Recent methodological advances in MALDI mass spectrometry

Decoding Sugars: Mass Spectrometric Advances in the Analysis of the Sugar Alphabet

Monosaccharides play a central role in metabolic networks and in the biosynthesis of glycomolecules, which perform essential functions across all domains of life. Thus, identifying and quantifying these building blocks is crucial in both research and industry. Routine methods have been established to facilitate the analysis of common monosaccharides. However, despite the presence of common metabolites, most organisms utilize distinct sets of monosaccharides and derivatives. These molecules therefore display a large diversity, potentially numbering in the hundreds or thousands, with many still unknown. This complexity presents significant challenges in the study of glycomolecules, particularly in microbes, including pathogens and those with the potential to serve as novel model organisms. This review discusses mass spectrometric techniques for the isomer-sensitive analysis of monosaccharides, their derivatives, and activated forms. Although mass spectrometry allows for untargeted analysis and sensitive detection in complex matrices, the presence of stereoisomers and extensive modifications necessitates the integration of advanced chromatographic, electrophoretic, ion mobility, or ion spectroscopic methods. Furthermore, stable-isotope incorporation studies are critical in elucidating biosynthetic routes in novel organisms.

Valorization of Grape Pomace: A Review of Phenolic Composition, Bioactivity, and Therapeutic Potential

Vitis vinifera L., commonly known as grapes, is one of the most widely cultivated crops worldwide, with over 80% used for wine production. However, the winemaking process generates substantial residues, including grape pomace (GP), wine lees, and wastewater, which can pose significant environmental and economic challenges. Among these, GP stands out not only as a waste product but also as a rich source of polyphenols-bioactive compounds with recognized antioxidant and anti-inflammatory properties. Recent advancements have expanded the application of GP-derived extracts, particularly in the health and food industries, due to their potent bioactive properties. This review provides a comprehensive overview of the valorization of GP, focusing on its phenolic composition and therapeutic potential. It evokes innovative, environmentally friendly extraction techniques and integrated methods for the chemical analysis of these valuable compounds. Additionally, the health benefits of GP polyphenols are explored, with recent experimental findings examining their metabolism and highlighting the key role of gut microbiota in these processes. These insights contribute to a deeper understanding of the biological activity of GP extracts and underscore their growing significance as a high-added-value product. By illustrating how winemaking by-products can be transformed into natural therapeutic agents, this review emphasizes the importance of sustainable development and eco-friendly waste management practices, significantly contributing to the advancement of a circular economy.

Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Applications for Metabolomics

Metabolomics is an interdisciplinary field that aims to study all metabolites < 1500 Da that are ubiquitously found within all organisms. Metabolomics is experiencing exponential growth and commonly relies on high-resolution mass spectrometry (HRMS). Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) is a form of HRMS that is particularly well suited for metabolomics research due to its exceptionally high resolution (105-106) and sensitivity with a mass accuracy in parts per billion (ppb). In this regard, FT-ICR-MS can provide valuable insights into the metabolomics analysis of complex biological systems due to unique capabilities such as the easy separation of isobaric and isomeric species, isotopic fine structure analysis, spatial resolution of metabolites in cells and tissues, and a high confidence (<1 ppm mass error) in metabolite identification. Alternatively, the large and complex data sets, long acquisition times, high cost, and limited access mainly through national mass spectrometry facilities may impede the routine adoption of FT-ICR-MS by metabolomics researchers. This review examines recent applications of FT-ICR-MS metabolomics in the search for clinical and non-human biomarkers; for the analysis of food, beverage, and environmental samples; and for the high-resolution imaging of tissues and other biological samples. We provide recent examples of metabolomics studies that highlight the advantages of FT-ICR-MS for the detailed and reliable characterization of the metabolome. Additionally, we offer some practical considerations for implementing FT-ICR-MS into a research program by providing a list of FT-ICR-MS facilities and by identifying different high-throughput interfaces, varieties of sample types, analysis methods (e.g., van Krevelen diagrams, Kendrick mass defect plot, etc.), and sample preparation and handling protocols used in FT-ICR-MS experiments. Overall, FT-ICR-MS holds great promise as a vital research tool for advancing metabolomics investigations.

Characterization of Synthetic Peptides by Mass Spectrometry

In the quality control of synthetic peptides, mass spectroscopy (MS) serves as an optimal method for evaluating authenticity and integrity. Typically, the sequence of a synthetic peptide is already established, thereby directing the focus of analysis towards validating its identity and purity. This chapter outlines straightforward methodologies for conducting MS analyses specifically tailored for synthetic peptides.

Development of mass spectrometry imaging techniques and its latest applications

Mass spectrometry imaging (MSI) is a novel molecular imaging technology that collects molecular information from the surface of samples in situ. The spatial distribution and relative content of various compounds can be visualized simultaneously with high spatial resolution. The prominent advantages of MSI promote the active development of ionization technology and its broader applications in diverse fields. This article first gives a brief introduction to the vital parts of the processes during MSI. On this basis, provides a comprehensive overview of the most relevant MS-based imaging techniques from their mechanisms, pros and cons, and applications. In addition, a critical issue in MSI, matrix effects is also discussed. Then, the representative applications of MSI in biological, forensic, and environmental fields in the past 5 years have been summarized, with a focus on various types of analytes (e.g., proteins, lipids, polymers, etc.) Finally, the challenges and further perspectives of MSI are proposed and concluded.

