Distinguishing methicillin-resistant Staphylococcus aureus from methicillin-sensitive strains by combining Fe3O4 magnetic nanoparticle-based affinity mass spectrometry with a machine learning strategy

Pathogenic bacteria, including drug-resistant variants such as methicillin-resistant Staphylococcus aureus (MRSA), can cause severe infections in the human body. Early detection of MRSA is essential for clinical diagnosis and proper treatment, considering the distinct therapeutic strategies for methicillin-sensitive S. aureus (MSSA) and MRSA infections. However, the similarities between MRSA and MSSA properties present a challenge in promptly and accurately distinguishing between them. This work introduces an approach to differentiate MRSA from MSSA utilizing matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) in conjunction with a neural network-based classification model. Four distinct strains of S. aureus were utilized, comprising three MSSA strains and one MRSA strain. The classification accuracy of our model ranges from ~ 92 to ~ 97% for each strain. We used deep SHapley Additive exPlanations to reveal the unique feature peaks for each bacterial strain. Furthermore, Fe3O4 MNPs were used as affinity probes for sample enrichment to eliminate the overnight culture and reduce the time in sample preparation. The limit of detection of the MNP-based affinity approach toward S. aureus combined with our machine learning strategy was as low as ~ 8 × 103 CFU mL-1. The feasibility of using the current approach for the identification of S. aureus in juice samples was also demonstrated.

Pulsed laser ablation synthesis of fresh Te nanoparticles for matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS) applications

This work aims to demonstrate the potential of pulsed laser ablation synthesis (PLA) of tellurium nanoparticles (Te NPs) for use in matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS) applications. An experimental laboratory setup for PLA synthesis of fresh Te NPs was designed to prevent unwanted aggregation of uncoated Te NPs and avoid the need to use additional modifiers. Performing pulsed laser ablation synthesis in liquid (PLAL) using acetone was found to be the optimal way of preparing Te NPs. Another possibility is to use commercially available laser ablation devices for laser ablation - inductively coupled plasma mass spectrometry (LA-ICP-MS) to perform PLA in a helium atmosphere, but this approach is less efficient and results in the formation of unwanted larger particles. The prepared Te NPs were studied using the transmission electron microscopy (TEM) and dynamic light scattering (DLS) methods. TEM images showed the formation of Te NP nanochains composed of many crystallized Te NPs with sizes ranging from 8 to 15 nm. The various size distributions of the synthesized Te NPs identified using the DLS method correspond to the size distributions of aggregations rather than individual Te NPs. The synthesized Te NPs were used for a pilot study of their possible use with the MALDI-MS technique. An important effect was observed when Te NPs were used to perform a MALDI-MS analysis of the α-cyclodextrin (α-CD) and cucurbit[7]uril (CB7) macrocycles, which consisted in a decline in the formation of matrix adducts. Furthermore, several changes in MALDI-MS mass spectra of intact cells and a positive effect of Te NPs on the crystallization of the MALDI-MS matrix were observed.

Transcriptomic, epigenomic, and spatial metabolomic cell profiling redefines regional human kidney anatomy

A large-scale multimodal atlas that includes major kidney regions is lacking. Here, we employed simultaneous high-throughput single-cell ATAC/RNA sequencing (SHARE-seq) and spatially resolved metabolomics to profile 54 human samples from distinct kidney anatomical regions. We generated transcriptomes of 446,267 cells and chromatin accessibility profiles of 401,875 cells and developed a package to analyze 408,218 spatially resolved metabolomes. We find that the same cell type, including thin limb, thick ascending limb loop of Henle and principal cells, display distinct transcriptomic, chromatin accessibility, and metabolomic signatures, depending on anatomic location. Surveying metabolism-associated gene profiles revealed non-overlapping metabolic signatures between nephron segments and dysregulated lipid metabolism in diseased proximal tubule (PT) cells. Integrating multimodal omics with clinical data identified PLEKHA1 as a disease marker, and its in vitro knockdown increased gene expression in PT differentiation, suggesting possible pathogenic roles. This study highlights previously underrepresented cellular heterogeneity underlying the human kidney anatomy.

Isolation and identification of Wickerhamiella tropicalis from blood culture by MALDI-MS

Wickerhamiella is a genus of budding yeast that is mainly isolated from environmental samples, and 40 species have been detected. The yeast isolated from human clinical samples usually only contain three species: W. infanticola, W. pararugosa and W. sorbophila. In this study, we isolated W. tropicalis from a blood sample of a six-year-old female with a history of B-cell precursor lymphoblastic leukemia in Japan in 2022. Though the strain was morphologically identified as Candida species by routine microbiological examinations, it was subsequently identified as W. tropicalis by sequencing the internal transcribed spacer (ITS) of ribosomal DNA (rDNA). The isolate had amino acid substitutions in ERG11 and FKS1 associated with azole and echinocandin resistance, respectively, in Candida species and showed intermediate-resistant to fluconazole and micafungin. The patient was successfully treated with micafungin. Furthermore, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) detected three novel peaks that are specific for W. tropicalis, indicating that MALDI-MS analysis is useful for rapid detection of Wickerhamiella species in routine microbiological examinations.

Novel Ag-modified vanadate nanosheets for determination of small organic molecules with laser desorption ionization mass spectrometry

Laser desorption ionization mass spectrometry (LDI-MS) aroused intensive concerns for the merits of label-free and high-throughput analysis. Here, we designed a silver nanoparticles (AgNP)-modified indium vanadate nanosheets with doping samarium (AgNP@InVO4:Sm) nanosheets. The developed AgNP@InVO4:Sm nanosheets (AIVON) were synthesized based on the microemulsion-mediated solvothermal method and ultraviolet-assisted in situ formation of AgNP, then for the first time applied as a matrix in LDI-MS analysis. With the advantages including enhanced MS signal, little matrix-related background, high reproducibility, and good salt tolerance, AIVON exhibited much better prospect than non-modified indium vanadate nanosheets with doping samarium (IVON) and traditional organic matrix, thus allowing sensitive MS detection for a wide range of low-molecular-weight (LMW) molecules. Moreover, by coupling with headspace sampling thin-film microextraction (TFME), a kind of representative pollutant chlorophenols were identified and quantified via AIVON-assisted LDI-MS in environmental and biological samples. Volatile LMW pollutants could be preconcentrated after TFME, hence a sensitive and rapid assay with negligible sample matrix effect was realized by using AIVON-assisted LDI-MS. It is anticipated that this novel nano-matrix AIVON and the proposed TFME coupling detection strategy were of competitive merits for LDI-MS analysis in the fields of environment, biomedicine, and agriculture.

Molecular diversity assessed by MALDI mass spectrometry of two scorpion species venom from two different locations in Morocco

Scorpion venom is a cocktail of molecules whose composition is remarkably plastic, controlled by several factors. The Moroccan scorpion fauna is characterized by its richness and high rate of endemism and the venom molecular variability of many species is not yet well characterized. The aim of the present study was to highlight the molecular variability of the venom composition of Androctonus amoreuxi and Buthacus stockmanni (endemic species), both belonging to the Buthidae family, collected from two Moroccan regions, Zagora and Tan-tan. Characterization of the molecular mass fingerprints (MFPs) of each specimen was performed by Matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS) using a sandwich (Sand) and a dried-droplet (DD) sample preparation and dilutions. Considering these two methods, a total of 828 ion signals were detected, and Sand method produced more adducts (56%) than DD (44%). We observed interspecific variations in the venom composition between these two species showing they share 235 ion signals, while 226 and 367 are specific for these two species, respectively. Moreover, B. stockmanni specimens showed a clear difference in their MFPs between the two geographical areas studied, suggesting intraspecific variations. Moreover, specimens from each population also show an intraspecific variability. In addition, for the same individual, a variation in the venom composition was also recorded depending on the milking frequency. Our results confirmed the presence of characteristic components in each extracted venom sample. In conclusion, MFPs assessed by MALDI-MS represent a fast, non-supervised, sensitive, reliable and cost-efficient approach for taxonomic identification and molecular variability characterization. This study undoubtedly represents a step forward for understanding the scorpion venom plasticity, intra/inter variations, and their temporal and geographical variability.

