Reducing Spatial Heterogeneity of MALDI Samples with Marangoni Flows During Sample Preparation

Critical Evaluation of Sphingolipids Detection by MALDI-MSI

The increasing interest in the role of sphingolipids in (patho)physiology has led to the demand for visualization of these lipids within tissue samples (both from animal models and patient specimens) using techniques such as matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). While increasingly adopted, detection of sphingolipids with MALDI-MSI is challenging due to: i) the significant structural variations of sphingolipid molecules, ii) the potential breakdown of the more complex molecules into structurally simpler species which may confound the analysis, and iii) the great difference in levels among sphingolipid classes and subspecies, with the low-abundant ones often being close to the detection limit. In this study, we adopted a multi-pronged approach to establish a robust pipeline for the detection of sphingolipids by MALDI-MSI and to establish best practices and limitations of this technology. First, we evaluated the more commonly adopted methods [2,5-Dihydroxyacetophenon (DHA) or 2,5-Dihydroxybenzoic acid (DHB) matrix in positive ion mode and 1,5-Diaminonaphthalene (DAN) matrix in negative ion mode] using MALDI-MS on reference standards. These standards were used at ratios similar to their relative levels in biological samples to evaluate signal artifacts originating from fragmentation of more complex sphingolipids and impacting low level species. Next, by applying the most appropriate protocol for each sphingolipid class, MALDI-MSI signals were validated in cell culture by modulating specific sphingolipid species using sphingolipid enzymes and inhibitors. Finally, the optimized parameters were utilized on breast cancer tissue from the PyMT mouse model. We report the optimal signal for sphingomyelin (SM) and, for the first time, Sph in DHB positive ion mode (in cells and PyMT tissue), and the validated detection of ceramides and glycosphingolipids in DAN negative ion mode. We document the extensive fragmentation of SM into sphingosine-1-phosphate (S1P) and even more so into ceramide-1-phosphate (C1P) using DAN in negative ion mode and its effect in generating an artifactual C1P tissue signal; we also report the lack of detectable signal for S1P and C1P in biological samples (cells and tissue) using the more suitable DHB positive ion mode protocol.

A Fast-Pass, Desorption Electrospray Ionization Mass Spectrometry Strategy for Untargeted Metabolic Phenotyping

Desorption electrospray ionization mass spectrometry imaging (DESI-MSI) provides direct analytical readouts of small molecules that can be used to characterize the metabolic phenotypes of genetically engineered bacteria. In an effort to accelerate the time frame associated with the screening of mutant libraries, we have developed a high-throughput DESI-MSI analytical workflow implementing a single raster line-scan strategy that facilitates the collection of location-resolved molecular information from engineered strains on a subminute time scale. Evaluation of this "Fast-Pass" DESI-MSI phenotyping workflow on analytical standards demonstrated the capability of acquiring full metabolic profiling information with a throughput of ∼40 s per sample. This Fast-Pass strategy was implemented in the analysis of genetically edited Escherichia coli strains that have been engineered to produce various free-fatty acids (FFAs) for applications relevant to biofuels. Due to the untargeted nature of DESI-MSI, the investigation of these strains yielded molecular information for both global metabolites and targeted detection of accumulated bioproducts, allowing simultaneous readouts of strain-specific chemical profiles and comparative measurements of FFA production levels.

Microarray-Based Methodology for Lipid Profiling, Enzymatic Activity, And Binding Assays in Printed Lipid Raft Membranes from Astrocytes and Neurons

Lipid rafts are liquid-ordered domains in which specific enzymes and receptors are located. These membrane platforms play crucial roles in a variety of signaling pathways. Alterations in the lipid environment, such as those elicited by oxidative stress, can lead to important functional disruptions in membrane proteins. Cell membrane microarrays have emerged in the past decade as a powerful methodology for the study of both lipids and membrane proteins at large scales. Based on that technology and the importance of liquid-ordered subdomains, we have developed a new printed lipid raft technology with a preserved native protein structure and lipid environment. To validate this technology and evaluate its potential for different aims, raft membrane microarrays (RMMAs) containing two different cell types (astrocytes and neurons) and three different conditions (astrocytes in control situation, metabolic stress, and oxidative stress) were developed. To study differences in lipid profiles between raft domains, the MALDI-MS assay was performed on RMMAs. To evaluate the preservation of native protein activities (enzymatic activity and ligand binding) in the printed raft domains, differences in NADH oxidoreductase, GAPDH, cholinesterase activities, and sigma-1 and sigma-2 binding assays were performed. We demonstrate the performance of this new microarray technology, adapted to membrane subdomains, as valid to explore changes in lipid composition and protein activities in raft domains from brain cell lines under different stress conditions relevant for neuropathology.

