Understanding zwitterionic ring-expansion polymerization through mass spectrometry.

Zwitterionic ring-expansion polymerization (ZREP) is a polymerization method in which a cyclic monomer is converted into a cyclic polymer through a zwitterionic intermediate. In this review, we explored the ZREP of various cyclic polymers and how mass spectrometry assists in identifying the product architectures and understanding their intricate reaction mechanism. For the majority of polymers (from a few thousand to a few million Da) matrix-assisted laser desorption/ionization time-of-flight mass spectrometry is the most effective mass spectrometry technique to determine the true molecular weight (MW) of the resultant product, but only when the dispersity is low (approximately below 1.2). The key topics covered in this study were the ZREP of cyclic polyesters, cyclic polyamides, and cyclic ethers. In addition, this study also addresses a number of other preliminary topics, including the ZREP of cyclic polycarbonates, cyclic polysiloxanes, and cyclic poly(alkylene phosphates). The purity and efficiency of those syntheses largely depend on the catalyst. Among several catalysts, N-heterocyclic carbenes have exhibited high efficiency in the synthesis of cyclic polyesters and polyamides, whereas tris(pentafluorophenyl)borane [B(C6F5)3] is the most optimal catalyst for cyclic polyether synthesis.

Integrated mass spectrometry imaging and single-cell transcriptome atlas strategies provide novel insights into taxoid biosynthesis and transport in Taxus mairei stems.

Taxol, which is a widely used important chemotherapeutic agent, was originally isolated from Taxus stem barks. However, little is known about the precise distribution of taxoids and the transcriptional regulation of taxoid biosynthesis across Taxus stems. Here, we used MALDI-IMS analysis to visualize the taxoid distribution across Taxus mairei stems and single-cell RNA sequencing to generate expression profiles. A single-cell T. mairei stem atlas was created, providing a spatial distribution pattern of Taxus stem cells. Cells were reordered using a main developmental pseudotime trajectory which provided temporal distribution patterns in Taxus stem cells. Most known taxol biosynthesis-related genes were primarily expressed in epidermal, endodermal, and xylem parenchyma cells, which caused an uneven taxoid distribution across T. mairei stems. We developed a single-cell strategy to screen novel transcription factors (TFs) involved in taxol biosynthesis regulation. Several TF genes, such as endodermal cell-specific MYB47 and xylem parenchyma cell-specific NAC2 and bHLH68, were implicated as potential regulators of taxol biosynthesis. Furthermore, an ATP-binding cassette family transporter gene, ABCG2, was proposed as a potential taxoid transporter candidate. In summary, we generated a single-cell Taxus stem metabolic atlas and identified molecular mechanisms underpinning the cell-specific transcriptional regulation of the taxol biosynthesis pathway.

Collisional experiences with Dr. Pietro Traldi and the incredible group in Padova.

Two Early Classic period (ca. 250-600 CE) Maya carved, greenstone jade pendants, Specimens A and B, were recovered from the Pacbitun site in Belize in 1987. The specimens were visually similar and may have been cut from a common jade piece. Mass spectrometry was considered as a technique that could possibly be used to explore the similarity of the specimens. However, at that time, neither electrospray ionization nor matrix-assisted laser desorption/ionization (MALDI) had been discovered; furthermore, only elemental analysis had been carried out with jade samples and there were no accounts of polyatomic ions being produced from jade. The discoverer of the greenstone jade pendants, a faculty member in Anthropology at Trent University, sought the assistance of the author of this piece but no immediate progress was accomplished. About 7 years after discovery of the greenstone jade pendants, this author was invited to spend a short sabbatical leave in the laboratory of Dr. Pietro Traldi in Padova, Italy. While this invitation was attractive for several reasons, the principal attraction was Dr. Traldi's new, and mysterious acquisition of MALDI instrumentation. There was, perhaps, a single iota of reason that appeared to suggest unusual assistance of a matrix in liberating polyatomic ions from jade using laser irradiation. This account is of a very interesting sojourn with Dr. Traldi and members of his laboratory which did not lead to any immediate understanding of MALDI; however, the belief was constant for the next 20 years after which some progress was made in the exploration of the structure of jade.