Application of aptamer-conjugated graphene oxide for specific enrichment of microcystin-LR in Achatina fulica prior to matrix-assisted laser desorption ionization mass spectrometry

Microcystin-LR (MC-LR), as a hepatotoxin, can cause liver swelling, hepatitis, and even liver cancer. In this study, MC-LR aptamer (Apt-3) modified graphene oxide (GO) was designed to enrich MC-LR in white jade snail (Achatina fulica) and pond water, followed by matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) analysis. Results indicated that the Apt-3/PEG/GO nanocomposites were highly specific to MC-LR, and the detection limit of MALDI-MS was 0.50 ng/mL. Moreover, the MC-LR can be released from nanocomposites at 75°C, thus, the reuse of Apt-3/PEG/GO is realized. Real sample analysis indicated that the Apt-3/PEG/GO nanocomposites coupled with MALDI-MS were efficient in detecting trace amounts of MC-LR in real samples. With the merits of being low cost, reusable, and easy to besynthesized, this Apt-3/PEG/GO MALDI-MS is expected to be comprehensively applied by anchoring suitable aptamers for different targets.

Deciphering the metabolic heterogeneity of hematopoietic stem cells with single-cell resolution

Metabolic status is crucial for stem cell functions; however, the metabolic heterogeneity of endogenous stem cells has never been directly assessed. Here, we develop a platform for high-throughput single-cell metabolomics (hi-scMet) of hematopoietic stem cells (HSCs). By combining flow cytometric isolation and nanoparticle-enhanced laser desorption/ionization mass spectrometry, we routinely detected >100 features from single cells. We mapped the single-cell metabolomes of all hematopoietic cell populations and HSC subpopulations with different division times, detecting 33 features whose levels exhibited trending changes during HSC proliferation. We found progressive activation of the oxidative pentose phosphate pathway (OxiPPP) from dormant to active HSCs. Genetic or pharmacological interference with OxiPPP increased reactive oxygen species level in HSCs, reducing HSC self-renewal upon oxidative stress. Together, our work uncovers the metabolic dynamics during HSC proliferation, reveals a role of OxiPPP for HSC activation, and illustrates the utility of hi-scMet in dissecting metabolic heterogeneity of immunophenotypically defined cell populations.

α-Cyano-3-aminocinnamic acid: A novel reactive matrix for qualitative and quantitative analysis of plant N-glycans by MALDI-MS

N-glycans have a diversity of crucial biological roles in organisms. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has become an indispensable analytical instrument for biomolecules. However, due to the inherent low abundance, high structural heterogeneity, and poor ionization efficiency of N-glycans, as well as the extremely inhomogeneous co-crystal property using traditional matrices, the qualitation and quantitation of N-glycans by MALDI-MS remains challenging. In the present study, α-cyano-3-aminocinnamic acid (3-CACA) was reasonably designed and synthesized as a novel reactive matrix for N-glycan analysis. Combining with traditional matrix α-cyano-4-hydroxycinnamic acid (CHCA) as an acidic catalyst, a combinational matrix 3-CACA/CHCA was obtained with homogeneous co-crystallization and high derivatization efficiency, achieving the sensitive qualitation with the limits of detection low to femtomole and reproducible quantitation with good linearity (R2 > 0.998). As a result, the established method was successfully applied to the on-target derivatization and high-throughput quantification of N-glycans in eight varieties of the peach complex system, indicating that N-glycan has the potential to become a new biomarker for food allergy, and elucidating the prospective correlation between N-glycan epitopes and allergic reactions.

Workflow for High-throughput Screening of Enzyme Mutant Libraries Using Matrix-assisted Laser Desorption/Ionization Mass Spectrometry Analysis of Escherichia coli Colonies

High-throughput molecular screening of microbial colonies and DNA libraries are critical procedures that enable applications such as directed evolution, functional genomics, microbial identification, and creation of engineered microbial strains to produce high-value molecules. A promising chemical screening approach is the measurement of products directly from microbial colonies via optically guided matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Measuring the compounds from microbial colonies bypasses liquid culture with a screen that takes approximately 5 s per sample. We describe a protocol combining a dedicated informatics pipeline and sample preparation method that can prepare up to 3,000 colonies in under 3 h. The screening protocol starts from colonies grown on Petri dishes and then transferred onto MALDI plates via imprinting. The target plate with the colonies is imaged by a flatbed scanner and the colonies are located via custom software. The target plate is coated with MALDI matrix, MALDI-MS analyzes the colony locations, and data analysis enables the determination of colonies with the desired biochemical properties. This workflow screens thousands of colonies per day without requiring additional automation. The wide chemical coverage and the high sensitivity of MALDI-MS enable diverse screening projects such as modifying enzymes and functional genomics surveys of gene activation/inhibition libraries. Key features • Mass spectrometry analyzes a range of compounds from E. coli colonies as a proxy for liquid culture testing enzyme mutant libraries. • Colonies are transferred to a MALDI target plate by a simple imprinting method. • The screen compares the ratio among several products or searches for the qualitative presence of specific compounds. • The protocol requires a MALDI mass spectrometer.

Automated High-Throughput Matrix Assisted Laser Desorption Ionization Mass Spectrometry Methodology for Formulation Assessment of Polyethylene-Glycol-Conjugated Cytokine Proteins

Biological therapeutics are major contributors to the pharmaceutical pipeline and continue to grow in sales and scope. Additionally, the field's understanding of cancer biology has advanced such that biopharmaceuticals can harness the power of the immune system for oncology treatments. Several of these novel therapeutics are engineered versions of naturally occurring proteins designed to improve therapeutic properties including potency, target engagement and half-life extension. Cytokines, such as interferons and interleukins, are a broad class of signaling proteins which modulate the body's immune response; engineered cytokines have entered the clinic as promising new immuno-oncology therapies. While these therapies hold great promise, their additional structural complexity introduces analytical challenges, and traditional analytical platforms may be ill-suited to effectively assess product development risks. Further, the pharmaceutical industry relies on streamlining approaches for high-throughput experimentation to achieve speed and efficiency for the discovery and development of new modalities. These demands necessitate the use of state-of-the-art techniques to rapidly characterize these new modalities and guide process development and optimization. Matrix Assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS) is a rapid, sensitive and automatable technique amenable for high-throughput analysis of proteins. In this work, we have developed an automated MALDI-MS platform to prepare, acquire and analyze molecular degradation in engineered PEGylated cytokines formulation samples. This orthogonal technique integrated seamlessly with current developability risk assessment workflows, ultimately enabling selection of a final formulation strategy for clinical development.

Fatal panresistant Lomentospora prolificans fungemia in a patient with aplastic anemia: First report from Türkiye

Lomentospora prolificans is an opportunistic pathogen that can cause invasive lomentosporiosis in immunocompromised patients. Patients with hematological malignancies and those who have undergone stem cell or solid organ transplantations are in the highest risk group. In addition to the limitations and delays in diagnostic possibilities, L. prolificans has a high mortality due to its resistance to all available antifungal drugs. In a patient diagnosed with aplastic anemia, we described the first case of L. prolificans in Türkiye. L. prolificans was identified in the blood culture, and despite the initiation of antifungal treatments, the fungemia resulted in mortality on the 7th day of intensive care hospitalization. This case highlights the importance of early recognition and prompt initiation of appropriate antifungal therapy to improve the outcome of patients with rare mold infections.

Boron nitride quantum dots-enhanced laser desorption/ionization mass spectrometry analysis and imaging of bisphenol A

Bisphenol A (BPA) displays harmful effects on the human health, including potent endocrine activity and potential impact on the development of cancer. Analysis BPA residues in water and plastic products attracted considerable attention in the past decades. However, dominantly used conventional analysis techniques are unable to directly and non-destructively identify the correct species of BPA in plastic products. Hence, this study demonstrates the effective utilisation of boron nitride quantum dots (BNQDs) as an inorganic matrix in matrix-assisted laser desorption/ionization mass spectrometry analysis and imaging (MALDI-MS & MSI) for BPA. The presence of abundant hydroxyl and amino groups on the BNQDs' surface is favourable for the formation of hydrogen bonds with BPA, and increases their ionization and chemoselectivity. Intriguingly, the BNQDs matrix offers a distinct signal for phenolic hazardous molecules featuring different hydroxyl groups. The method was applied to detect BPA at nanomolar level in environmental water, and also allowed non-destructive and in situ mapping of BPA in plastics and pacifiers. This research provides a novel strategy for adapting nanomaterials as inorganic matrices for analysis of small molecular pollutants in environmentally relevant samples using MALDI-MS & MSI.

