. Tandem (MS/MS) analyses at the single cell level were conducted for selected adduct ions for molecular identification. The utilization of the dicationic compounds in the single-probe MS technique provides an effective approach to the detection of a broad range of metabolites at the single cell level.

Mass Spectrometry in Plant-omics

Plant-omics is rapidly becoming an important field of study in the scientific community due to the urgent need to address many of the most important questions facing humanity today with regard to agriculture, medicine, biofuels, environmental decontamination, ecological sustainability, etc. High-performance mass spectrometry is a dominant tool for interrogating the metabolomes, peptidomes, and proteomes of a diversity of plant species under various conditions, revealing key insights into the functions and mechanisms of plant biochemistry.

Nanomanipulation-Coupled Matrix-Assisted Laser Desorption/ Ionization-Direct Organelle Mass Spectrometry: A Technique for the Detailed Analysis of Single Organelles

We describe a novel technique combining precise organelle microextraction with deposition and matrix-assisted laser desorption/ionization (MALDI) for a rapid, minimally invasive mass spectrometry (MS) analysis of single organelles from living cells. A dual-positioner nanomanipulator workstation was utilized for both extraction of organelle content and precise co-deposition of analyte and matrix solution for MALDI-direct organelle mass spectrometry (DOMS) analysis. Here, the triacylglycerol (TAG) profiles of single lipid droplets from 3T3-L1 adipocytes were acquired and results validated with nanoelectrospray ionization (NSI) MS. The results demonstrate the utility of the MALDI-DOMS technique as it enabled longer mass analysis time, higher ionization efficiency, MS imaging of the co-deposited spot, and subsequent MS/MS capabilities of localized lipid content in comparison to NSI-DOMS. This method provides selective organellar resolution, which complements current biochemical analyses and prompts for subsequent subcellular studies to be performed where limited samples and analyte volume are of concern. Graphical Abstract ᅟ.

Surface-enhanced laser desorption ionization time-of-flight mass spectrometry used to screen serum diagnostic markers of colon cancer recurrence in situ following surgery

The aim of the present study was to identify specific serum biomarkers in patients with colon cancer recurrence in situ following surgery. The study was conducted at the Renmin Hospital of Wuhan University (Wuhan, China) between January 2012 and January 2014. Surface-enhanced laser desorption ionization time-of-flight mass spectrometry was used to compare and analyze the serum protein profiles of patients with (n=50) and patients without (n=50) recurrence in situ. Biomarker Wizard software was used to analyze and obtain the protein spectrum. In total, nine protein peaks demonstrated statistically significant differences between the recurrence and non-recurrence group (P<0.05), which included two protein peaks (7,731.3 Da and 8,266.5 Da). The two protein peaks were highly expressed in patients with colon cancer recurrence in situ following surgery, but lowly expressed in patients without recurrence. Therefore, the two protein peaks may represent potential biomarkers for the prediction of colon cancer recurrence in situ following surgical treatment.

Proteome-wide characterization of signalling interactions in the hippocampal CA4/DG subfield of patients with Alzheimer's disease

Alzheimer’s disease (AD) is the most common form of dementia; however, mechanisms and biomarkers remain unclear. Here, we examined hippocampal CA4 and dentate gyrus subfields, which are less studied in the context of AD pathology, in post-mortem AD and control tissue to identify possible biomarkers. We performed mass spectrometry-based proteomic analysis combined with label-free quantification for identification of differentially expressed proteins. We identified 4,328 proteins, of which 113 showed more than 2-fold higher or lower expression in AD hippocampi than in control tissues. Five proteins were identified as putative AD biomarkers (MDH2, PCLO, TRRAP, YWHAZ, and MUC19 isoform 5) and were cross-validated by immunoblotting, selected reaction monitoring, and MALDI imaging. We also used a bioinformatics approach to examine upstream signalling interactions of the 113 regulated proteins. Five upstream signalling (IGF1, BDNF, ZAP70, MYC, and cyclosporin A) factors showed novel interactions in AD hippocampi. Taken together, these results demonstrate a novel platform that may provide new strategies for the early detection of AD and thus its diagnosis.

Membrane electrospray ionization for direct ultrasensitive biomarker quantitation in biofluids using mass spectrometry

The ability of rapid biomarker quantitation in raw biological samples would expand the application of mass spectrometry in clinical diagnosis. Up until now, the conventional chromatography-mass spectrometry method is time-consuming in both sample preparation and chromatography separation processes, while ambient ionization methods normally suffer from sensitivity. The membrane electrospray ionization (MESI) introduced in this study could not only achieve sensitive biomolecule quantitation, but also minimize the sample handling process. As a unique feature of MESI, both vertical and horizontal chemical separations could be achieved in real-time. With the capability of mass-selectively minimizing matrix effects from salts, small molecules, and macromolecules, ultrasensitive detection of cytochrome C (>500-fold sensitivity improvement) in raw urine samples was demonstrated in less than 20 min.

Biomarker Characterization by MALDI-TOF/MS

Mass spectrometric techniques frequently used in clinical diagnosis, such as gas chromatography-mass spectrometry, liquid chromatography-mass spectrometry, ambient ionization mass spectrometry, and matrix-assisted laser desorption ionization/time-of-flight mass spectrometry (MALDI-TOF/MS), are discussed. Due to its ability to rapidly detect large biomolecules in trace amounts, MALDI-TOF/MS is an ideal tool for characterizing disease biomarkers in biologic samples. Clinical applications of MS for the identification and characterization of microorganisms, DNA fragments, tissues, and biofluids are introduced. Approaches for using MALDI-TOF/MS to detect various disease biomarkers including peptides, proteins, and lipids in biological fluids are further discussed. Finally, various sample pretreatment methods which improve the detection efficiency of disease biomarkers are introduced.