Advancing carbohydrate quantification in MALDI mass spectrometry by the rapidly freeze-drying droplet (RFDD) method

Quantitative carbohydrate analysis faces challenges in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), including insufficient sensitivity and inconsistent spatial distribution of ion intensity. This study introduces an innovative sample preparation approach, the Rapidly Freeze-Drying Droplet (RFDD) method, aimed at overcoming these challenges by enhancing the homogeneity of the sample morphology and signal intensity in MALDI. Compared to conventional preparation methods, the RFDD method reduces the laser energy threshold and demonstrates a remarkable increase in signal intensity for carbohydrates, facilitating the detection of high-molecular-weight polysaccharides (>10 kDa). The RFDD-prepared samples exhibit a uniformly distributed signal intensity that overcomes the 'sweet spot' issue in MALDI. The enhanced signal intensity and reproducibility lead to reliable quantitative analysis of carbohydrates, eliminating the need for expensive isotopic standards in each sample. A straightforward and accessible approach is presented for general laboratories, revolutionizing carbohydrate analysis in MALDI-MS.

Advances in high-resolution mass spectrometry techniques for analysis of high mass-to-charge ions

A major challenge in modern mass spectrometry (MS) is achieving high mass resolving power and accuracy for precision analyses in high mass-to-charge (m/z) regions. To advance the capability of MS for increasingly demanding applications, understanding limitations of state-of-the-art techniques and their status in applied sciences is essential. This review summarizes important instruments in high-resolution mass spectrometry (HRMS) and related advances to extend their working range to high m/z regions. It starts with an overview of HRMS techniques that provide adequate performance for macromolecular analysis, including Fourier-transform, time-of-flight (TOF), quadrupole-TOF, and related data-processing techniques. Methodologies and applications of HRMS for characterizing macromolecules in biochemistry and material sciences are summarized, such as top-down proteomics, native MS, drug discovery, structural virology, and polymer analyses.

M. T, Cho G, Lee J. Control of the Drying Patterns for Complex Colloidal Solutions and Their Applications

The uneven deposition at the edges of an evaporating droplet, termed the coffee-ring effect, has been extensively studied during the past few decades to better understand the underlying cause, namely the flow dynamics, and the subsequent patterns formed after drying. The non-uniform evaporation rate across the colloidal droplet hampers the formation of a uniform and homogeneous film in printed electronics, rechargeable batteries, etc., and often causes device failures. This review aims to highlight the diverse range of techniques used to alleviate the coffee-ring effect, from classic methods such as adding chemical additives, applying external sources, and manipulating geometrical configurations to recently developed advancements, specifically using bubbles, humidity, confined systems, etc., which do not involve modification of surface, particle or liquid properties. Each of these methodologies mitigates the edge deposition via multi-body interactions, for example, particle-liquid, particle-particle, particle-solid interfaces and particle-flow interactions. The mechanisms behind each of these approaches help to find methods to inhibit the non-uniform film formation, and the corresponding applications have been discussed together with a critical comparison in detail. This review could pave the way for developing inks and processes to apply in functional coatings and printed electronic devices with improved efficiency and device yield.

Microbowls with Controlled Concavity for Accurate Microscale Mass Spectrometry

Patterned surfaces can enhance the sensitivity of laser desorption ionization mass spectrometry by segregating and concentrating analytes, but their fabrication can be challenging. Here, a simple method to fabricate substrates patterned with micrometer-scale wells that yield more accurate and sensitive mass spectrometry measurements compared to flat surfaces is described. The wells can also concentrate and localize cells and beads for cell-based assays.

Controllable dried patterns of colloidal drops

HYPOTHESIS

When an aqueous colloidal drop dries on a solid substrate, the final pattern of the dried deposit can be manipulated through controlling the internal flow states of the drop.

EXPERIMENTS

We report a strategy to control the dried patterns of aqueous colloidal drop by controlling the drop configurations and relative humidity. For this purpose, both sessile and pendant drops are studied.