IsoMatchMS: Open-Source Software for Automated Annotation and Visualization of High Resolution MALDI-MS Spectra

Due to its speed, accuracy, and adaptability to various sample types, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has become a popular method to identify molecular isotope profiles from biological samples. Often MALDI-MS data do not include tandem MS fragmentation data, and thus the identification of compounds in samples requires external databases so that the accurate mass of detected signals can be matched to known molecular compounds. Most relevant MALDI-MS software tools developed to confirm compound identifications are focused on small molecules (e.g., metabolites, lipids) and cannot be easily adapted to protein data due to their more complex isotopic distributions. Here, we present an R package called IsoMatchMS for the automated annotation of MALDI-MS data for multiple datatypes: intact proteins, peptides, and glycans. This tool accepts already derived molecular formulas or, for proteomics applications, can derive molecular formulas from a list of input peptides or proteins including proteins with post-translational modifications. Visualization of all matched isotopic profiles is provided in a highly accessible HTML format called a trelliscope display, which allows users to filter and sort by several parameters such as match scores and the number of peaks matched. IsoMatchMS simplifies the annotation and visualization of MALDI-MS data for downstream analyses.

Utilizing linkage-specific ethyl-esterification approach to perform in-depth analysis of sialylated N-glycans present on milk whey glycoproteins

Glycosylation of milk whey proteins, specifically the presence of sialic acid-containing glycan residues, causes functional changes in these proteins. This study aimed to analyze the N-glycome of milk whey glycoproteins from various milk sources using a linkage-specific ethyl esterification approach with MALDI-MS (matrix-assisted laser desorption/ionization-mass spectrometry). The results showed that the N-glycan profiles of bovine and buffalo whey mostly overlapped. Acetylated N-glycans were only detected in donkey milk whey at a rate of 16.06%. a2,6-linked N-Acetylneuraminic acid (a2,6-linked NeuAc, E) was found to be the predominant sialylation type in human milk whey (65.16%). The amount of a2,6-linked NeuAc in bovine, buffalo, goat, and donkey whey glycoproteomes was 42.33%, 44.16%, 39.00%, and 34.86%, respectively. The relative abundances of a2,6-linked N-Glycolylneuraminic acid (a2,6-linked NeuGc, Ge) in bovine, buffalo, goat, and donkey whey were 7.52%, 5.41%, 28.24%, and 17.31%, respectively. Goat whey exhibited the highest amount of a2,3-linked N-Glycolylneuraminic acid (a2,3-linked NeuGc, Gl, 8.62%), while bovine and donkey whey contained only 2.14% and 1.11%, respectively.

N-glycomic profiling reveals dysregulated N-glycans of peripheral neuropathy in type 2 diabetes

Given the increasing morbidity of diabetes mellitus type 2 (T2DM) with peripheral neuropathy (PN), efficient screening for T2DM-PN is of great significance. Altered N-glycosylation is closely associated with T2DM progression, whereas its association with T2DM-PN remains uncharacterized. In this study, N-glycomic profiling was performed to identify the N-glycan features between T2DM patients with (n = 39, T2DM-PN) and without PN (n = 36, T2DM-C). Another independent set of T2DM patients (n = 29 for both T2DM-C and T2DM-PN) were utilized to validate these N-glycomic features. There were 10 N-glycans varied significantly between T2DM-C and T2DM-PN (p < 0.05 and 0.7 < AUC < 0.9), of which T2DM-PN was associated with increased oligomannose and core-fucosylation of sialylated glycans, and decreased bisected mono-sialylated glycan. Notably, these results were validated by an independent set of T2DM-C and T2DM-PN. This is the first profiling for N-glycan features in T2DM-PN patients, which reliably differentiates them from T2DM controls, thus providing a prospective profile of glyco-biomarkers for the screening and diagnosis of T2DM-PN.

Evaluation of strategies to narrow the product chain-length distribution of microbially synthesized free fatty acids

The dominant strategy for tailoring the chain-length distribution of free fatty acids (FFA) synthesized by heterologous hosts is expression of a selective acyl-acyl carrier protein (ACP) thioesterase. However, few of these enzymes can generate a precise (greater than 90% of a desired chain-length) product distribution when expressed in a microbial or plant host. The presence of alternative chain-lengths can complicate purification in situations where blends of fatty acids are not desired. We report the assessment of several strategies for improving the dodecanoyl-ACP thioesterase from the California bay laurel to exhibit more selective production of medium-chain free fatty acids to near exclusivity. We demonstrated that matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS) was an effective library screening technique for identification of thioesterase variants with favorable shifts in chain-length specificity. This strategy proved to be a more effective screening technique than several rational approaches discussed herein. With this data, we isolated four thioesterase variants which exhibited a more selective FFA distribution over wildtype when expressed in the fatty acid accumulating E. coli strain, RL08. We then combined mutations from the MALDI isolates to generate BTE-MMD19, a thioesterase variant capable of producing free fatty acids consisting of 90% of C₁₂ products. Of the four mutations which conferred a specificity shift, we noted that three affected the shape of the binding pocket, while one occurred on the positively charged acyl carrier protein landing pad. Finally, we fused the maltose binding protein (MBP) from E. coli to the N - terminus of BTE-MMD19 to improve enzyme solubility and achieve a titer of 1.9 g per L of twelve-carbon fatty acids in a shake flask.

Recent Trends In MALDI-MS Drugs Analysis In Human Hair: Pre-Analytical And Analytical Challenges And Pitfalls

The value of hair in forensic toxicology has already been widely demonstrated. It offers a much wider detection window than other matrices and its segmental analysis allows the documentation of a single, occasional or regular consumption of a large number of molecules. To date, considerable efforts are being made to achieve very high sensitivity using increasingly effective techniques in the forensic analysis of hair (GC-EI/MS, GC-CI/MS, GC-MS/MS, HPLC-MS/MS and UPLC-MS/MS). Since the early 2000s, work has been carried out to analyze hair using matrix-assisted laser desorption/ionization (MALDI) coupled with imaging mass spectrometry (IMS). Intact, cut or pulverized, human head hairs are analyzed in all their forms. With a simplified and rapid sample preparation protocol, MALDI-IMS appears to be an attractive option for the forensic interpretation of hair analysis. The high spatial resolution clearly competes with conventional methods and strand segmentation. This article provides a complete overview on MALDI techniques used and its applications to better understand the pre-analytical and the analytical parts in the hair analysis.

Single drop analysis of mercury ions by rational design of peptide coated gold nanoparticles integrated with MALDI-MS measurement

In this study, a novel and rapid method for specific identification and accurate quantification of Hg²⁺ in environmental water was developed by using laser cleavable cysteine containing peptides modified gold nanoparticles coupled with high resolution matrix-assisted laser desorption ionization time-of-flight mass spectrometer (MALDI-TOF MS) measurement. First, gold nanoparticles were prepared by the reduction of tetrachloroauric (III) acid (HAuCl₄) solution. Various cysteine containing peptides, photolabile linkers, including mercury ion binding motif with a proper molecular mass and amino acids were synthesized by solid phase peptide synthesis (SPPS). Subsequently, thiol-containing peptides were coated onto the surface of gold nanoparticles via the formation of gold-thiol (Au-S) bond. The resulting cysteine containing peptides modified gold nanoparticles were designed to specifically capture Hg²⁺ in water samples. After conjugated complex formation, ions of Hg²⁺-peptide complex were directly liberated by ultraviolet laser radiation by way of MALDI-MS using α-Cyano-4-hydroxycinnamic acid (CHCA) as matrix. The linear dynamic range of Hg²⁺ concentration in this study was 1-100 pmol/μL with coefficient of determination 0.9987. The limit of detection (LOD) and limit of quantification (LOQ) were 0.19 and 0.63 pmol/μL, respectively. Notably, the developed method allows rapid quantification of Hg²⁺ in 5 min and the desired sample volume was down to few μL.