Correlation between small-cell lung cancer serum protein/peptides determined by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and chemotherapy efficacy.

BACKGROUND: Currently, no effective measures are available to predict the curative efficacy of small-cell lung cancer (SCLC) chemotherapy. We expect to develop a method for effectively predicting the SCLC chemotherapy efficacy and prognosis in clinical practice in order to offer more pertinent therapeutic protocols for individual patients. METHODS: We adopted matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and ClinPro Tools system to detect serum samples from 154 SCLC patients with different curative efficacy of standard chemotherapy and analyze the different peptides/proteins of SCLC patients to discover predictive tumor markers related to chemotherapy efficacy. Ten peptide/protein peaks were significantly different in the two groups. RESULTS: A genetic algorithm model consisting of four peptides/proteins was developed from the training group to separate patients with different chemotherapy efficacies. Among them, three peptides/proteins (m/z 3323.35, 6649.03 and 6451.08) showed high expression in the disease progression group, whereas the peptide/protein at m/z 4283.18 was highly expressed in the disease response group. The classifier exhibited an accuracy of 91.4% (53/58) in the validation group. The survival analysis showed that the median progression-free survival (PFS) of 30 SCLC patients in disease response group was 9.0 months; in 28 cases in disease progression group, the median PFS was 3.0 months, a statistically significant difference (χ2 = 46.98, P < 0.001). The median overall survival (OS) of the two groups was 13.0 months and 7.0 months, a statistically significant difference (χ2 = 40.64, P < 0.001). CONCLUSIONS: These peptides/proteins may be used as potential biological markers for prediction of the curative efficacy and prognosis for SCLC patients treated with standard regimen chemotherapy.

Imaging plant metabolism in situ.

Mass spectrometry imaging (MSI) has emerged as an invaluable analytical technique for investigating the spatial distribution of molecules within biological systems. In the realm of plant science, MSI is increasingly employed to explore metabolic processes across a wide array of plant tissues, including those in leaves, fruits, stems, roots, and seeds, spanning various plant systems such as model species, staple and energy crops, and medicinal plants. By generating spatial maps of metabolites, MSI has elucidated the distribution patterns of diverse metabolites and phytochemicals, encompassing lipids, carbohydrates, amino acids, organic acids, phenolics, terpenes, alkaloids, vitamins, pigments, and others, thereby providing insights into their metabolic pathways and functional roles. In this review, we present recent MSI studies that demonstrate the advances made in visualizing the plant spatial metabolome. Moreover, we emphasize the technical progress that enhances the identification and interpretation of spatial metabolite maps. Within a mere decade since the inception of plant MSI studies, this robust technology is poised to continue as a vital tool for tackling complex challenges in plant metabolism.

Pipette-tip solid-phase extraction coupled with matrix-assisted laser desorption/ionization mass spectrometry enables rapid and high-throughput analysis of antidepressants in rat serum.

Therapeutic drug monitoring is essential for ensuring the efficacy and safety of medications. This study introduces a streamlined approach that combines pipette-tip solid-phase extraction (PT-SPE) with matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), facilitating rapid and high-throughput monitoring of drug concentrations. As a demonstration, this method was applied to the extraction and quantification of antidepressants in serum. Utilizing Zip-Tip C18, the method enabled the extraction of antidepressants from complex biological matrices in less than 2 min, with the subsequent MALDI-MS analysis yielding results in just 1 min. Optimal extraction recoveries were achieved using a sampling solution at pH 9.0 and a 10 µL ethanol desorption solution containing 0.1% phosphoric acid. For MALDI analysis, 2,5-dihydroxybenzoic acid was identified as the most effective matrix for producing the highest signal intensity. The quantification strategy exhibited robust linearities (R2 ≥ 0.997) and satisfactory limits of quantification, ranging from 0.05 to 0.5 µg/mL for a suite of antidepressants. The application for monitoring dynamic concentration changes of antidepressants in rat serum emphasized the method's efficacy. This strategy offers the advantages of high throughput, minimal sample usage, environmental sustainability, and simplicity, providing ideas and a reference basis for the subsequent development of methods for therapeutic drug monitoring.