FINDING

The capillary flow, which is responsible for coffee-ring, is suppressed by increasing the relative humidity. Then, surprisingly, the internal convection in the pendant drop is significantly stronger than that in the sessile drop. This phenomenon leads to the formation of the disc-like and spot-like dried patterns in the sessile and pendant drop, respectively, which are the results of different interactions between the Marangoni and (buoyancy-induced) natural convections in the sessile and pendant drops. In the sessile drop, the Marangoni and natural convections mutually restrain each other due to their opposite flow directions. In contrast, in the pendant drop, the two convections mutually enhance each other, due to their same flow directions. Thisnew strategy offers a foreign-material-free and external-force-free means to control the dried patterns of the drop.

Mass Spectrometry Imaging of Biological Tissues by Laser Desorption Ionization from Silicon Nanopost Arrays

Mass spectrometry imaging (MSI) plays an expanding role in the label-free spatial mapping of hundreds of molecules simultaneously. Currently, matrix-assisted laser desorption ionization (MALDI) is among the most widely adopted MSI techniques. However, matrix application can impact the fidelity of spatial distributions, and matrix selection and related spectral interferences in the low mass range can lead to biased molecular coverage. Nanophotonic ionization from silicon nanopost arrays (NAPA) is an emerging matrix-free MSI platform with enhanced sensitivity for several molecular classes, for example, neutral lipids and biooligomers. Here, we describe a protocol with minimal sample preparation for NAPA-MSI of metabolites, lipids, and biooligomers from biological tissues.

Re-exploring α-Cyano-4-Hydroxycinnamic Acid as a Reactive Matrix for Selective Detection of Glutathione via MALDI-MS

Herein, we re-explored α-cyano-4-hydroxycinnamic acid (CHCA) as a reactive matrix for selective and sensitive analysis of glutathione (GSH) by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). CHCA efficiently reacted with GSH, and the resulting CHCA-GSH conjugate was readily detected by MALDI-MS without interferences. The detection limit of the CHCA-GSH conjugate decreased to 200 pmol μL^-1, which was 2 orders of magnitude lower than that of pure GSH.Forapplication, CHCA was successfully applied for the detection of GSH, present in HepG2 cell lysates. The results demonstrated detection advantages of simple, high-throughput, and selective and screening of GSH in biological samples by MALDI-MS.

Material-assisted mass spectrometric analysis of low molecular weight compounds for biomedical applications

Low molecular weight compounds play an important role in encoding the current physiological state of an individual. Laser desorption/ionization mass spectrometry (LDI MS) offers high sensitivity with low cost for molecular detection, but it is not able to cover small molecules due to the drawbacks of the conventional matrix. Advanced materials are better alternatives, showing little background interference and high LDI efficiency. Herein, we first classify the current materials with a summary of compositions and structures. Matrix preparation protocols are then reviewed, to enhance the selectivity and reproducibility of MS data better. Finally, we highlight the biomedical applications of material-assisted LDI MS, at the tissue, bio-fluid, and cellular levels. We foresee that the advanced materials will bring far-reaching implications in LDI MS towards real-case applications, especially in clinical settings.

ANALYSIS OF CARBOHYDRATES AND GLYCOCONJUGATES BY MATRIX-ASSISTED LASER DESORPTION/IONIZATION MASS SPECTROMETRY: AN UPDATE FOR 2015-2016

This review is the ninth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2016. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented over 30 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show no sign of deminishing. © 2020 Wiley Periodicals, Inc.

Microarray and Mass Spectrometry-Based Methodology for Lipid Profiling of Tissues and Cell Cultures

The recent developments in mass spectrometry have revealed the importance of lipids as biomarkers in the context of different diseases and as indicators of the cell's homeostasis. However, further advances are required to unveil the complex relationships between lipid classes and lipid species with proteins. Here, we present a new methodology that combines microarrays with mass spectrometry to obtain the lipid fingerprint of samples of a different nature in a standardized and fast way, with minimal sample consumption. As a proof of concept, we use the methodology to obtain the lipid fingerprint of 20 rat tissues and to create a lipid library for tissue classification. Then, we combine those results with immunohistochemistry and enzymatic assays to unveil the relationship between some lipid species and two enzymes. Finally, we demonstrate the performance of the methodology to explore changes in lipid composition of the nucleus accumbens from mice subjected to two lipid diets.