Integration of Non-targeted Proteomics Mass Spectrometry with Machine Learning for Screening Cooked Beef Adulterated Samples

The degradation of ingredients in heat-processed meat products makes their authentication challenging. In this study, protein profiles of raw beef, chicken, duck, pork, and binary simulated adulterated beef samples (chicken-beef, duck-beef, and pork-beef) and their heat-processed samples were obtained by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Heat-stable characteristic proteins were found by screening the overlapping characteristic protein ion peaks of the raw and corresponding heat-processed samples, which were discovered by partial least-squares discriminant analysis. Based on the 36 heat-stable characteristic proteins, qualitative classification for the raw and heat-processed meats was achieved by extreme gradient boosting. Moreover, quantitative analysis via partial least squares regression was applied to determine the adulteration ratio of the simulated adulterated beef samples. The validity of the approach was confirmed by a blind test with the mean accuracy of 97.4%. The limit of detection and limit of quantification of this method were determined to be 5 and 8%, respectively, showing its practical aspect for the beef authentication.

Quantitative Mass Spectrometry Imaging of Bleomycin in Skin Using a Mimetic Tissue Model for Calibration

The aim of Quantitative mass spectrometry imaging (Q-MSI) is to provide distribution analysis and quantitation from one single mass-spectrometry-based experiment, and several quantitation methods have been devised for Q-MSI. Mimetic tissue models based on spiked tissue homogenates are considered one of the most accurate ways to perform Q-MSI, since the analyte is present in a well-defined concentration in a sample matrix highly similar to the one of the unknown sample to be analyzed. The delivery of drugs in skin is among the most frequent types of pharmaceutical MSI studies. Here, a mimetic tissue model is extended for use on the skin, which, due to its high collagen content, is different from most other tissue as the homogenates become extremely viscous. A protocol is presented which overcomes this by the addition of water and the handling of the homogenate at an elevated temperature where the viscosity is lower. Using a mimetic tissue model, a method was developed for the quantitative imaging of bleomycin in skin. To compensate for the signal drift and the inhomogeneities in the skin, an internal standard was included in the method. The method was tested on skin from a pig which had had an electropneumatic injection of bleomycin into the skin. Quantification was made at several regions in a cross section of the skin at the injection site, and the results were compared to the results of a quantitative LC-MS on a neighboring tissue biopsy from the same animal experiment. The overall tissue concentration determined by the LC-MS was within the range of the different regions quantified by the Q-MSI. As the model provides the results of the same order of magnitude as a LC-MS, it can either be used to replace LC-MS in skin studies where MSI and LC-MS are today carried out in combination, or it can add quantitative information to skin studies which are otherwise carried out by MSI alone.

Modulating the lipid profile of blastocyst cell membrane with DPPC multilamellar vesicles

The aim of this study was to evaluate the effect of multilamellar vesicles (MLVs) of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) in co-culture with in vitro-produced bovine embryos (IVPEs). The stability of five concentrations of MLVs (1.0, 1.25, 1.5, 1.75, and 2.0 mM) produced using ultrapure water or embryonic culture medium with 24 or 48 h of incubation at 38.5 °C with 5% CO₂ was assessed. In addition, the toxicity of MLVs and their modulation of the lipid profile of the plasma membrane of IVPEs were evaluated after 48 h of co-culture. Both media allowed the production of MLVs. Incubation (24 and 48 h) did not impair the MLV structure but affected the average diameter. The rate of blastocyst production was not reduced, demonstrating the nontoxicity of the MLVs even at 2.0 mmol/L. The lipid profile of the embryos was different depending on the MLV concentration. In comparison with control embryos, embryos cultured with MLVs at 2.0 mmol/L had a higher relative abundance of six lipid ions (m/z 720.6, 754.9, 759.0, 779.1, 781.2, and 797.3). This study sheds light on a new culture system in which the MLV concentration could change the lipid profile of the embryonic cell membrane in a dose-dependent manner.

Mass spectrometry-based N-glycosylation analysis in kidney disease

Kidney disease is a global health concern with an enormous expense. It is estimated that more than 10% of the population worldwide is affected by kidney disease and millions of patients would progress to death prematurely and unnecessarily. Although creatinine detection and renal biopsy are well-established tools for kidney disease diagnosis, they are limited by several inevitable defects. Therefore, diagnostic tools need to be upgraded, especially for the early stage of the disease and possible progression. As one of the most common post-translational modifications of proteins, N-glycosylation plays a vital role in renal structure and function. Deepening research on N-glycosylation in kidney disease provides new insights into the pathophysiology and paves the way for clinical application. In this study, we reviewed recent N-glycosylation studies on several kidney diseases. We also summarized the development of mass spectrometric methods in the field of N-glycoproteomics and N-glycomics.

Enzyme-assisted ReMALDI-MS assay for quantification of cholesterol in food

Cholesterol is a vital building block for animal cell membranes and participates in the synthesis of various hormones. Accurate quantitation of cholesterol in food is crucial for healthy diets. Here, we describe an enzyme-assisted reactive matrix-assisted laser desorption/ionization mass spectrometry (ReMALDI-MS) assay for the quantification of cholesterol in food. First, cholesterol was converted to 4-cholesten-3-one using the cholesterol oxidase, and then reacted with a reactive matrix, 4-hydrazinoquinazoline (4-HQ), to form a hydrazone bond. Utilizing 4-HQ significantly improved the ionization efficiency of cholesterol, which possesses poor ionization efficiency in MALDI-MS, and no additional tedious derivatization/purification steps were needed. Thus, the proposed assay was successfully used for the quantification of cholesterol in bovine milk and cream. The standard recovery tests show a recovery range of 95.3-103.0% with a relative standard deviation of 0.3-3.1%. Therefore, the proposed enzyme-assisted ReMALDI-MS assay has great potential for quantification of cholesterol in other foods.

NH2NH-MOF: a reaction matrix for the specific determination of small aldehydes by MALDI-MS

Efficient determination of aldehydes by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is hampered mainly by the low mass and unstable nature of analytes. In the present work, we propose a combined strategy of a reactive metal-organic framework (MOF) matrix for the derivatization and detection of aldehydes. A novel reactive MOF matrix (NH₂NH-MOF) was synthesized in two steps. First, NR₃⁺-MOF was synthesized via Cu²⁺ and the quaternary amine ligand 4,4'-bipyridinium, 1,1″-(1,2-ethanediyl)bis-, dibromide (PyEtBr). Then, -NHNH₂ was introduced to NR₃⁺-MOF through electrostatic adsorption between the -NR₃⁺ and -HSO₃^- of 4-hydrazinylbenzenesulfonic acid to synthesize NH₂NH-MOF. The acid-base chemistry of NH₂NH-MOF led to uniform cocrystallization of the aldehyde-matrix mixtures and helped to achieve the detection of low-weight aldehydes with good relative standard deviations (RSDs = 0.07-12.35%). It was confirmed that this strategy can accurately quantify formaldehyde, valeraldehyde, and benzaldehyde with good linearity (r > 0.97). Furthermore, this strategy was applied to quantitatively detect benzaldehyde in wastewater, thus showing potential applications in environmental pollutant detection.

Iminodiacetic acid (IDA)-generated mesoporous nanopolymer: a template to relate surface area, hydrophilicity, and glycopeptides enrichment

A three-step strategy is introduced to develop inherent iminodiacetic (IDA)-functionalized nanopolymer. SEM micrographs show homogenous spherical beads with a particle size of 500 nm. Further modification to COOH-functionalized 1,2-epoxy-5-hexene/DVB mesoporous nanopolymer enriches glycopeptides via hydrophilic interactions followed by their MS determination. Significantly high BET surface area 433.4336 m² g^-1 contributes to the improved surface hydrophilicity which is also shown by high concentration of ionizable carboxylic acids, 14.59 ± 0.25 mmol g^-1. Measured surface area is the highest among DVB-based polymers and in general much higher in comparison to the previously reported BET surface areas of co-polymers, terpolymers, MOFs, and graphene-based composites. Thirty-one, 19, and 16 N-glycopeptides are enriched/identified by nanopolymer beads from tryptic digests of immunoglobulin G, horseradish peroxidase, and chicken avidin, respectively, without additional desalting steps. Material exhibits high selectivity (1:400 IgG:BSA), sensitivity (down to 0.1 fmol), regeneration ability up to three cycles, and batch-to-batch reproducibility (RSD > 1%). Furthermore, from 1 μL of digested human serum, 343 N-glycopeptide characteristics of 134 glycoproteins including 30 FDA-approved serum biomarkers are identified via nano-LC-MS/MS. The developed strategy to self-generate IDA on polymeric surface with improved surface area, porosity, and ordered morphology is insignia of its potential as chromatographic tool contributing to future developments in large-scale biomedical glycoproteomics studies.