Matrix- and surface-assisted laser desorption/ionization-mass spectrometry analysis of fingermark components for forensic studies: current trends and future prospects.

The chemical analysis of fingermarks (FMs) has attracted considerable attention in the realm of forensic investigations. Techniques based on direct ionization of a sample by laser irradiation, specifically matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS), have provided excellent figures of merit for analyzing high molecular-weight compounds. However, it can be challenging to analyze low molecular-weight compounds using MALDI-MS owing to potential interference produced by the organic matrices in the low molecular-weight region, which can impede the detection of small molecules (m/z < 700 Da). Alternately, surface-assisted laser desorption/ionization-mass spectrometry (SALDI-MS) has shown great promise for small molecules analysis owing to the unique properties of the nanostructures used, particularly, minimal chemical background in low m/z region improved the production of ions involved in this method. The advancement of MALDI-MS and SALDI-MS has propelled their application in the analysis of FM components, focused on gaining deep insights into individual traits. This review aims to outline the current role of MALDI-MS and SALDI-MS in the chemical analysis of FMs. It also describes the latest achievements in forensic intelligence derived from fingermark analysis using these powerful methods. The accomplishments include the understanding of certain characteristics and lifestyles of donors. The review offers a comprehensive overview of the challenges and demands in this field. It suggests potential enhancements in this rapidly expanding domain to bridge the gap between research and practical police casework.

Pseudonectria keratitis-emerging pathogenic fungi in the eye.

BACKGROUND: Infectious keratitis, a significant contributor to blindness, with fungal keratitis accounting for nearly half of cases, poses a formidable diagnostic and therapeutic challenge due to its delayed clinical presentation, prolonged culture times, and the limited availability of effective antifungal medications. Furthermore, infections caused by rare fungal strains warrant equal attention in the management of this condition. CASE PRESENTATION: A case of fungal keratitis was presented, where corneal scraping material culture yielded pink colonies. Lactophenol cotton blue staining revealed distinctive spore formation consistent with the Fusarium species. Further analysis using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) identified the causative agent as Fusarium proliferatum. However, definitive diagnosis of Pseudonectria foliicola infection was confirmed through ITS sequencing. The patient's recovery was achieved with a combination therapy of voriconazole eye drops and itraconazole systemic treatment. CONCLUSION: Pseudonectria foliicola is a plant pathogenic bacterium that has never been reported in human infections before. Therefore, ophthalmologists should consider Pseudonectria foliicola as a possible cause of fungal keratitis, as early identification and timely treatment can help improve vision in most eyes.

Extracellular Microenvironment Alterations in Ductal Carcinoma In Situ and Invasive Breast Cancer Pathologies by Multiplexed Spatial Proteomics.

Ductal carcinoma in situ (DCIS) is a heterogeneous breast disease that remains challenging to treat due to its unpredictable progression to invasive breast cancer (IBC). Contemporary literature has become increasingly focused on extracellular matrix (ECM) alterations with breast cancer progression. However, the spatial regulation of the ECM proteome in DCIS has yet to be investigated in relation to IBC. We hypothesized that DCIS and IBC present distinct ECM proteomes that could discriminate between these pathologies. Tissue sections of pure DCIS, mixed DCIS-IBC, or pure IBC (n = 22) with detailed pathological annotations were investigated by multiplexed spatial proteomics. Across tissues, 1,005 ECM peptides were detected in pathologically annotated regions and their surrounding extracellular microenvironments. A comparison of DCIS to IBC pathologies demonstrated 43 significantly altered ECM peptides. Notably, eight fibrillar collagen peptides could distinguish with high specificity and sensitivity between DCIS and IBC. Lesion-targeted proteomic imaging revealed heterogeneity of the ECM proteome surrounding individual DCIS lesions. Multiplexed spatial proteomics reported an invasive cancer field effect, in which DCIS lesions in closer proximity to IBC shared a more similar ECM profile to IBC than distal counterparts. Defining the ECM proteomic microenvironment provides novel molecular insights relating to DCIS and IBC.