In situ analysis of volatile oil in Angelica sinensis roots by fluorescence imaging combined with mass spectrometry imaging

In this study, the spatial distribution and accumulation dynamics of volatile oil in Angelica sinensis roots was realized by fluorescence imaging combined with mass spectrometry imaging. The laser scanning confocal microscopy was used to determine the optimal excitation wavelength and the fluorescent stability of volatile oil in the sections of Angelica sinensis roots. The results demonstrated that 488 nm was the most suitable excitation wavelength for the identification and quantitative analysis of volatile oil. It was observed that volatile oil accumulated in the oil chamber of the phelloderm and secondary phloem, and the oil canal of the secondary xylem. The results also indicated that there were differences in content during different periods. Furthermore, the MALDI-TOF-MSI technology was used to study the spatial distribution and compare the chemical compositions of different parts of Angelica sinensis roots during the harvest period. A total of 55, 49, 50 and 30 compounds were identified from the head, body, tail of the root and root bark, respectively. The spatial distribution of phthalides, organic acids and other compounds were revealed in Angelica sinensis roots. The method developed in this study could be used for the in situ analysis of volatile oil in Angelica sinensis roots.

Advances in Mass Spectrometry-Based Single Cell Analysis

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

Recent advances in mass spectrometry analysis of neuropeptides

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

Desorption and ablation regimes in UV-MALDI: the critical fluence

Although MALDI is a widely used technique, there is so far no theoretical description able to reproduce some critical aspects of the experimental results. For example, there is experimental as well as theoretical controversy regarding the minimum laser fluence, i.e., the so-called fluence threshold (F T), required to evaporate a sample. Furthermore, although the different processes involved in ion production have been the focus of many investigations, the fact is that the primary process for ion formation in MALDI is not desorption but ablation. In this work, we present a new phenomenological approach for understanding MALDI results based on a simple, but physically intuitive, idea consisting of limiting the laser-matter interaction process to three layers. This description allows us to consider the different processes that dominate ion formation, i.e., heat dissipation, as well as the different existing regimes. Concretely, we present the results for three different matrices, i.e., DHB, ferulic acid (FA) and α-cyano-4-hydroxycinnamic acid (CHCA), in the limit of low fluence. The simulations we carried out show great qualitative and pseudo-quantitative agreement with the experimental results. Also, based on the simulation results, it is possible to distinguish clearly between the two dominant regimes, i.e., desorption and ablation, and it is possible, therefore, to estimate the critical fluence (F C) that defines the transition from one regime to another.

Measurement of kinetic isotope effects on peptide hydroxylation using MALDI-MS

Primary kinetic isotope effects (KIEs) provide unique insight into enzymatic reactions, as they can reveal rate-limiting steps and detailed chemical mechanisms. HIF hydroxylases, part of a family of 2-oxoglutarate (2OG) oxygenases are central to the regulation of many crucial biological processes through O2-sensing, but present a challenge to monitor due to the large size of the protein substrate and the similarity between native and hydroxylated substrate. MALDI-TOF MS is a convenient tool to measure peptide masses, which can also be used to measure the discontinuous kinetics of peptide hydroxylation for Factor Inhibiting HIF (FIH). Using this technique, rate data can be observed from the mole-fraction of CTAD and CTAD-OH in small volumes, allowing noncompetitive H/D KIEs to be measured. Slow dCTAD substrate leads to extensive uncoupling of O2 consumption from peptide hydroxylation, leading to enzyme autohydroxylation, which is observed using UV-vis spectroscopy. Simultaneously measuring both the normal product, CTAD-OH, and the uncoupled product, autohydroxylated enzyme, the KIE on the microscopic step of hydrogen atom transfer (HAT) can be estimated. MALDI-MS analysis is a strong method for monitoring reactions that hydroxylate peptides, and can be generalized to other similar reactions, and simultaneous kinetic detection of branched products can provide valuable insight on microscopic KIEs at intermediate mechanistic steps.

A Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Assay Identifies Nilotinib as an Inhibitor of Inflammation in Acute Myeloid Leukemia

Inflammatory responses are important in cancer, particularly in the context of monocyte-rich aggressive myeloid neoplasm. We developed a label-free cellular phenotypic drug discovery assay to identify anti-inflammatory drugs in human monocytes derived from acute myeloid leukemia (AML), by tracking several features ionizing from only 2500 cells using matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry. A proof-of-concept screen showed that the BCR-ABL inhibitor nilotinib, but not the structurally similar imatinib, blocks inflammatory responses. In order to identify the cellular (off-)targets of nilotinib, we performed thermal proteome profiling (TPP). Unlike imatinib, nilotinib and other later-generation BCR-ABL inhibitors bind to p38α and inhibit the p38α-MK2/3 signaling axis, which suppressed pro-inflammatory cytokine expression, cell adhesion, and innate immunity markers in activated monocytes derived from AML. Thus, our study provides a tool for the discovery of new anti-inflammatory drugs, which could contribute to the treatment of inflammation in myeloid neoplasms and other diseases.

Nanoporous Substrates with Molecular-Level Perfluoroalkyl/Alkylamide Surface for Laser Desorption/Ionization Mass Spectrometry of Small Proteins

The rapid detection of biomolecules greatly contributes to health management, clinical diagnosis, and prevention of diseases. Mass spectrometry (MS) is effective for detecting and analyzing various molecules at high throughput. However, there are problems with the MS analysis of biological samples, including complicated separation operations and essential pretreatments. In this study, a nanostructured organosilica substrate for laser desorption/ionization mass spectrometry (LDI-MS) is designed and synthesized to detect peptides and small proteins efficiently and rapidly. The surface functionality of the substrate is tuned by perfluoroalkyl/alkylamide groups mixed at a molecular level. This contributes to both lowering the surface free energy and introducing weak anchoring sites for peptides and proteins. Analyte molecules applied onto the substrate are homogeneously distributed and readily desorbed by the laser irradiation. The organosilica substrate enables the efficient LDI of various compounds, including peptides, small proteins, phospholipids, and drugs. An amyloid β protein fragment, which is known as a biomarker for Alzheimer's disease, is detectable at 0.05 fmol μL^-1. The detection of the amyloid β at 0.2 fmol μL^-1 is also confirmed in the presence of blood components. Nanostructured organosilica substrates incorporating a molecular-level surface design have the potential to enable easy detection of a wide range of biomolecules.