Apo-H (beta-2-glycoprotein) intact N-glycan analysis by MALDI-TOF-MS using sialic acid derivatization

Apo-H is a plasma glycoprotein. Nearly 19% of the molecular weight of this protein is composed of glycans. Up- and down-regulation and structural changes in protein glycans provide diagnostic value for disease detection. Here, an efficient, sensitive, and optimized method is developed for Apo-H N-glycans analysis by MALDI-TOF-MS in positive mode. This bioanalytical method includes sample preparation, sample purification, and detection. An Apo-H enrichment method is developed using standard proteins by anti-Apo-H beads followed by enrichment from plasma samples. SDS-PAGE confirms the Apo-H protein enrichment, which is further verified by LC-MS/MS analysis. The lower ionization efficiency of sialylated glycan hampers their analysis by MALDI-MS. For this, stabilization of sialic acids is done by selective derivatization of carboxyl groups to differentiate between α(2,3)- and α(2,6)-linked sialic acids. Glycans are further purified by HILIC-SPE and analyzed by MALDI-MS. Several branched bi- and tri-antennary glycans with fucosylation and sialylation are identified. The reproducibility of the developed method is tested by analyzing multiple replicates of human plasma, where the same glycans are consistently identified. This method could be applied for the Apo-H glycan profiling of large clinical cohorts for diagnostic purposes.

Machine Learning of Serum Metabolic Patterns Encodes Asymptomatic SARS-CoV-2 Infection

Asymptomatic COVID-19 has become one of the biggest challenges for controlling the spread of the SARS-CoV-2. Diagnosis of asymptomatic COVID-19 mainly depends on quantitative reverse transcription PCR (qRT-PCR), which is typically time-consuming and requires expensive reagents. The application is limited in countries that lack sufficient resources to handle large-scale assay during the COVID-19 outbreak. Here, we demonstrated a new approach to detect the asymptomatic SARS-CoV-2 infection using serum metabolic patterns combined with ensemble learning. The direct patterns of metabolites and lipids were extracted by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) within 1 s with simple sample preparation. A new ensemble learning model was developed using stacking strategy with a new voting algorithm. This approach was validated in a large cohort of 274 samples (92 asymptomatic COVID-19 and 182 healthy control), and provided the high accuracy of 93.4%, with only 5% false negative and 7% false positive rates. We also identified a biomarker panel of ten metabolites and lipids, as well as the altered metabolic pathways during asymptomatic SARS-CoV-2 Infection. The proposed rapid and low-cost approach holds promise to apply in the large-scale asymptomatic COVID-19 screening.

Toward Revealing Microcystin Distribution in Mouse Liver Tissue Using MALDI-MS Imaging

Cyanotoxins can be found in water and air during cyanobacterial harmful algal blooms (cHABs) in lakes and rivers. Therefore, it is very important to monitor their potential uptake by animals and humans as well as their health effects and distribution in affected organs. Herein, the distribution of hepatotoxic peptide microcystin-LR (MC-LR) is investigated in liver tissues of mice gavaged with this most common MC congener. Preliminary matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) imaging experiments performed using a non-automated MALDI matrix deposition device and a MALDI-time-of-flight (TOF) mass spectrometer yielded ambiguous results in terms of MC-LR distribution in liver samples obtained from MC-LR-gavaged mice. The tissue preparation for MALDI-MS imaging was improved by using an automated sprayer for matrix deposition, and liver sections were imaged using an Nd:YAG MALDI laser coupled to a 15 Tesla Fourier-transform ion cyclotron resonance (FT-ICR)-mass spectrometer. MALDI-FT-ICR-MS imaging provided unambiguous detection of protonated MC-LR (calculated m/z 995.5560, z = +1) and the sodium adduct of MC-LR (m/z 1017.5380, z = +1) in liver sections from gavaged mice with great mass accuracy and ultra-high mass resolution. Since both covalently bound and free MC-LR can be found in liver of mice exposed to this toxin, the present results indicate that the distribution of free microcystins in tissue sections from affected organs, such as liver, can be monitored with high-resolution MALDI-MS imaging.

Matrix-assisted laser desorption ionization mass spectrometry based quantitative analysis of cordycepin from Cordyceps militaris

Cordycepin, which has great immunomodulatory activities such as anticancer, antifungal, antivirus, antileukemia and lipid-lowering ones, is the secondary metabolite of Cordyceps militaris (C. militaris). Liquid submerged fermentation is the common cultivation process to produce cordycepin. To optimize the fermentation process and improve production, monitoring the cordycepin secretion in the fermentation is essential. The measurement based on chromatography-mass spectrometry methods is generally involved in the complex sample pretreatments and time-consuming separation, so more rapid and convenient methods are required. Matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) is more attractive for faster and direct detection. Therefore, MALDI-MS detection combined with isotope-labeled internal standard was applied to the measurement of cordycepin content in the fermentation broth and mycelium. This method made accurate quantification of cordycepin in the range of 5–400 μg/mL with a relative standard deviation of 5.6%. The recovery rates of fermentation samples after the 1, 13, and 25 days were 90.15%, 94.27%, and 95.06%, respectively. The contents of cordycepin in the mycelium and fermentation broth were 136 mg/g and 148.39 mg/mL on the 20th culture day, respectively. The cordycepin secretion curve of the liquid fermentation of C. militaris was real-time traced over 25 days.

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A rapid quantification method of cordycepin based on MALDI-MS is proposed.

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The quantification relies on the stable isotope standard method.

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Rapid determination of the cordycepin content in the liquid fermentation broth of Cordyceps militaris without pre-treatment.

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Monitoring the fermentation state of C. militaris fermentation broth is benefit to improve the yield of cordycepin.

Functional magnetic nanoparticle-based affinity probe for MALDI mass spectrometric detection of ricin B

The use of lactosylated Fe₃O₄ magnetic nanoparticles (MNP@LAC) has been explored as affinity probes against ricin B based on galactose-ricin B binding interactions. Lactose was bound onto the surface of aminated MNPs through the Maillard reaction. The enrichment of ricin B took ~1 h by incubating MNP@LAC with samples under shaking at room temperature, followed by magnetic isolation. The resultant MNP@LAC-ricin B conjugates were characterized by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The limit of detection toward ricin B was ~3 nM by using the developed method. It was possible to detect the peptides derived from the tryptic digest of trace ricin B (~0.39 nM) enriched by the MNP@LAC probes followed by tryptic digestion and MALDI-MS analysis. The feasibility of using the developed method for detection of ricin B from complex white corn starch samples spiked with trace ricin B was demonstrated.

Lipidomic Profiling of Algae with Microarray MALDI-MS toward Ecotoxicological Monitoring of Herbicide Exposure

Misuse of agrochemicals has a long-lasting negative impact on aquatic systems. Mismanagement of herbicides in agri-food sectors is often linked to a simultaneous decline in the health of downstream waterways. However, monitoring the herbicide levels in these areas is a laborious task, and modern analytical approaches, such as solid-phase extraction-liquid chromatography-mass spectrometry (SPE-LC-MS) and enzyme-linked immunosorbent assay, are low-throughput and require significant sample preparation. We report here the use of microchip technology in combination with matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) for the assessment of the ecotoxicological effect of agrochemicals on aquatic species at the single-cell level. This approach quantifies the fluctuations in lipid content in sentinel organisms and targets the microalga, Chlamydomonas reinhardtii (C. reinhardtii), as the model system. Specifically, we investigated the cytotoxicity of three herbicides (atrazine, clomazone, and norflurazon) on C. reinhardtii by analyzing the lipid component variation upon assorted herbicide exposure. Lipidomic profiling reveals a significantly altered lipid content at >EC₅₀ in atrazine-exposed cells. The response for norflurazon showed similar trends but diminished in magnitude, while the result for clomazone was near muted. At lower herbicide concentrations, digalactosyldiacylglycerols showed a rapid decrease in abundance, while several other lipids displayed a moderate increase. The microchip-based MALDI technique demonstrates the ability to achieve lipidomic profiling of aquatic species exposed to different stressors, proving effective for high-throughput screening and single-cell analysis in ecotoxicity studies.