Effective analysis of degree of polymerization of polysialic acids in mass spectrometry by combining novel sample preparation and dynamic instrument optimization methods

This work demonstrates a mass spectrometry technique to improve data reliability when analyzing degree of polymerization (DP) of high-mass polysialic acids (PSAs). Matrix-assisted laser-desorption/ionization (MALDI) time-of-flight mass spectrometry is the technique of choice for analyzing large molecules due to its wide mass working range; however, the observed DP of PSAs using such an instrument is unreliable owing to sensitivity bias towards low-mass ions. A multi-layer MALDI sample preparation protocol is demonstrated in the current study to improve PSA sensitivity, and a dynamic instrument optimization method (DIOM) is employed to minimize detector saturation over a wide mass range. The DP information obtained in the DIOM combines a series of mass spectral data obtained with individually optimized instrument parameters to minimize the problem of sensitivity bias in respective mass ranges. The resultant mass spectra facilitate unambiguous determination of DP in the high-mass range due to significantly improved spectral quality. The main instrument parameters involved in the optimization process include extraction delay in MALDI ion source as well as the cutoff mass of the ion detector. In comparison to conventional methods, the DIOM doubles the maximum DP that can be unambiguously identified by mass spectrometry.

An Efficient Sample Preparation Method to Enhance Carbohydrate Ion Signals in Matrix-assisted Laser Desorption/Ionization Mass Spectrometry

Sample preparation is a critical process in mass spectrometry (MS) analysis of carbohydrates. Although matrix-assisted laser desorption/ionization (MALDI) MS is the method of choice in carbohydrate analysis, poor ion signal and data reproducibility of carbohydrate samples continue to be severe problems. For quantitative analysis of carbohydrates, an effective analytical protocol providing superior data quality is necessary. This video demonstrates sample preparation protocols to improve signal intensity and minimize data variation of carbohydrates in MALDI-MS. After drying and crystallization of sample droplets, the crystal morphology is reformed by methanol before mass spectrometric analysis. The enhancement in carbohydrate signal is examined with MALDI imaging mass spectrometry (IMS). Experimental results show that crystal reformation adjusts crystalline structures and redistributes carbohydrate analytes. In comparison with the dried droplet preparation method in conventional MALDI-MS, reforming carbohydrate crystal morphologies with methanol shows significantly better signal intensity, ion image distribution, and data stability. Since the protocols demonstrated herein do not involve changes in sample composition, they are generally applicable to various carbohydrates and matrixes.

Impact of uneven sample morphology on mass resolving power in linear MALDI-TOF mass spectrometry: A comprehensive theoretical investigation

This work discusses the correlation between the mass resolving power of matrix-assisted laser desorption/ionization time-of-flight mass analyzers and extraction condition with an uneven sample morphology. Previous theoretical calculations show that the optimum extraction condition for flat samples involves an ideal ion source design and extraction delay. A general expression of spectral feature takes into account ion initial velocity, and extraction delay is derived in the current study. The new expression extends the comprehensive calculation to uneven sample surfaces and above 90% Maxell-Boltzmann initial velocity distribution of ions to account for imperfect ionization condition. Calculation shows that the impact of uneven sample surface or initial spatial spread of ions is negligible when the extraction delay is away from the ideal value. When the extraction delay approaches the optimum value, the flight-time topology shows a characteristic curve shape, and the time-domain mass spectral feature broadens with an increase in initial spatial spread of ions. For protonated 2,5-dihydroxybenzoic acid, the mass resolving power obtained from a sample of 3-μm surface roughness is approximately 3.3 times lower than that of flat samples. For ions of m/z 3000 coexpanded with 2,5-dihydroxybenzoic acid, the mass resolving power in the 3-μm surface roughness case only reduces roughly 7%. Comprehensive calculations also show that the mass resolving power of lighter ions is more sensitive to the accuracy of the extraction delay than heavier ions.

A review on suppression and utilization of the coffee-ring effect

Evaporation of sessile droplets containing non-volatile solutes dispersed in a volatile solvent leaves behind ring-like solid stains. As the volatile species evaporates, pinning of the contact line gives rise to capillary flows that transport non-volatile solutes to the contact line. This phenomenon, called the coffee-ring effect, compromises the overall performance of industrially relevant manufacturing processes involving evaporation such as printing, biochemical analysis, manufacturing of nano-structured materials through colloidal and macromolecular patterning. Various approaches have been developed to suppress this phenomenon, which is otherwise difficult to avoid. The coffee-ring effect has also been leveraged to prepare new materials through convection induced assembly. This review underlines not only the strategies developed to suppress the coffee-ring effect but also sheds light on approaches to arrive at novel processes and materials. Working principles and applicability of these strategies are discussed together with a critical comparison.