A MATLAB-based app to improve LC-MS/MS data analysis for N-linked glycan peak identification.

BACKGROUND: Glycosylation is an important modification to proteins that plays a significant role in biological processes. Glycan structures are characterized by liquid chromatography (LC) combined with mass spectrometry (MS), but data interpretation of LC/MS and MS/MS data can be time-consuming and arduous when analyzed manually. Most of glycan analysis requires dedicated glycobioinformatics tools to process MS data, identify glycan structure, and display the results. However, software tools currently available are either too costly or heavily focused on academic applications, limiting their use within the biopharmaceutical industry for implementing the standardized LC/MS glycan analysis in high-throughput manner. Additionally, few tools provide the capability to generate report-ready annotated MS/MS glycan spectra. RESULTS: Here, we present a MATLAB-based app, GlyKAn AZ, which can automate data processing, glycan identification, and customizable result displays in a streamlined workflow. MS1 and MS2 mass search algorithms along with glycan databases were developed to confirm the fluorescent labeled N-linked glycan species based on accurate mass. A user-friendly graphical user interface (GUI) streamlines the data analysis process, making it easy to implement the software tool in biopharmaceutical analytical laboratories. The databases provided with the app can be expanded through the Fragment Generator functionality which automatically identifies fragmentation patterns for new glycans. The GlyKAn AZ app can automatically annotate the MS/MS spectra, yet this data display feature remains flexible and customizable by users, saving analysts' time in generating individual report-ready spectra figures. This app accepts both OrbiTrap and matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) MS data and was successfully validated by identifying all glycan species that were previously identified manually. CONCLUSIONS: The GlyKAn AZ app was developed to expedite glycan analysis while maintaining a high level of accuracy in positive identifications. The app's customizable user inputs, polished figures and tables, and unique calculated outputs set it apart from similar software and greatly improve the current manual analysis workflow. Overall, this app serves as a tool for streamlining glycan identification for both academic and industrial needs.

Noncanonical atherosclerosis as the driving force in tricuspid aortic valve associated aneurysms - A trace collection.

Pathogenic mechanisms in degenerative thoracic aortic aneurysms (TAA) are still unclear. There is an ongoing debate about whether TAAs are caused by uniform or distinct processes, which would obviously have a major impact on future treatment strategies. Clearly, the ultimate outcome of TAA subgroups associated with a tricuspid aortic valve (TAV) or a bicuspid aortic valve (BAV) is the same, namely a TAA. Based on results from our own and others' studies, we decided to compare the different TAAs (TAV and BAV) and controls using a broad array of analyses, i.e., metabolomic analyses, gene expression profiling, protein expression analyses, histological characterization, and matrix-assisted laser desorption ionization imaging. Central findings of the present study are the presence of noncanonical atherosclerosis, pathological accumulation of macrophages, and disturbances of lipid metabolism in the aortic media. Moreover, we have also found that lipid metabolism is impaired systemically. Importantly, all of the above-described phenotypes are characteristic for TAV-TAA only, and not for BAV-TAA. In summary, our results suggest different modes of pathogenesis in TAV- and BAV-associated aneurysms. Intimal atherosclerotic changes play a more central role in TAV-TAA formation than previously thought, particularly as the observed alterations do not follow classical patterns. Atherosclerotic alterations are not limited to the intima but also affect and alter the TAV-TAA media. Further studies are needed to i) clarify patho-relevant intima-media interconnections, ii) define the origin of the systemic alteration of lipid metabolism, and iii) to define valid biomarkers for early diagnosis, disease progression, and successful treatments in TAV-TAAs.