Fullerenol as a water-soluble MALDI-MS matrix for rapid analysis of small molecules and efficient quantification of saccharin sodium in foods

Due to the strong background interferences in the low-mass region and poor reproducibility of conventional organic matrices, it is of great importance to develop a novel matrix for matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) to qualitatively and quantitatively analyze small molecules. In this work, water-soluble fullerenol C₆₀(OH)_24-26 was selected as a MALDI matrix for the analysis of low-molecular-weight compounds in consideration of optical absorption property, water solubility and stability. Compared with the traditional matrices, fullerenol demonstrated lower background interference and stronger peak intensity. In addition, the hydrophilic fullerenol could avoid the heterogeneous crystallization in sample preparation, increase the reproducibility and sensitivity of MALDI-MS, and ameliorate quantitative analysis of small molecules. With saccharin as model analyte, quantitative analysis was carried out using fullerenol as matrix. The results demonstrated satisfying reproducibility and good tolerance to salt. The limit-of-detection of the quantitative analysis was as low as 4 pmol, and the linear range is 1-100 μg mL^-1 with R² greater than 0.99. The analytical results also showed excellent precision and accuracy, low matrix effect and good recovery rate. Fullerenol as a potential matrix was further validated in the quantification of saccharin sodium in different real food samples, such as nuts and drinks. This work not only confirms the potential of fullerenol for the quantitative analysis in food field, but also provides a new technique for rapid analysis of small molecules.

Clinical, molecular and glycophenotype insights in SLC39A8-CDG

BACKGROUND

SLC39A8, a gene located on chromosome 4q24, encodes for the manganese (Mn) transporter ZIP8 and its detrimental variants cause a type 2 congenital disorder of glycosylation (CDG). The common SLC39A8 missense variant A391T is associated with increased risk for multiple neurological and systemic disorders and with decreased serum Mn. Patients with SLC39A8-CDG present with different clinical and neuroradiological features linked to variable transferrin glycosylation profile. Galactose and Mn supplementation therapy results in the biochemical and clinical amelioration of treated patients.

RESULTS

Here, we report clinical manifestations, neuroradiological features and glycophenotypes associated with novel SLC39A8 variants (c.1048G > A; p.Gly350Arg and c.131C > G; p.Ser44Trp) in two siblings of the same Italian family. Furthermore, we describe a third patient with overlapping clinical features harbouring the homozygous missense variant A391T. The clinical phenotype of the three patients was characterized by severe developmental disability, dystonic postural pattern and dyskinesia with a more severe progression of the disease in the two affected siblings. Neuroimaging showed a Leigh syndrome-like pattern involving the basal ganglia, thalami and white matter. In the two siblings, atrophic cerebral and cerebellum changes consistent with SLC39A8-CDG were detected as well. Serum transferrin isoelectric focusing (IEF) yielded variable results with slight increase of trisialotransferrin isoforms or even normal pattern. MALDI-MS showed the presence of hypogalactosylated transferrin N-glycans, spontaneously decreasing during the disease course, only in one affected sibling. Total serum N-glycome depicted a distinct pattern for the three patients, with increased levels of undergalactosylated and undersialylated precursors of fully sialylated biantennary glycans, including the monosialo-monogalacto-biantennary species A2G1S1.

CONCLUSIONS

Clinical, MRI and glycosylation features of patients are consistent with SLC39A8-CDG. We document two novel variants associated with Leigh syndrome-like disease presentation of SLC39A8-CDG. We show, for the first time, a severe neurological phenotype overlapping with that described for SLC39A8-CDG in association with the homozygous A391T missense variant. We observed a spontaneous amelioration of transferrin N-glycome, highlighting the efficacy of MS-based serum glycomics as auxiliary tool for the diagnosis and clinical management of therapy response in patients with SLC39A8-CDG. Further studies are needed to analyse more in depth the influence of SLC39A8 variants, including the common missense variant, on the expression and function of ZIP8 protein, and their impact on clinical, biochemical and neuroradiological features.

Mineralization of 3D Osteogenic Model Based on Gelatin-Dextran Hybrid Hydrogel Scaffold Bioengineered with Mesenchymal Stromal Cells: A Multiparametric Evaluation

Gelatin–dextran hydrogel scaffolds (G-PEG-Dx) were evaluated for their ability to activate the bone marrow human mesenchymal stromal cells (BM-hMSCs) towards mineralization. G-PEG-Dx1 and G-PEG-Dx2, with identical composition but different architecture, were seeded with BM-hMSCs in presence of fetal bovine serum or human platelet lysate (hPL) with or without osteogenic medium. G-PEG-Dx1, characterized by a lower degree of crosslinking and larger pores, was able to induce a better cell colonization than G-PEG-Dx2. At day 28, G-PEG-Dx2, with hPL and osteogenic factors, was more efficient than G-PEG-Dx1 in inducing mineralization. Scanning electron microscopy (SEM) and Raman spectroscopy showed that extracellular matrix produced by BM-hMSCs and calcium-positive mineralization were present along the backbone of the G-PEG-Dx2, even though it was colonized to a lesser degree by hMSCs than G-PEG-Dx1. These findings were confirmed by matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI), detecting distinct lipidomic signatures that were associated with the different degree of scaffold mineralization. Our data show that the architecture and morphology of G-PEG-Dx2 is determinant and better than that of G-PEG-Dx1 in promoting a faster mineralization, suggesting a more favorable and active role for improving bone repair.

Enhanced and Selective MALDI-MS Detection of Peptides via the Nanomaterial-Dependent Coffee Ring Effect

Nanomaterials have been explored as alternative matrices in MALDI-MS to overcome some of the limitations of conventional matrices. Recently, we demonstrated a new means by which nanomaterials can improve peptide ionization and detection in MALDI-MS analyses by exploiting the tendency of nanomaterials to form "coffee rings" upon drying from liquids. In the current work, we investigate how nanomaterial size and composition affect the signal enhancement of peptides through the coffee-ring effect. From studies of eight different types of nanomaterials ranging in size and composition, we find that most nanomaterials can provide signal enhancement ranging from 2- to 10-fold for individual peptides, as long as a coffee ring is formed. However, when a mixture of peptides is present in a sample, the signal enhancement is the greatest for peptides whose net charge is complementary to the nanomaterial's surface charge. These results suggest that careful design of NM surface properties could allow for selective, enhanced MALDI-MS detection of specific peptides in complex mixtures.

Visualization Analysis of Glyceollin Production in Germinating Soybeans by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometric Imaging Technique

Apart from the physiological functions of soybean phytoalexins, the production sites in soybeans remain unknown. In this study, the dynamic production of phytoalexins, glyceollins, in germinating soybeans inoculated with Aspergillus oryzae was visually investigated using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) imaging. During a 3-day sensitization using a fungus, glyceollins I-III were produced in germinating soybeans (from 0.03 mg/g for glyceollin III to 0.96 mg/g for glyceollin I). Imaging analysis provided visual evidence that glyceollins were produced only in the regions of seed coat and germinated root of the soybeans, while no production was observed in other regions, including the cotyledons. In contrast, their precursor, isoflavone, was distributed throughout the soybean. The evidence that the inoculation of the inactivated fungi also caused glyceollin production at the seed coat led us to speculate that glyceollins could be produced in the region of soybean attached to the fungus body.