Life sciences and mass spectrometry: some personal reflections

Molecular analysis of biological systems by mass spectrometry was in focus of technological developments in the second half of the 20th century, in which the issues of chemical identification of high molecular diversity by biophysical instrumental methods appeared as a mission impossible. By developing dialogs between researchers dealing with life sciences and medicine on one side and technology developers on the other, new horizons toward deciphering, identifying and quantifying of complex systems became a reality. Contributions toward this goal can be today considered as pioneering efforts delivered by a number of researchers, including generations of motivated students and associates.

Development of MALDI MS peptide array for thrombin inhibitor screening

The development of in situ methods for the analysis and visualization of enzyme activity is of paramount importance in drug discovery, research, and development. In this work, the functionalized and array patterned indium tin oxide (ITO) glass slides were fabricated by non-covalent immobilization of amphipathic phospholipid-tagged peptides encompassing the thrombin cleavage site on steric acid-modified ITO slides. The fabricated peptide arrays provide 60 spots per slide, and are compatible with matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) measurement, free matrix peak interference, and tolerance to repeated aqueous washing. The peptide arrays were used for the investigation of thrombin activity and screening for its potential inhibitors. The thrombin activity and its Michaelis-Menten constant (K_m) for immobilized peptide substrate was determined using developed MALDI MS peptide array. To investigate the applicability and effectiveness of peptide arrays, the anti-thrombin activity of grape seed proanthocyanidins with different degrees of polymerization (DP) was monitored and visualized. MALDI MS imaging results showed that the fractions of proanthocyanidins with the mean DP of 4.61-6.82 had good thrombin inhibitory activity and their half-maximal inhibitory concentration (IC₅₀) were below 10 μg/mL. Therefore, the developed peptide array is a reliable platform for the discovery of natural thrombin inhibitors.

MALDI Matrices for the Analysis of Low Molecular Weight Compounds: Rational Design, Challenges and Perspectives

The analysis of low molecular weight (LMW) compounds is of great interest to detect small pharmaceutical drugs rapidly and sensitively, or to trace and understand metabolic pathways. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) plays a central role in the analysis of high molecular weight (bio)molecules. However, its application for LMW compounds is restricted by spectral interferences in the low m/z region, which are produced by conventional organic matrices. Several strategies regarding sample preparation have been investigated to overcome this problem. A different rationale is centred on developing new matrices which not only meet the fundamental requirements of good absorption and high ionization efficiency, but are also vacuum stable and "MALDI silent", i. e., do not give matrix-related signals in the LMW area. This review gives an overview on the rational design strategies used to develop matrix systems for the analysis of LMW compounds, focusing on (i) the modification of well-known matrices, (ii) the search for high molecular weight matrices, (iii) the development of binary, hybrid and nanomaterial-based matrices, (iv) the advance of reactive matrices and (v) the progress made regarding matrices for negative or dual polarity mode.

Three-dimensional (3D) imaging of lipids in skin tissues with infrared matrix-assisted laser desorption electrospray ionization (MALDESI) mass spectrometry

Three-dimensional (3D) mass spectrometry imaging (MSI) has become a growing frontier as it has the potential to provide a 3D representation of analytes in a label-free, untargeted, and chemically specific manner. The most common 3D MSI is accomplished by the reconstruction of 2D MSI from serial cryosections; however, this presents significant challenges in image alignment and registration. An alternative method would be to sequentially image a sample by consecutive ablation events to create a 3D image. In this study, we describe the use of infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) in ablation-based 3D MSI for analyses of lipids within fresh frozen skin tissue. Depth resolution using different laser energy levels was explored with a confocal laser scanning microscope to establish the imaging parameters for skin. The lowest and highest laser energy level resulted in a depth resolution of 7 μm and 18 μm, respectively. A total of 594 lipids were putatively detected and detailed lipid profiles across different skin layers were revealed in a 56-layer 3D imaging experiment. Correlated with histological information, the skin structure was characterized with differential lipid distributions with a lateral resolution of 50 μm and a z resolution of 7 μm.

A nanoparticle co-matrix for multiple charging in matrix-assisted laser desorption ionization imaging of tissue

RATIONALE

A two-component matrix of 2-nitrophloroglucinol (2-NPG) and silica nanoparticles was used for matrix-assisted laser desorption ionization (MALDI) mass spectrometry imaging of high-charge-state biomolecules in tissue. Potential advantages include increased effective mass range and efficiency of fragmentation.

METHODS

A mixture of 2-NPG matrix and silica nanoparticles was applied to cyrosectioned 10 μm thick mouse brain tissue. The mixture was pipetted onto the tissue for profiling and sprayed for tissue imaging. MALDI images were obtained under high vacuum in a commercial time-of-flight mass spectrometer.

RESULTS

The combined 2-NPG and nanoparticle matrix produced highly charged ions from tissue with high-vacuum MALDI. Nanoparticles of 20, 70, 400, and 1000 nm in diameter were tested, the 20 nm particles producing the highest charge states. Images of mouse brain tissue obtained from highly charged ions show similar spatial localization.

CONCLUSIONS

The combined 2-NPG and nanoparticle matrix produces highly charged ions from tissue through a mechanism that may rely on the high surface area of the particles which can dry the tissue, and their ability to bind analyte molecules thereby assisting in crystal formation and production of multiply charged ions on laser irradiation.