Complex-Type N-Glycans Are Associated with Cartilage Degeneration within Different Loading Sites of the Tibial Plateau for Knee Osteoarthritis Patients.

Abnormal N-glycosylation has been shown to play an important role in the pathogenesis of multiple diseases. However, little is known about the relationship between N-glycosylation and knee osteoarthritis (KOA) progression at the tissue level. Thus, the aim of this study was to quantify the cartilage histomorphometric changes in formalin-fixed paraffin-embedded (FFPE) tissue collected from the lateral and medial compartments of the tibial plateau KOA patients (n = 8). Subsequently, N-glycans were analyzed by matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) followed by in situ MS/MS fragmentation. Overall, the Osteoarthritis Research Society International (OARSI) histological grade and cartilage surface fibrillation index were significantly higher, and chondrocyte size in the superficial zone was much larger, for the medial high-loaded cartilage compared to the lateral less-loaded cartilage. Among 92 putative N-glycans observed by MALDI-MSI, 3 complex-type N-glycans, (Hex)4(HexNAc)3, (Hex)4(HexNAc)4, and (Hex)5(HexNAc)4, and 1 oligomannose-type N-glycan, (Hex)9(HexNAc)2, were significantly higher in intensity in the medial cartilage compared to the lateral cartilage, whereas 2 tetra-antennary fucosylated-type N-glycans, (Hex)3(HexNAc)6(Fuc)2 and (Hex)3(HexNAc)6(Fuc)3, were significantly higher in intensity in the lateral cartilage than the medial cartilage. Our findings indicate that complex-type N-glycans are associated with higher severity of cartilage degeneration and may influence the cellular processes of KOA.

Evaluation of the Qvella FAST System and the FAST-PBC cartridge for rapid species identification and antimicrobial resistance testing directly from positive blood cultures.

Blood culture diagnostics require rapid and accurate identification (ID) of pathogens and antimicrobial susceptibility testing (AST). Standard procedures, involving conventional cultivation on agar plates, may take up to 48 hours or more until AST completion. Recent approaches aim to shorten the processing time of positive blood cultures (PBC). The FAST System is a new technology, capable of purifying and concentrating bacterial/fungal pathogens from positive blood culture media and producing a bacterial suspension called "liquid colony" (LC), which can be further used in downstream analyses (e.g., ID and AST). Here, we evaluated the performance of the FAST System LC generated from PBC in comparison to our routine workflow including ID by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using Sepsityper, AST by automatized MicroScan WalkAway plus and directly inoculated disk diffusion (DD), and MICRONAUT-AM for yeast/fungi. A total of 261 samples were analyzed, of which 86.6% (226/261) were eligible for the comparative ID and AST analyses. In comparison to the reference technique (culture-grown colonies), ID concordance of the FAST System LC and Sepsityper was 150/154 (97.4%) and 123/154 (79.9%), respectively, for Gram positive; 67/70 (95.7%) and 64/70 (91.4%), respectively, for Gram negative. For AST, categorical agreement (CA) of the FAST System LC in comparison to the routine workflow for Gram-positive bacteria was 96.1% and 98.7% for MicroScan and DD, respectively. Similar results were obtained for Gram-negative bacteria with 96.6% and 97.5% of CA for MicroScan and DD, respectively. Taken together, the FAST System LC allowed the laboratory to significantly reduce the time to obtain correct ID and AST (automated MicroScan) results 1 day earlier and represents a promising tool to expedite the processing of PBC.

MALDI mass spectrometry imaging shows a gradual change in the proteome landscape during mouse ovarian folliculogenesis.