Selective Capture and Identification of Methicillin-Resistant Staphylococcus aureus by Combining Aptamer-Modified Magnetic Nanoparticles and Mass Spectrometry

A nucleic acid aptamer that specifically recognizes methicillin-resistant Staphylococcus aureus (MRSA) has been immobilized on magnetic nanoparticles to capture the target bacteria prior to mass spectrometry analysis. After the MRSA species were captured, they were further eluted from the nanoparticles and identified using matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). The combination of aptamer-based capture/enrichment and MS analysis of microorganisms took advantage of the selectivity of both techniques and should enhance the accuracy of MRSA identification. The capture and elution efficiencies for MRSA were optimized by examining factors such as incubation time, temperature, and elution solvents. The aptamer-modified magnetic nanoparticles showed a capture rate of more than 90% under the optimized condition, whereas the capture rates were less than 11% for non-target bacteria. The as-prepared nanoparticles exhibited only a 5% decrease in the capture rate and a 9% decrease in the elution rate after 10 successive cycles of utilization. Most importantly, the aptamer-modified nanoparticles revealed an excellent selectivity towards MRSA in bacterial mixtures. The capture of MRSA at a concentration of 10² CFU/mL remained at a good percentage of 82% even when the other two species were at 10⁴ times higher concentration (10⁶ CFU/mL). Further, the eluted MRSA bacteria were successfully identified using MALDI mass spectrometry.

Investigation of the lipidomic changes in differentiated glioblastoma cells after drug treatment using MALDI-MS

Lipids differences between tumor and normal tissue have been proved to be of diagnostic and therapeutic significance. The research of lipidomics in tumor is more and more important. Mass spectrometry like matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS) can be more convenient and informative for lipids researching in biological and clinical researches. Most of malignant tumors like glioblastoma are characterized by incomplete differentiation, so differentiation therapy has made important progress in tumor treatment. Lipid profiles changes after therapy are worthy investigating. In our study, glioblastoma cell line U87-MG cells were treated by inducers of sodium phenylbutyrate (SPB) and all-trans retinoic acid (ATRA). The changes in lipids on cell membrane were profiled by MALDI-MS. The differentiation degree was assessed by cell proliferation, cell cycle, morphology and protein expression before MALDI-MS analysis. Comparing the inducer treated and untreated U87-MG cells, reduced proliferation rate, blocked cell cycle, benign nucleus morphology and changed expression of protein CD133 and glial fibrillary acidic protein (GFAP), were found after drug treatment. Moreover, the lipids of cell membrane presented distinguished differences in the drug treated cells. Most of the glycerophosphocholines (PC) with an increasing abundance are unsaturated PCs (PC (38:1), 816 m/z; PC (36:1), 788 m/z; PC (31:1), 725 m/z), and those decreasing are saturated PCs (PC (32:0), 734 m/z). These results provide the lipidomic differentiation which may be a significant guidance for evaluating the therapeutic effect of tumor therapy.

Bioactive Compounds in Waste By-Products from Olive Oil Production: Applications and Structural Characterization by Mass Spectrometry Techniques

In recent years, a remarkable increase in olive oil consumption has occurred worldwide, favoured by its organoleptic properties and the growing awareness of its health benefits. Currently, olive oil production represents an important economic income for Mediterranean countries, where roughly 98% of the world production is located. Both the cultivation of olive trees and the production of industrial and table olive oil generate huge amounts of solid wastes and dark liquid effluents, including olive leaves and pomace and olive oil mill wastewaters. Besides representing an economic problem for producers, these by-products also pose serious environmental concerns, thus their partial reuse, like that of all agronomical production residues, represents a goal to pursue. This aspect is particularly important since the cited by-products are rich in bioactive compounds, which, once extracted, may represent ingredients with remarkable added value for food, cosmetic and nutraceutical industries. Indeed, they contain considerable amounts of valuable organic acids, carbohydrates, proteins, fibers, and above all, phenolic compounds, that are variably distributed among the different wastes, depending on the employed production process of olive oils and table olives and agronomical practices. Yet, extraction and recovery of bioactive components from selected by-products constitute a critical issue for their rational valorization and detailed identification and quantification are mandatory. The most used analytical methods adopted to identify and quantify bioactive compounds in olive oil by-products are based on the coupling between gas- (GC) or liquid chromatography (LC) and mass spectrometry (MS), with MS being the most useful and successful detection tool for providing structural information. Without derivatization, LC-MS with electrospray (ESI) or atmospheric pressure chemical (APCI) ionization sources has become one of the most relevant and versatile instrumental platforms for identifying phenolic bioactive compounds. In this review, the major LC-MS accomplishments reported in the literature over the last two decades to investigate olive oil processing by-products, specifically olive leaves and pomace and olive oil mill wastewaters, are described, focusing on phenolics and related compounds.

A concise discussion on the potential spectral tools for the rapid COVID-19 detection

Developing robust methods to detect the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a causative agent for the current global health pandemic, is an exciting area of research. Nevertheless, the currently used conventional reverse transcription-polymerase chain reaction (RT-PCR) technique in COVID-19 detection endures with some inevitable limitations. Consequently, the establishment of rapid diagnostic tools and quick isolation of infected patients is highly essential. Furthermore, the requirement of point-of-care testing is the need of the hour. Considering this, we have provided a brief review of the use of very recently reported robust spectral tools for rapid COVID-19 detection. The spectral tools include, colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), with the admittance of principal component analysis (PCA) and machine learning (ML) for meeting the high-throughput and fool-proof platforms for the detection of SARS-CoV-2, are reviewed. Recently, these techniques have been readily applied to screen a large number of suspected patients within a short period and they demonstrated higher sensitivity for the detection of COVID-19 patients from unaffected human subjects.

Experimental and Computational Study of Aminoacridines as MALDI(-)-MS Matrix Materials for the Analysis of Complex Samples

Monoaminoacridines (1-, 2-, 3-, 4-, and 9-aminoacridine) were studied for suitability as matrices in the negative ion mode matrix-assisted laser desorption/ionization mass spectrometry (MALDI(-)-MS) analysis of various samples. This is the first study to examine 1-, 2-, and 4-aminoacridine as potential matrix material candidates for MALDI(-)-MS. In addition, spectral (UV-Vis absorption and fluorescence), proton transfer-related (basicity and autoprotolysis), and crystallization properties of these compounds were characterized experimentally and/or computationally. For testing the capabilities of these aminoacridines as matrix materials, four samples related to cultural heritage materials-stearic acid, colophony resin, dyer's madder dye, and a resinous case-study sample from a shipwreck-were analyzed with MALDI(-)-MS. A novel algorithm (implemented as an executable Python script) for MS data analysis was developed to compare the five matrix materials and to help mass spectrometrists rapidly identify peaks originating from the sample and matrix material. It was determined that all five of the studied aminoacridines can successfully be used as matrix materials in MALDI(-)-MS analysis. As an interesting finding, in several cases, the best mass spectra were obtained by using a relatively small amount of matrix material mixed with an excess amount of sample. 3- and 4-aminoacridine outperformed the other aminoacridines in the ease of obtaining acceptable spectra, average number of ions identified in the mass spectra, and low dependence of the sample-to-matrix mass ratio on experimental results.

Identification of peptides in blood following oral administration of β-conglycinin to Wistar rats

In this study, β-conglycinin (100 mg/kg) was orally administered to Wistar rats in order to identify peptides that may be derived from the protein in the blood. Plasma samples taken from the tail vein up to 8 h after administration were analyzed by matrix-assisted laser desorption/ionization (MALDI) and liquid chromatography-time-of-flight (LC-TOF) mass spectrometry (MS). In total, 126 signals were detected by MALDI-MS. Among the signals, nine oligopeptides (SEL, KGPL, SILGA, DSEL, GDANI, SYFV, CLQSC, GEQPRPF, and LVINEGDA) were successfully identified as β-conglycinin-derived peptides by LC-TOF/MS at a plasma concentration of 0.75-756 pmol/mL. The results demonstrated that β-conglycinin could be the dietary source protein for the oligopeptides produced prior to entering the circulating bloodstream of rats.

A procedure for method development and protein binding ratio as the indicator of sensitivity with anticancer agents on MALDI mass spectrometry imaging

The concentration and distribution of a drug and its metabolites in tissues are key factors for elucidating both drug efficacy and toxicity in drug development. In this study we developed a pharamaco-imaging procedure for 12 agents and investigated the relationship between the properties of target compounds and the sensitivities of detection in matrix-assisted laser desorption/ionization-mass spectrometer imaging (MALDI-MSI). We prepared mock samples with mouse liver homogenates diluted with gelatin solution, limit of detection concentrations of each compound was confirmed. The correlation was evaluated between the intensities of mass signals obtained in MALDI-MSI with each test compound (the intensities of the test compounds) at a consistent concentration and the properties of each test compound. The liver homogenate diluted with gelatin solution showed easier handling and lower coefficients of variation than did liver homogenate only, and can be used as a good surrogate matrix. Based on the analysis of 12 agents, the protein binding ratios showed significant correlation to the detection sensitivities. We presented a procedure for standardization of pharmaco-imaging method development with an in-tissue method using MALDI-MS. Our results indicated the correlation between test compound's sensitivity and their protein binding ratios in plasma or serum.