Direct nanoimprinting of nanoporous organosilica films consisting of covalently crosslinked photofunctional frameworks

Nanoimprinting methods have been used widely to prepare various patterned or nanostructured thin films from inorganic or organic components. However, the accumulation of large functional aromatic groups in covalently crosslinked nanoimprints is challenging, due to the difficulty in controlling the fluidity and reactivity of the precursor films. In this work, nanoimprinting of naphthalimide-silica sol-gel films results in vertically oriented nanoporous structures consisting of covalently crosslinked UV-absorbing frameworks. The nanoimprinted films demonstrate potential as robust analytical substrates for laser desorption/ionization mass spectrometry (LDI-MS). The sol-gel polycondensation behavior of the precursors is examined using 29Si NMR spectroscopy to determine reaction conditions suitable for nanoimprinting. The inorganic-organic hybrid frameworks containing a high density of naphthalimide groups exhibit small volume shrinkage during the polycondensation reactions, which leads to desired nanoimprinting. Various bio-related compounds on the order of picomole to femtomole quantities are detectable by LDI-MS measurements using the nanoimprinted substrates. To improve their user-friendliness and signal intensity in LDI-MS analysis, the nanoimprinted substrates are patterned with surface-modified silica nanoparticles. The direct formation of surface nanostructures by nanoimprinting of functional organosilica films may open a new path to developing optically and electronically functional materials, thereby widening their utility.

Ultraviolet-Laser-Induced Electron Transfer from Peptides to an Oxidizing Matrix: Study of the First Step of MALDI In-Source Decay Mass Spectrometry

Although the N-H bond in peptide backbones is stronger than the C-H bond, hydrogen abstraction from the amide nitrogen is considered to be the initial step in the C_α-C bond cleavage of peptide backbones by matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD) when using an oxidizing matrix. MALDI-ISD induces C_α-C bond cleavage in most amino acid residues, whereas the N-terminal sides of proline (Pro) residues preferentially undergo peptide bond cleavage, which cannot be explained by the previously proposed mechanism involving hydrogen abstraction from peptides. To explain the whole MALDI-ISD process, electron abstraction from peptides by the oxidizing matrix is proposed as the initial step in the MALDI-ISD process. The electron abstraction occurs from either nitrogen or oxygen in the peptide backbone and induces the cleavage of both C_α-C and N-H bonds in most amino acid residues, except for those on the N-terminal sides of Pro residues. Electron abstraction from the Pro residues induces the cleavage of both peptide and C_α-C bonds, which is consistent with MALDI-ISD experimental results. The electron transfer from the peptide to the oxidizing matrix occurs simultaneously with the formation of matrix ions, which is considered to be the initial ion formation process in MALDI. The resultant peptide radical cation produces protonated and neutral molecules/radicals, which undergo subsequent ion-molecule reactions in the MALDI plume, finally yielding the ions that are observed in MALDI-ISD spectrum. As a result, the fragment ions formed by MALDI-ISD are observed as both positive and negative ions.

Emerging role of clinical mass spectrometry in pathology

Mass spectrometry-based assays have been increasingly implemented in various disciplines in clinical diagnostic laboratories for their combined advantages in multiplexing capacity and high analytical specificity and sensitivity. It is now routinely used in areas including reference methods development, therapeutic drug monitoring, toxicology, endocrinology, paediatrics, immunology and microbiology to identify and quantify biomolecules in a variety of biological specimens. As new ionisation methods, instrumentation and techniques are continuously being improved and developed, novel mass spectrometry-based clinical applications will emerge for areas such as proteomics, metabolomics, haematology and anatomical pathology. This review will summarise the general principles of mass spectrometry and specifically highlight current and future clinical applications in anatomical pathology.

Laser Desorption Combined with Laser Postionization for Mass Spectrometry

Lasers with pulse lengths from nanoseconds to femtoseconds and wavelengths from the mid-infrared to extreme ultraviolet (UV) have been used for desorption or ablation in mass spectrometry. Such laser sampling can often benefit from the addition of a second laser for postionization of neutrals. The advantages offered by laser postionization include the ability to forego matrix application, high lateral resolution, decoupling of ionization from desorption, improved analysis of electrically insulating samples, and potential for high sensitivity and depth profiling while minimizing differential detection. A description of postionization by vacuum UV radiation is followed by a consideration of multiphoton, short pulse, and other postionization strategies. The impacts of laser pulse length and wavelength are considered for laser desorption or laser ablation at low pressures. Atomic and molecular analysis via direct laser desorption/ionization using near-infrared ultrashort pulses is described. Finally, the postionization of clusters, the role of gaseous collisions, sampling at ambient pressure, atmospheric pressure photoionization, and the addition of UV postionization to MALDI are considered.

Mass Spectrometry for Proteomics and Recent Developments in ESI, MALDI and other Ionization Methodologies

Background:

Mass spectrometry is a tool used in analytical chemistry to identify components in a chemical compound and it is of tremendous importance in the field of biology for high throughput analysis of biomolecules, among which protein is of great interest.

Objective:

Advancement in proteomics based on mass spectrometry has led the way to quantify multiple protein complexes, and proteins interactions with DNA/RNA or other chemical compounds which is a breakthrough in the field of bioinformatics.

Methods:

Many new technologies have been introduced in electrospray ionization (ESI) and Matrixassisted Laser Desorption/Ionization (MALDI) techniques which have enhanced sensitivity, resolution and many other key features for the characterization of proteins.

Results:

The advent of ambient mass spectrometry and its different versions like Desorption Electrospray Ionization (DESI), DART and ELDI has brought a huge revolution in proteomics research. Different imaging techniques are also introduced in MS to map proteins and other significant biomolecules. These drastic developments have paved the way to analyze large proteins of >200kDa easily.

Conclusion:

Here, we discuss the recent advancement in mass spectrometry, which is of great importance and it could lead us to further deep analysis of the molecules from different perspectives and further advancement in these techniques will enable us to find better ways for prediction of molecules and their behavioral properties.

