Proteome Imaging: From Classic to Modern Mass Spectrometry-Based Molecular Histology

Applications of tandem mass spectrometry (MS/MS) in antimicrobial peptides field: Current state and new applications

Antimicrobial peptides (AMPs) constitute a group of small molecular peptides that exhibit a wide range of antimicrobial activity. These peptides are abundantly present in the innate immune system of various organisms. Given the rise of multidrug-resistant bacteria, microbiological studies have identified AMPs as potential natural antibiotics. In the context of antimicrobial resistance across various human pathogens, AMPs hold considerable promise for clinical applications. However, numerous challenges exist in the detection of AMPs, particularly by immunological and molecular biological methods, especially when studying of newly discovered AMPs in proteomics. This review outlines the current status of AMPs research and the strategies employed in their development, considering resent discoveries and methodologies. Subsequently, we focus on the advanced techniques of mass spectrometry for the quantification of AMPs in diverse samples, and analyzes their application, advantages, and limitations. Additionally, we propose suggestions for the future development of tandem mass spectrometry for the detection of AMPs.

Investigation on property differences of ginseng and American ginseng by spatial metabolomics of neurochemicals with desorption electrospray ionization mass spectrometry imaging

ETHNOPHARMACOLOGICAL RELEVANCE

The properties are the body's response to traditional Chinese medicine (TCM). The essence of traditional Chinese medicine properties are cold, hot, warm, and cool. In the theory of traditional Chinese medicine, ginseng is warm and American ginseng is cool, they present two opposite properties. The material basis of property differences and effect mechanism of property degree need further investigation.

AIM OF THE STUDY

The aim of this work was to screen out the neurochemicals related to warm and cool properties of ginseng and American ginseng, and investigate the distributions of identified neurochemicals in rat brain and the metabolic mechanism.

MATERIALS AND METHODS

Spatial metabolomics was applied to study the effects of ginseng and American ginseng on the distributions of neurochemicals in rat brain by desorption electrospray ionization mass spectrometry imaging (DESI-MSI). Based on discriminant coefficients in partial least square discriminant analysis (PLS-DA) processing, neurochemicals related to warm and cool properties were classified. In addition, the score contributions of the neurochemicals markers could be used to evaluate the warm and cool property degrees.

RESULTS

A total of 25 neurochemicals were imaged and identified in brain section. The distribution regions of main neurochemicals were consistent with in sagittal and coronal sections of brain reported in literature. 17 neurochemicals were classified as warm markers. Meanwhile, 8 neurochemicals were identified as cool markers, correlated with the cool properties of American ginseng. It demonstrated that the score contributions of the 25 neurochemicals markers could be used to evaluate the warm and cool property degrees. Based on the regulatory effects of neurochemicals, the warm markers could promote the body's energy metabolism, improve the function of endocrine system, and enhance the excitability of central nervous system. The cool property markers have reduced excitability of central nervous system, weakened metabolism and stress response ability, thus presented the biological activity of cool and cold.

CONCLUSIONS

Our findings provided a rapid and effective visualization method for the spatial distribution and metabolism of small molecular neurochemicals in rat brain. DESI-MSI was a reference methodology for evaluating the properties of TCM.

Key defatting tissue pretreatment protocol for enhanced MALDI MS Imaging of peptide biomarkers visualization in the castor beans and their attribution applications

INTRODUCTION

Castor bean or ricin-induced intoxication or terror events have threatened public security and social safety. Potential resources or materials include beans, raw extraction products, crude toxins, and purified ricin. The traceability of the origins of castor beans is thus essential for forensic and anti-terror investigations. As a new imaging technique with label-free, rapid, and high throughput features, matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) has been gradually stressed in plant research. However, sample preparation approaches for plant tissues still face severe challenges, especially for some lipid-rich, water-rich, or fragile tissues. Proper tissue washing procedures would be pivotal, but little information is known until now.

METHODS

For castor beans containing plenty of lipids that were fragile when handled, we developed a comprehensive tissue pretreatment protocol. Eight washing procedures aimed at removing lipids were discussed in detail. We then constructed a robust MALDI-MSI method to enhance the detection sensitivity of RCBs in castor beans.