Enhancing carbohydrate ion yield by controlling crystalline structures in matrix-assisted laser desorption/ionization mass spectrometry

Carbohydrate analysis is challenging due to lack of sensitive detection and efficient separation methods. Although matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is a sensitive tool, the low ionization efficiency of carbohydrates makes mass analyses inefficient. This work systematically examines the correlation between MALDI-MS sensitivity and carbohydrate sample morphology. Depending on the properties of the matrix used, the morphology changes through sample recrystallization after drying or imposition of hydrodynamic flows during droplet drying. Observation shows that amorphous solids and finer crystals offer higher carbohydrate sensitivity and spatial homogeneity than larger crystals. Clear evidences of an inverse correlation between sensitivity and crystal size are obtained when various kinds of carbohydrates are mixed with different matrixes. Similar experiments on proteins and peptides showed a negative or negligible effect. The result serves as a general guideline for improving efficiency in routine carbohydrate analysis.

Enhanced Laser Desorption/Ionization Mass Spectrometric Detection of Biomolecules Using Gold Nanoparticles, Matrix, and the Coffee Ring Effect

Nanomaterials have been extensively used as alternate matrices to minimize the low molecular weight interferences observed in typical MALDI but such nanomaterials typically do not improve the spot-to-spot variability that is commonly seen. In this work, we demonstrate that nanoparticles and low matrix concentrations (<2.5 mg/mL) can be used to homogeneously concentrate analytes into a narrow ring by taking advantage of the "coffee ring" effect. Concentration of the samples in this way leads to enhanced signals when compared to conventional MALDI, with higher m/z analytes being enhanced to the greatest extent. Moreover, the ionization suppression often observed in samples with high salt concentrations can be overcome by preparing samples in this way. The ring that is formed is readily visible, allowing the laser to be focused only on spots that contain analyte. The coffee-ring effect represents a new mode by which nanomaterials can be used to enhance the MALDI-based detection of biomolecules.

A cool and high salt-tolerant ionic liquid matrix for preferential ionization of phosphopeptides by negative ion MALDI-MS

An optimized ILM G₃THAP/PA matrix significantly improved the detection of phosphopeptides by negative ion MALDI-MS compared with using 3-AQ/CHCA/ADP and DHB/PA matrices.

Preparation of Homogeneous MALDI Samples for Quantitative Applications

This protocol demonstrates a simple sample preparation to reduce spatial heterogeneity in ion signals during matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. The heterogeneity of ion signals is a severe problem in MALDI, which results in poor data reproducibility and makes MALDI unsuitable for quantitative analysis. By regulating sample plate temperature during sample preparation, thermal-induced hydrodynamic flows inside droplets of sample solution are able to reduce the heterogeneity problem. A room-temperature sample preparation chamber equipped with a temperature-regulated copper base block that holds MALDI sample plates facilitates precise control of the sample drying condition. After drying of sample droplets, the temperature of sample plates is returned to room temperature and removed from the chamber for subsequent mass spectrometric analysis. The areas of samples are examined with MALDI-imaging mass spectrometry to obtain the spatial distribution of all components in the sample. In comparison with the conventional dried-droplet method that prepares samples under ambient conditions without temperature control, the samples prepared with the method demonstrated herein show significantly better spatial distribution and signal intensity. According to observations using carbohydrate and peptide samples, decreasing substrate temperature while maintaining the surroundings at ambient temperature during the drying process can effectively reduce the heterogeneity of ion signals. This method is generally applicable to various combinations of samples and matrices.

Critical factors determining the quantification capability of matrix-assisted laser desorption/ionization- time-of-flight mass spectrometry

Quantitative analysis with mass spectrometry (MS) is important but challenging. Matrix-assisted laser desorption/ionization (MALDI) coupled with time-of-flight (TOF) MS offers superior sensitivity, resolution and speed, but such techniques have numerous disadvantages that hinder quantitative analyses. This review summarizes essential obstacles to analyte quantification with MALDI-TOF MS, including the complex ionization mechanism of MALDI, sensitive characteristics of the applied electric fields and the mass-dependent detection efficiency of ion detectors. General quantitative ionization and desorption interpretations of ion production are described. Important instrument parameters and available methods of MALDI-TOF MS used for quantitative analysis are also reviewed.This article is part of the themed issue 'Quantitative mass spectrometry'.