Piezoelectric matrix-assisted ionization

We have developed a new actuation method for matrix-assisted ionization with good temporal and spatial resolution using piezoelectric cantilever. A strike from the piezoelectric bimorph cantilever on a thin metal foil was used to remove materials deposited on the opposite side facing the mass spectrometer inlet. Highly charged ions of peptides and proteins were generated from dried droplet deposits and sampled into the inlet of the mass spectrometer. A lateral resolution of 1 mm was obtained with the piezoelectric sampling configuration. Singly charged lipids and gangliosides were detected from tissue with piezoelectric matrix-assisted ionization using a silica nanoparticle co-matrix.

High Throughput Complementary Analysis and Quantitation of Metabolites by MALDI- and Silicon Nanopost Array-Laser Desorption/Ionization-Mass Spectrometry

Silicon nanopost array (NAPA) structures have been shown to be effective substrates for laser desorption/ionization-mass spectrometry (LDI-MS) and have been used to analyze a variety of samples including peptides, metabolites, drugs, explosives, and intact cells, as well as to image lipids and metabolites in tissue sections. However, no direct comparison has yet been conducted between NAPA-MS and the most commonly used LDI-MS technique, matrix-assisted laser desorption/ionization (MALDI)-MS. In this work, we compare the utility of NAPA-MS to that of MALDI-MS using two common matrices for the analysis of metabolites in cellular extracts and human urine. Considerable complementarity of molecular coverage was observed between the two techniques. Of 178 total metabolites assigned from cellular extracts, 68 were uniquely detected by NAPA-MS and 62 were uniquely detected by MALDI-MS. NAPA-MS was found to provide enhanced coverage of low-molecular weight compounds such as amino acids, whereas MALDI afforded better detection of larger, labile compounds including nucleotides. In the case of urine, a sample largely devoid of higher-mass labile compounds, 88 compounds were uniquely detected by NAPA-MS and 13 by MALDI-MS. NAPA-MS also favored more extensive alkali metal cation adduction relative to MALDI-MS, with the [M + 2Na/K - H]⁺ species accounting for as much as 97% of the total metabolite ion signal in positive mode. The capability of NAPA-MS for targeted quantitation of endogenous metabolites in urine via addition of isotopically labeled standards was also examined. Both NAPA-MS and MALDI-MS provided quantitative results in good agreement with one another and the concentrations reported in the literature, as well as good sample-to-sample reproducibility (RSD < 10%).

Towards Point-of-Care Insulin Detection

Good glucose management through an insulin dose regime based on the metabolism of glucose helps millions of people worldwide manage their diabetes. Since Banting and Best extracted insulin, glucose management has improved due to the introduction of insulin analogues that act from 30 minutes to 28 days, improved insulin dose regimes, and portable glucose meters, with a current focus on alternative sampling sites that are less invasive. However, a piece of the puzzle is still missing-the ability to measure insulin directly in a Point-of-Care device. The ability to measure both glucose and insulin concurrently will enable better glucose control by providing an improved estimate for insulin sensitivity, minimizing variability in control, and maximizing safety from hypoglycaemia. However, direct detection of free insulin has provided a challenge due to the size of the molecule, the low concentration of insulin in blood, and the selectivity against interferants in blood. This review summarizes current insulin detection methods from immunoassays to analytical chemistry, and sensors. We also discuss the challenges and potential of each of the methods towards Point-of-Care insulin detection.

Determination of copper and lead in tequila by conventional matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and partial least squares regression

RATIONALE

Quantification of small molecules by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) is challenging yet attractive, due to micro-scale procedural simplicity, high throughput and lack of memory effects. Since these features are important while analyzing trace elements in quality control schemes, MALDI-TOFMS was used for the determination of copper (Cu) and lead (Pb) in tequila with quantification carried out by partial least squares regression (PLS2) and by univariate calibration (UC).

METHODS

In the proposed procedure, Bi(III) was added as internal standard (IS), diethyldithiocarbamate complexes were formed (pH 7.4) and extracted into chloroform; after solvent evaporation and re-constitution in acetonitrile, the sample was co-crystallized with α-cyano-4-hydroxycinnamic acid on a steel target. From the acquired mass spectra, UC was performed using IS-normalized signals of the monoisotopic ions of analytes, and the m/z range 350-513 was used for PLS2. Accuracy was tested by recovery experiments and by inductively coupled plasma (ICP)-MS analysis.

RESULTS

When compared with direct analyte signal measurements, application of IS yielded enhanced analytical performance using either UC or PLS2; the method quantification limits were: 11.1 μg L^-1 , 23.4 μg L^-1 for Cu and 89.8 μg L^-1 , 97.1 μg L^-1 for Pb, respectively. In tequila, MALDI-TOFMS and ICP-MS provided consistent results for Cu (165-2599 μg L^-1 ); Pb was not detected in any sample by MALDI-TOFMS, yet recoveries obtained after standard addition were indicative of acceptable accuracy (400 μg L^-1 Pb added; recoveries: 91.2-108% for UC and 98.8-120% for PLS2).

CONCLUSIONS

New experimental evidence has been provided supporting the inclusion of trace metals quantification within a range of MALDI-TOFMS applications. Slightly better results were obtained for UC as compared with PLS2 yet both methods can be recommended for testing the compliance of Cu and Pb levels with Official Mexican Norm. Of note, while using PLS2, there is no need for signal integration nor for IS normalization.

Generation and Propagation of MALDI Ion Packets Probed by Sheet-Like Nanosecond UV Laser Light

A sheet-like ultraviolet (UV) probe laser is used to investigate the ejection and propagation of ion packets of matrix CHCA, which are produced by matrix-assisted laser desorption and ionization (MALDI). Laser irradiation of the expanding MALDI plume induced photodissociation of the CHCA-related ions, which existed in a sheet-like volume, leading to their absence in their MALDI signal profiles. The MALDI spectra were measured under varying conditions: the temporal delay of the lasers and the distance of the sheet-like probe laser from the MALDI sample surface. It was found that the center of the (CHCA)H⁺ packets were ejected at 46±11 ns after MALDI laser irradiation, while the (CHCA)₂H⁺ packets were ejected at 64±12 ns, regardless of the magnitude of acceleration static high-voltage in 3.5–5.5 kV. This suggests that (CHCA)₂H⁺ is formed by a proton transfer reaction from (CHCA)H⁺ to (CHCA)₂ in the heated condensed phase and/or near the surface. This study represents the first experimental determination of ion ejection time in the MALDI process, which is also applicable to other species in the MALDI plume.