RESULTS AND DISCUSSION

A modified six-step washing procedure was chosen as the most critical parameter regarding the MSI visualization of peptides. The method was further applied to visualize and quantify the defense peptides, Ricinus communis biomarkers (RCBs) in castor bean tissue sections from nine different geographic sources from China, Pakistan, and Ethiopia. Multivariate statistical models, including deep learning network, revealed a valuable classification clue concerning nationality and altitude.

Three-dimensional imaging and reconstruction of the whole ovary and testis: a new frontier for the reproductive scientist

The 3D functional reconstruction of a whole organ or organism down to the single cell level and to the subcellular components and molecules is a major future scientific challenge. The recent convergence of advanced imaging techniques with an impressively increased computing power allowed early attempts to translate and combine 2D images and functional data to obtain in-silico organ 3D models. This review first describes the experimental pipeline required for organ 3D reconstruction: from the collection of 2D serial images obtained with light, confocal, light-sheet microscopy or tomography, followed by their registration, segmentation and subsequent 3D rendering. Then, we summarise the results of investigations performed so far by applying these 3D image analyses to the study of the female and male mammalian gonads. These studies highlight the importance of working towards a 3D in-silico model of the ovary and testis as a tool to gain insights into their biology during the phases of differentiation or adulthood, in normal or pathological conditions. Furthermore, the use of 3D imaging approaches opens to key technical improvements, ranging from image acquisition to optimisation and development of new processing tools, and unfolds novel possibilities for multidisciplinary research.

MALDI-MSI-A Step Forward in Overcoming the Diagnostic Challenges in Ovarian Tumors

This study presents the use of matrix-assisted laser desorption and ionization mass spectrometry imaging (MALDI-MSI) directly on the tissue of two ovarian tumors that often present a diagnostic challenge, a low-grade serous borderline ovarian tumor and ovarian fibrothecoma. Different spatial distribution of m/z values within the tissue samples was observed, and regiospecific peaks were identified. Among the 106 peaks in the borderline ovarian tumor five, regiospecific peaks (m/z: 2861.35; 2775.79; 3368.34; 3438.43; 4936.37) were selected using FlexImaging software. Subsequently, the distribution of those selected peaks was visualized on the fibrothecoma tissue section, which demonstrated the differences in the tissue homo-/heterogeneous structure of both tumors. The comparison with the histopathological staining of the ovarian borderline tumor tissue section, obtained during serial sectioning, showed a close correlation of the molecular map with the morphological and histopathological features of the tissue and allowed the identification of different tissue types within the sample. This study highlights the potential significance of MSI in enabling morphological characterization of ovarian tumors as well as correct diagnosis and further prognosis than thus far seen in the literature. Osteopontin, tropomyosin and orosomucoid are only a couple of the molecules investigated using MALDI-MSI in ovarian cancer research. This study, in line with the available literature, proves the potential of MALDI-MSI to overcome the current limitations of classic histopathological examination giving a more in-depth insight into the tissue structure and thus lead to the more accurate differential diagnosis of ovarian tumors, especially in the most challenging cases.

Mass Spectrometry Analysis of Intact Proteins from Crude Samples

Analysis of intact proteins by native mass spectrometry has emerged as a powerful tool for obtaining insight into subunit diversity, post-translational modifications, stoichiometry, structural arrangement, stability, and overall architecture. Typically, such an analysis is performed following protein purification procedures, which are time consuming, costly, and labor intensive. As this technology continues to move forward, advances in sample handling and instrumentation have enabled the investigation of intact proteins in situ and in crude samples, offering rapid analysis and improved conservation of the biological context. This emerging field, which involves various ion source platforms such as matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) for both spatial imaging and solution-based analysis, is expected to impact many scientific fields, including biotechnology, pharmaceuticals, and clinical sciences. In this Perspective, we discuss the information that can be retrieved by such experiments as well as the current advantages and technical challenges associated with the different sampling strategies. Furthermore, we present future directions of these MS-based methods, including current limitations and efforts that should be made to make these approaches more accessible. Considering the vast progress we have witnessed in recent years, we anticipate that the advent of further innovations enabling minimal handling of MS samples will make this field more robust, user friendly, and widespread.