Our knowledge regarding the role proteins play in the mutual relationship among oocytes, surrounding follicle cells, stroma, and the vascular network inside the ovary is still poor and obtaining insights into this context would significantly aid our understanding of folliculogenesis. Here, we describe a spatial proteomics approach to characterize the proteome of individual follicles at different growth stages in a whole prepubertal 25-day-old mouse ovary. A total of 401 proteins were identified by nano-scale liquid chromatography-electrospray ionization-tandem mass spectrometry (nLC-ESI-MS/MS), 69 with a known function in ovary biology, as demonstrated by earlier proteomics studies. Enrichment analysis highlighted significant KEGG and Reactome pathways, with apoptosis, developmental biology, PI3K-Akt, epigenetic regulation of gene expression, and extracellular matrix organization being well represented. Then, correlating these data with the spatial information provided by matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) on 276 follicles enabled the protein profiles of single follicle types to be mapped within their native context, highlighting 94 proteins that were detected throughout the secondary to the pre-ovulatory transition. Statistical analyses identified a group of 37 proteins that showed a gradual quantitative change during follicle differentiation, comprising 10 with a known role in follicle growth (NUMA1, TPM2), oocyte germinal vesicle-to-metaphase II transition (SFPQ, ACTBL, MARCS, NUCL), ovulation (GELS, CO1A2), and preimplantation development (TIF1B, KHDC3). The proteome landscape identified includes molecules of known function in the ovary, but also those whose specific role is emerging. Altogether, this work demonstrates the utility of performing spatial proteomics in the context of the ovary and offers sound bases for more in-depth investigations that aim to further unravel its spatial proteome.

On-tissue chemical derivatization in mass spectrometry imaging.

Mass spectrometry imaging (MSI) combines molecular and spatial information in a valuable tool for a wide range of applications. Matrix-assisted laser desorption/ionization (MALDI) is at the forefront of MSI ionization due to its wide availability and increasing improvement in spatial resolution and analysis speed. However, ionization suppression, low concentrations, and endogenous and methodological interferences cause visualization problems for certain molecules. Chemical derivatization (CD) has proven a viable solution to these issues when applied in mass spectrometry platforms. Chemical tagging of target analytes with larger, precharged moieties aids ionization efficiency and removes analytes from areas of potential isobaric interferences. Here, we address the application of CD on tissue samples for MSI analysis, termed on-tissue chemical derivatization (OTCD). MALDI MSI will remain the focus platform due to its popularity, however, alternative ionization techniques such as liquid extraction surface analysis and desorption electrospray ionization will also be recognized. OTCD reagent selection, application, and optimization methods will be discussed in detail. MSI with OTCD is a powerful tool to study the spatial distribution of poorly ionizable molecules within tissues. Most importantly, the use of OTCD-MSI facilitates the analysis of previously inaccessible biologically relevant molecules through the adaptation of existing CD methods. Though further experimental optimization steps are necessary, the benefits of this technique are extensive.

ADVANCES IN HIGH-RESOLUTION MALDI MASS SPECTROMETRY FOR NEUROBIOLOGY.

Research in the field of neurobiology and neurochemistry has seen a rapid expansion in the last several years due to advances in technologies and instrumentation, facilitating the detection of biomolecules critical to the complex signaling of neurons. Part of this growth has been due to the development and implementation of high-resolution Fourier transform (FT) mass spectrometry (MS), as is offered by FT ion cyclotron resonance (FTICR) and Orbitrap mass analyzers, which improves the accuracy of measurements and helps resolve the complex biological mixtures often analyzed in the nervous system. The coupling of matrix-assisted laser desorption/ionization (MALDI) with high-resolution MS has drastically expanded the information that can be obtained with these complex samples. This review discusses notable technical developments in MALDI-FTICR and MALDI-Orbitrap platforms and their applications toward molecules in the nervous system, including sequence elucidation and profiling with de novo sequencing, analysis of post-translational modifications, in situ analysis, key advances in sample preparation and handling, quantitation, and imaging. Notable novel applications are also discussed to highlight key developments critical to advancing our understanding of neurobiology and providing insight into the exciting future of this field. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.