Comparison and application of fluorescence EEMs and DRIFTS combined with chemometrics for tracing the geographical origin of Radix Astragali

Selection of the appropriate method for traceability may be of great interest for the characterization of food authenticity and to reveal falsifications. The possibility of tracing the geographical origins of Radix Astragali based on diffuse reflectance mid-infrared Fourier transform spectroscopy (DRIFTS) technique and fluorescence fingerprints (EEMs) technique was investigated in this work. DRIFTS technique combined with PCA and PLS-DA and EEMs technique combined with M-PCA and N-PLS-DA were used to determine the geographical origin of Radix Astragali samples, respectively. DRIFTS-PLS-DA provided total recognition rates of 98.4% for all Radix Astragali samples in the training sets and 94.6% in the predicted sets. Compared with the DRIFTS, EEMs combined with chemometrics obtained more accurate recognition results. The total recognition rates (RRs) of the training sets and prediction sets obtained with EEMs-N-PLS-DA were all 100%. The good classification results of fluorescence fingerprints technique should be attributed mainly to two reasons. One reason is that three-dimensional fluorescence spectrum can provide more information than two-dimensional DRIFTS, and the other reason is that fluorescence spectrum has higher sensitivity and selectivity than the DRIFTS. Therefore, fluorescence fingerprint (EEMs) technique combined with chemometrics results more adequate for tracing the food geographical origin. It should be noted that the more the analysis target contains fluorescent substances, the more accurate results are obtained by using the fluorescent fingerprint method. Conversely, if the classification object contains very few fluorescent substances, the classification result may not be as good as the DRIFTS method. Furthermore, due to relatively cumbersome operation of fluorescence method, EEMs fluorescence method is unsuitable for rapid analysis as compared to infrared method.

Two-dimensional TiO2 nanoflakes enable rapid SALDI-TOF-MS detection of toxic small molecules (dyes and their metabolites) in complex environments

High surface area (136 m² g^-1) nanoporous two-dimensional TiO₂ nanoflakes are applied as an adsorbent and meanwhile a matrix for toxic small molecule analysis using positive-ion surface-assisted laser desorption/ionization time-of-flight mass spectrometry (SALDI-TOF MS). The TiO₂ nanoflakes enable one-step enrichment and analysis, greatly simplifying the analysis technique. Due to the high enrichment efficiency and low background noise, small molecule organic contaminants at ppt or even sub-ppt concentrations such as malachite green (10 pg/mL), leucomalachite green (10 pg/mL), cetyltrimethylammonium bromide (0.001 pg/mL), rhodamine B (0.001 pg/mL), and crystal violet (0.1 pg/mL) were detected. In addition, malachite green and its metabolite leucomalachite green at ng/mL concentrations were successfully detected from fish blood and fish extracts, and crystal violet and its homologues at ng/cm² concentrations were detected from inks on thermal receipt papers obtained from local supermarket.

A highly efficient magnetically confined ion source for real time on-line monitoring of trace compounds in ambient air

We fabricate a high-efficient ion source for real time on-line monitoring of trace compounds in ambient air by introducing a weak longitudinal magnetic field to a micro-fabricated DC glow discharge. Mass spectrometric detection of various samples indicates that the signal intensity increases by an order of magnitude and the limit of detection can be lowered to 1/10 of the original level. This improvement results from the increasing ion transport efficiency through the magnetic confinement.

Small- and large-sized iron(II, III) oxide nanoparticles for surface-assisted laser desorption/ionization mass spectrometry of small biomolecules

RATIONALE

Common surface-assisted laser desorption/ionization (SALDI) surfaces are functionalized to improve mass spectrometric detection. Such surfaces are selective to certain group(s) of compounds. The application of universal and sensitive SALDI surfaces with appropriate size/surface area is paramount. In this study, two different sizes/surface areas of Fe3 O4 are compared as SALDI surfaces.

METHODS

For accurate surface area comparisons, the physical properties of the Fe3 O4 nanoparticles used as SALDI surfaces were determined using scanning electron microscopy, X-ray diffractometry, and N2 Brunauer-Emmet-Teller adsorption techniques. SALDI mass spectrometry (MS) data were acquired using a time-of-flight (TOF) mass spectrometer operated in the linear mode and equipped with a 50-Hz pulsed nitrogen laser (at 337 nm). Small biomolecules (adenosine, glucose, sucrose, tryptophan, and tripeptide) and a real sample (human serum) were analyzed.

RESULTS

The average sizes/specific surface areas of the SALDI surfaces of the small- and large-sized Fe3 O4 nanoparticles were ~21 nm/~82 m2 /g and ~39 nm/~38 m2 /g, respectively. An overall ~2.0-fold enhancement in signal-to-noise ratios was observed for the ionic species of the analyzed biomolecules in SALDI-MS using small-sized Fe3 O4 in comparison to large-sized Fe3 O4 nanoparticles. MS sensitivity from adenosine calibration curves (concentration between 0.05 and 10.0 mM) was ~2.0-fold higher for small-sized than large-sized Fe3 O4 nanoparticles as SALDI surfaces.

CONCLUSIONS

We have shown that transition-metal oxides such as Fe3 O4 nanoparticles are suitable and efficient surfaces for SALDI-TOF-MS analysis of small biomolecules. We observed improvement in signal-to-noise ratios and detection sensitivity for the analyzed samples from SALDI surfaces using small-sized (possessing larger surface area) than large-sized Fe3 O4 nanoparticles.