Ultra-high-throughput SPE-MALDI workflow: Blueprint for efficient purification and screening of peptide libraries

At the forefront of synthetic endeavors in the pharmaceutical industry, including drug discovery and high-throughput screening, timelines are tight and large quantities of pure chemical targets are rarely available. In this regard, the development of novel and increasingly challenging chemistries requires a commensurate level of innovation to develop reliable analytical assays and purification workflows with rapid turnaround that enables accelerated pharmacological evaluation. A small-scale automation platform enabling high-throughput analysis and purification to streamline the selection of candidate leads would be a transformative advance. Herein, we introduce an automation-friendly solid-phase extraction-matrix-assisted laser desorption/ionization (SPE-MALDI) platform applied to the high-throughput purification and analysis of peptide libraries. This advance enabled us to purify peptides from microgram levels in less than a day with results comparable to traditional high-performance liquid chromatography-diode array detection-mass spectrometry (HPLC-DAD-MS).

Quantitative MALDI-MS assay of steroid hormones in plasma based on hydroxylamine derivatization

Measuring the concentrations of steroid hormones in plasma is critical for understanding their role in various vital physiological processes. The detection of underivatized steroid hormones in biofluids through mass spectrometry (MS) is typically hindered by low ionization efficiency. We described a novel matrix-assisted laser desorption/ionization-MS (MALDI-MS) approach based on hydroxylamine derivatization (HA-D) to analyze low-concentration steroid hormones in plasma. The ketonic carbonyl group containing steroid hormones could be derivatized using HA to form oxime derivatives, which considerably enhanced the MS sensitivity for detecting steroid hormones. By using the optimized conditions, estrone (E1), testosterone (T), and progesterone (Prog), could be simultaneously quantified in plasma with a limit of detection (LOD) from 0.019 to 0.031 nM, recoveries from 86% to 108%, and coefficient of variation (CV%) from 4.59% to 11.90%. HA-D/MALDI-MS exhibited higher sensitivity than those using Girard T (GT). To establish potential utility of our method, we characterized fatty liver patient plasmas to demonstrate that the HA-D/MALDI-MS procedure could generate quantitative results comparable to the current clinical liquid chromatography-electrospray ionization tandem MS (LC-ESI MS/MS) method. This approach facilitates the rapid and accurate characterization of plasma hormones, and renders the MALDI-MS approach for steroid hormones more adaptable for clinical research and use.

Ionic matrices for matrix-assisted laser desorption/ionization mass spectrometry analysis of microRNA biomarkers

The use of ionic matrices (IMs) was evaluated as an alternative to conventional matrices to analyze microRNAs (miRNAs) by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). 2, 4, 6-Trihydroxyacetophenone (THAP), 6-aza-2-thiothymine (ATT) and 3-hydroxypicolinic acid (3-HPA) and their IMs with pyridine (PYR) and butylamine (BA) were studied to analyze a standard mixture of miRNAs: miR-21, let-7g and iso-miR-16. Among all the studied matrices, ATT-PYR at 75 mg/mL in acetonitrile (MeCN):H₂O (50:50, v/v) was selected as the optimal. Furthermore, addition of ammonium citrate dibasic (AC) as signal enhancer was mandatory to obtain an appropriate miRNA detection. ATT-PYR provided the best sensitivity, with limit of detection (LOD) up to 5 nM (equivalent to 1 fmol in the spot) and excellent spot-to-spot repeatability due to the improved homogeneity of the spots compared to the conventional matrices. The applicability of the established method to direct, multiplex and untargeted analysis of miRNAs in serum samples was also investigated.

A robust glycan labeling strategy using a new cationic hydrazide tag for MALDI-MS-based rapid and sensitive glycomics analysis

Chemical derivatization of glycans is a common strategy to increase the analytical performance of MALDI-MS-based glycan profiling techniques. Hydrazide, one of the most popular tags, offers important advantages including allowing purification-free procedures. Several hydrazides have thus been used for glycomics combined with an on-target strategy to further simplify the analytical procedures. Usually, gentle heating and mildly acidic conditions with somewhat long reaction times are needed for these hydrazide derivatizations to reach a high reaction efficiency, which makes the current hydrazide tags not yet perfectly conducive to high-throughput analysis. To further optimize these hydrazide tags for high-throughput analysis, based on the structure of a reported hydrazide and the theoretical calculations, a new cationic hydrazide tag, 4-(hydrazinecarbonyl)-N,N,N-trimethylbenzenaminium (HTMBA), was designed, synthesized and tested in this work. HTMBA could completely derivatize glycans at room temperature in several seconds under very mildly acidic conditions (<3% acetic acid). A 19-fold enhancement in the signal intensity was obtained without interference from alkali adduct ions in the MALDI-MS detection of HTMBA-labeled maltoheptaose. To broaden the applicability of HTMBA, an HTMBA on-target derivatization (HOD) strategy was developed and fully validated with maltoheptaose and RNase B, and the method showed a good repeatability and stability. Finally, the HOD strategy was successfully applied to serum samples, 44 glycans in human serum were detected, and the O-acetylation information of sialic acid in horse serum was preserved. These results showed that the HOD strategy was suitable for the MS-based rapid analysis of all glycoforms in complex biological samples.

Mass spectrometry imaging reveals glycine distribution in the developing and adult mouse brain

Glycine is an important amino acid in the central nervous system. The aberrant conditions of glycine concentrations cause sever neurological disorders, such as nonketotic-hyperglycinemia (NKH), also known as glycine encephalopathy. Therefore, a better understanding of its relative abundance and distribution in the developing and adult brains would provide insights into the pathogeneses of this kind of disorders. Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) imaging has been used for direct molecular-specific compound detection, distribution mapping, and identifying molecular species in tissue sections. Although a few reports have already shown the imaging of glycine using MALDI-MS in the adult mouse brain, they lack detailed neuroanatomical and developmental evaluations. We, thus, investigated the detailed distribution and abundance of glycine not only in the adult mouse brain but also in the developing mouse brain using this technique. In both brains, we detected derivatized glycine throughout the mouse brain. Interestingly, in both brains, derivatized glycine was abundantly detected in the brain stem. The other areas showed relatively lower signal intensities. As many model mice are used for glycine-related diseases, MALDI-MS is a suitable technique to analyze the pathogenesis of these diseases.

Fast saccharide mapping method for quality consistency evaluation of commercial xylooligosaccharides collected in China

Due to the extensive use of xylooligosaccharides (XOS) as functional food ingredients, many inferior goods and even adulterants are generally found in the market, which may pose a health hazard to certain populations. Chromatography method such as high-performance liquid chromatography (HPLC) and high-performance thin-layer chromatography (HPTLC) is traditionally applied for the quality analysis of XOS. However, it is time consuming due to the prolonged separation and pre- or post- derivatization procedure. In this study, a fast saccharide mapping method based on matrix-assisted laser desorption/time-of-flight mass spectrometry (MALDI-TOF-MS) was developed for the quality consistency analysis of 22 batches of XOS collected from different manufacturers in China. The time needed for saccharides analysis using MALDI-MS was less than 30 min for one plate, at least 6 times faster than that by the traditional HPTLC chromatography method. In addition, MALDI-MS possessed higher resolution for XOS with DP4-DP7 based on the difference of m/z, which is hardly separated using HPTLC. The results showed that XOS were present only in samples XY01-XY11, samples XY12-XY14 only consisted of hex oligosaccharides, and samples XY15-XY22 were free of oligosaccharides. These indicate that the quality consistency of XOS products in the China market was poor, which should be carefully investigated.

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Fast saccharide mapping method was developed based on MADLI-TOF-MS.

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Quality consistency of commercial xylooligosaccharides collected in China was evaluated.

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Glycosidic linkage analysis was also used for identification of xylooligosaccharides.

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Fifty percent of commercial xylooligosaccharides are mislabeled.