Advances in Imaging Mass Spectrometry for Biomedical and Clinical Research.

Imaging mass spectrometry (IMS) allows for the untargeted mapping of biomolecules directly from tissue sections. This technology is increasingly integrated into biomedical and clinical research environments to supplement traditional microscopy and provide molecular context for tissue imaging. IMS has widespread clinical applicability in the fields of oncology, dermatology, microbiology, and others. This review summarizes the two most widely employed IMS technologies, matrix-assisted laser desorption/ionization (MALDI) and desorption electrospray ionization (DESI), and covers technological advancements, including efforts to increase spatial resolution, specificity, and throughput. We also highlight recent biomedical applications of IMS, primarily focusing on disease diagnosis, classification, and subtyping.

Multiple multi-sample testing under arbitrary covariance dependency.

Modern high-throughput biomedical devices routinely produce data on a large scale, and the analysis of high-dimensional datasets has become commonplace in biomedical studies. However, given thousands or tens of thousands of measured variables in these datasets, extracting meaningful features poses a challenge. In this article, we propose a procedure to evaluate the strength of the associations between a nominal (categorical) response variable and multiple features simultaneously. Specifically, we propose a framework of large-scale multiple testing under arbitrary correlation dependency among test statistics. First, marginal multinomial regressions are performed for each feature individually. Second, we use an approach of multiple marginal models for each baseline-category pair to establish asymptotic joint normality of the stacked vector of the marginal multinomial regression coefficients. Third, we estimate the (limiting) covariance matrix between the estimated coefficients from all marginal models. Finally, our approach approximates the realized false discovery proportion of a thresholding procedure for the marginal p-values for each baseline-category logit pair. The proposed approach offers a sensible trade-off between the expected numbers of true and false findings. Furthermore, we demonstrate a practical application of the method on hyperspectral imaging data. This dataset is obtained by a matrix-assisted laser desorption/ionization (MALDI) instrument. MALDI demonstrates tremendous potential for clinical diagnosis, particularly for cancer research. In our application, the nominal response categories represent cancer (sub-)types.

Complete and selective nitration of tyrosine residue in peptides caused by ultraviolet matrix-assisted laser desorption/ionization.

Complete and highly selective nitration of tyrosine (Tyr) as a residue-specific modification in peptides was found without side reactions, using ultraviolet matrix-assisted laser desorption/ionization (UV-MALDI) with a nitroaromatic reagent 3, 5-dinitrosalicylic acid (3,5-DNSA). The tyrosine nitration supported two propositions, namely, the UV-induced. NO2 attack reaction mechanism by Long et al. and the C-NO2 homolysis as a thermal process by Wiik et al. and Furman et al. With the UV-MALDI of peptides, a residue-specific reaction was observed in glycine (Gly) residue, i.e., an oxidation of the alpha-carbon of Gly due to attack of hydroxyl radical (.OH).

Desorption electrospray ionization and matrix-assisted laser desorption/ionization as imaging approaches for biological samples analysis.

The imaging of biological tissues can offer valuable information about the sample composition, which improves the understanding of analyte distribution in such complex samples. Different approaches using mass spectrometry imaging (MSI), also known as imaging mass spectrometry (IMS), enabled the visualization of the distribution of numerous metabolites, drugs, lipids, and glycans in biological samples. The high sensitivity and multiple analyte evaluation/visualization in a single sample provided by MSI methods lead to various advantages and overcome drawbacks of classical microscopy techniques. In this context, the application of MSI methods, such as desorption electrospray ionization-MSI (DESI-MSI) and matrix-assisted laser desorption/ionization-MSI (MALDI-MSI), has significantly contributed to this field. This review discusses the evaluation of exogenous and endogenous molecules in biological samples using DESI and MALDI imaging. It offers rare technical insights not commonly found in the literature (scanning speed and geometric parameters), making it a comprehensive guide for applying these techniques step-by-step. Furthermore, we provide an in-depth discussion of recent research findings on using these methods to study biological tissues.