Molecular imaging mass spectrometry for probing protein dynamics in neurodegenerative disease pathology

Recent advances in the understanding of basic pathological mechanisms in various neurological diseases depend directly on the development of novel bioanalytical technologies that allow sensitive and specific chemical imaging at high resolution in cells and tissues. Mass spectrometry-based molecular imaging (IMS) has gained increasing popularity in biomedical research for mapping the spatial distribution of molecular species in situ. The technology allows for comprehensive, untargeted delineation of in situ distribution profiles of metabolites, lipids, peptides and proteins. A major advantage of IMS over conventional histochemical techniques is its superior molecular specificity. Imaging mass spectrometry has therefore great potential for probing molecular regulations in CNS-derived tissues and cells for understanding neurodegenerative disease mechanism. The goal of this review is to familiarize the reader with the experimental workflow, instrumental developments and methodological challenges as well as to give a concise overview of the major advances and recent developments and applications of IMS-based protein and peptide profiling with particular focus on neurodegenerative diseases. This article is part of the Special Issue "Proteomics".

Strategy for marker-based differentiation of pro- and anti-inflammatory macrophages using matrix-assisted laser desorption/ionization mass spectrometry imaging

Macrophages are large phagocytes playing a crucial role in the development and progression of atherosclerosis. The phenotypic polarization and activation of macrophages in atherosclerotic plaques depends on their complex micro-environment and at the same time has a major impact on the vulnerability or stability of advanced atherosclerotic lesions. Many in vitro and in vivo studies have been designed to define markers for macrophage subtypes to better understand the mechanism of plaque progression but they have rather added to the confusion. Nonetheless, some of the in vitro defined macrophage subtypes, like the pro-inflammatory M1 or the anti-inflammatory M2a/b/c macrophage, have been shown to be present in atherosclerotic plaques. Herein, we developed a comprehensive workflow to distinguish between human in vitro differentiated pro-inflammatory M1 and anti-inflammatory M2a and M2c macrophages. The cells were analyzed using qPCR and FACS analyses for defining suitable markers on the transcript (mRNA) and protein level as well as MALDI MSI for the assignment of metabolic markers, which can be used for the identification of the corresponding macrophage subtypes in atherosclerotic plaques. Data obtained using both qPCR and FACS analyses were in agreement with the literature. For the analysis of the macrophages with MALDI MSI, a comprehensive workflow was developed and the obtained data were subjected to different statistical analysis methods like principal component analysis (PCA) to define markers for each macrophage type. Our MALDI MSI results revealed that the method produces reliable and reproducible results but that the heterogeneity of the monocytes derived from different donors is too high to define universal markers on the metabolic level. Moreover, the results show that a sample set of three biological replicates is not sufficient to obtain representative data and therefore we recommend performing ring experiments in which the samples are measured by different laboratories.

Phosphonate coating of SiO2 nanoparticles abrogates inflammatory effects and local changes of the lipid composition in the rat lung: a complementary bioimaging study

BACKGROUND

The well-known inflammatory and fibrogenic changes of the lung upon crystalline silica are accompanied by early changes of the phospholipid composition (PLC) as detected in broncho-alveolar lavage fluid (BALF). Amorphous silica nanoparticles (NPs) evoke transient lung inflammation, but their effect on PLC is unknown. Here, we compared effects of unmodified and phosphonated amorphous silica NP and describe, for the first time, local changes of the PLC with innovative bioimaging tools.

METHODS

Unmodified (SiO₂-n), 3-(trihydroxysilyl) propyl methylphosphonate coated SiO₂-n (SiO₂-p) as well as a fluorescent surrogate of SiO₂-n (SiO₂-FITC) nanoparticles were used in this study. In vitro toxicity was tested with NR8383 alveolar macrophages. Rats were intratracheally instilled with SiO₂-n, SiO₂-p, or SiO₂-FITC, and effects on lungs were analyzed after 3 days. BALF from the right lung was analyzed for inflammatory markers. Cryo-sections of the left lung were subjected to fluorescence microscopy and PLC analyses by matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MS), Fourier transform infrared microspectroscopy (FT-IR), and tandem mass spectrometry (MS/MS) experiments.

RESULTS

Compared to SiO₂-p, SiO₂-n NPs were more cytotoxic to macrophages in vitro and more inflammatory in the rat lung, as reflected by increased concentration of neutrophils and protein in BALF. Fluorescence microscopy revealed a typical patchy distribution of SiO₂-FITC located within the lung parenchyma and alveolar macrophages. Superimposable to this particle distribution, SiO₂-FITC elicited local increases of phosphatidylglycerol (PG) and phosphatidylinositol (PI), whereas phoshatidylserine (PS) and signals from triacylgyceride (TAG) were decreased in the same areas. No such changes were found in lungs treated with SiO₂-p or particle-free instillation fluid.

CONCLUSIONS

Phosphonate coating mitigates effects of silica NP in the lung and abolishes their locally induced changes in PLC pattern. Bioimaging methods based on MALDI-MS may become a useful tool to investigate the mode of action of NPs in tissues.

Integrating Mass Spectrometry with Microphysiological Systems for Improved Neurochemical Studies

Microphysiological systems, often referred to as "organs-on-chips", are in vitro platforms designed to model the spatial, chemical, structural, and physiological elements of in vivo cellular environments. They enhance the evaluation of complex engineered biological systems and are a step between traditional cell culture and in vivo experimentation. As neurochemists and measurement scientists studying the molecules involved in intercellular communication in the nervous system, we focus here on recent advances in neuroscience using microneurological systems and their potential to interface with mass spectrometry. We discuss a number of examples - microfluidic devices, spheroid cultures, hydrogels, scaffolds, and fibers - highlighting those that would benefit from mass spectrometric technologies to obtain improved chemical information.

Mass spectrometry in pathology - Vision for a future workflow

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

Remote Atmospheric Pressure Infrared Matrix-Assisted Laser Desorption-Ionization Mass Spectrometry (Remote IR-MALDI MS) of Proteins

Remote Infrared Matrix-Assisted Laser Desorption/Ionization (Remote IR-MALDI) system using tissue endogenous water as matrix was shown to enable in vivo real-time mass spectrometry analysis with minimal invasiveness. Initially the system was used to detect metabolites and lipids. Here, we demonstrate its capability to detect and analyze peptides and proteins. Very interestingly, the corresponding mass spectra show ESI-like charge state distribution, opening many applications for structural elucidation to be performed in real-time by Top-Down strategy. The charge states show no dependence toward laser wavelength or length of the transfer tube. Indeed, remote analysis can be performed 5 m away from the mass spectrometer without modification of spectra. On the contrary, addition of glycerol to water shift the charge state distributions toward even higher charge states. The desorption/ionization process is very soft, allowing to maintain protein conformation as in ESI. Observation of proteins and similar spectral features on tissue, when protein standards are deposited on raw tissue pieces, could potentially open the way to their direct analysis from biological samples. This also brings interesting features that could contribute to the understanding of IR MALDI ionization mechanism.

The inherent matrix properties of lichen metabolites in matrix-assisted laser desorption ionization time-of-flight mass spectrometry

RATIONALE

Light-absorbing secondary metabolites from lichens were recently reported to exhibit promising Laser Desorption Ionization (LDI) properties, enabling their direct detection from crude lichen extracts. In addition, many of them display close structural homologies to commercial Matrix-Assisted Laser Desorption Ionization (MALDI) matrices, which is incentive for the evaluation of their matrical properties. The current study systematically evaluated the matrix effects of several structural classes of lichen metabolites: monoaromatic compounds, quinone derivatives, dibenzofuran-related molecules and the shikimate-derived vulpinic acid. Their matrical properties were tested against a wide range of structurally diverse analytes including alkaloids, coumarins, flavonoids and peptides.

METHODS

Triplicate automatic positive-ion mode MALDI analyses were carried out and ionization efficiencies were compared with those of structurally related reference matrices (i.e. DHB, HCCA, dithranol and usnic acid) in terms of (i) analyte absolute intensities and (ii) Matrix Suppressing Effect (MSE) scores.

RESULTS

Monoaromatic lichen metabolites revealed matrical properties similar to those of DHB when obtained under comparable experimental conditions. Likewise, anthraquinone metabolites triggered ionization of tested analytes in a similar way to the structurally related dithranol. Finally, dibenzofuran derivatives displayed a broad ionization profile, reminiscent of that of (+)-usnic acid.

CONCLUSIONS

Lichen metabolites exhibit interesting MALDI matrix properties, especially for medium and low molecular weight analytes. For many of the tested molecules, matrix ion formation was very limited. This proof-of-concept study paves the way for follow-up investigations to assess the matrix properties of lichen metabolites against a wider array of analytes as well as adapting experimental settings to individually optimize the performance of successfully tested candidates.

Identifying Inhibitors of Inflammation: A Novel High-Throughput MALDI-TOF Screening Assay for Salt-Inducible Kinases (SIKs)

Matrix-assisted laser desorption/ionization time-of-flight (MALDI TOF) mass spectrometry has become a promising alternative for high-throughput drug discovery as new instruments offer high speed, flexibility and sensitivity, and the ability to measure physiological substrates label free. Here we developed and applied high-throughput MALDI TOF mass spectrometry to identify inhibitors of the salt-inducible kinase (SIK) family, which are interesting drug targets in the field of inflammatory disease as they control production of the anti-inflammatory cytokine interleukin-10 (IL-10) in macrophages. Using peptide substrates in in vitro kinase assays, we can show that hit identification of the MALDI TOF kinase assay correlates with indirect ADP-Hunter kinase assays. Moreover, we can show that both techniques generate comparable IC50 data for a number of hit compounds and known inhibitors of SIK kinases. We further take these inhibitors to a fluorescence-based cellular assay using the SIK activity-dependent translocation of CRTC3 into the nucleus, thereby providing a complete assay pipeline for the identification of SIK kinase inhibitors in vitro and in cells. Our data demonstrate that MALDI TOF mass spectrometry is fully applicable to high-throughput kinase screening, providing label-free data comparable to that of current high-throughput fluorescence assays.

Proteomics in Inflammatory Bowel Disease: Approach Using Animal Models

Recently, proteomics studies have provided important information on the role of proteins in health and disease. In the domain of inflammatory bowel disease, proteomics has shed important light on the pathogenesis and pathophysiology of inflammation and has contributed to the discovery of some putative clinical biomarkers of disease activity. By being able to obtain a large number of specimens from multiple sites and control for confounding environmental, genetic, and metabolic factors, proteomics studies using animal models of colitis offered an alternative approach to human studies. Our aim is to review the information and lessons acquired so far from the use of proteomics in animal models of colitis. These studies helped understand the importance of different proteins at different stages of the disease and unraveled the different pathways that are activated or inhibited during the inflammatory process. Expressed proteins related to inflammation, cellular structure, endoplasmic reticulum stress, and energy depletion advanced the knowledge about the reaction of intestinal cells to inflammation and repair. The role of mesenteric lymphocytes, exosomes, and the intestinal mucosal barrier was emphasized in the inflammatory process. In addition, studies in animal models revealed mechanisms of the beneficial effects of some therapeutic interventions and foods or food components on intestinal inflammation by monitoring changes in protein expression and paved the way for some new possible inflammatory pathways to target in the future. Advances in proteomics technology will further clarify the interaction between intestinal microbiota and IBD pathogenesis and investigate the gene-environmental axis of IBD etiology.