Identification of proteins directly from tissue: in situ tryptic digestions coupled with imaging mass spectrometry

A novel method for on-tissue identification of proteins in spatially discrete regions is described using tryptic digestion followed by matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) with MS/MS analysis. IMS is first used to reveal the protein and peptide spatial distribution in a tissue section and then a serial section is robotically spotted with small volumes of trypsin solution to carry out in situ protease digestion. After hydrolysis, 2,5-Dihydroxybenzoic acid (DHB) matrix solution is applied to the digested spots, with subsequent analysis by IMS to reveal the spatial distribution of the various tryptic fragments. Sequence determination of the tryptic fragments is performed using on-tissue MALDI MS/MS analysis directly from the individual digest spots. This protocol enables protein identification directly from tissue while preserving the spatial integrity of the tissue sample. The procedure is demonstrated with the identification of several proteins in the coronal sections of a rat brain.     

An approach for visualizing the spatial metabolome of an entire plant root system inspired by the Swiss‐rolling technique

The spatial configuration and morphology of roots are commonly monitored for a better understanding of plant health and development. However, this approach provides minimal details about the biochemistry regulating the observable traits. Therefore, the ability to metabolically map the entire root structure would be of major value. Here, we developed a sample preparation approach that enables imaging of the entire root within a restricted space (width of microscope slide), which was influenced by the Swiss‐rolling technique. We were able to image and confidently identify molecules along the entire root structure from rolled‐root tissue sections using multiple spatially resolved mass spectrometry approaches.     

Applications of MALDI-MS/MS-Based Proteomics in Biomedical Research

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is one of the most widely used techniques in proteomics to achieve structural identification and characterization of proteins and peptides, including their variety of proteoforms due to post-translational modifications (PTMs) or protein–protein interactions (PPIs). MALDI-MS and MALDI tandem mass spectrometry (MS/MS) have been developed as analytical techniques to study small and large molecules, offering picomole to femtomole sensitivity and enabling the direct analysis of biological samples, such as biofluids, solid tissues, tissue/cell homogenates, and cell culture lysates, with a minimized procedure of sample preparation. In the last decades, structural identification of peptides and proteins achieved by MALDI-MS/MS helped researchers and clinicians to decipher molecular function, biological process, cellular component, and related pathways of the gene products as well as their involvement in pathogenesis of diseases. In this review, we highlight the applications of MALDI ionization source and tandem approaches for MS for analyzing biomedical relevant peptides and proteins. Furthermore, one of the most relevant applications of MALDI-MS/MS is to provide “molecular pictures”, which offer in situ information about molecular weight proteins without labeling of potential targets. Histology-directed MALDI-mass spectrometry imaging (MSI) uses MALDI-ToF/ToF or other MALDI tandem mass spectrometers for accurate sequence analysis of peptide biomarkers and biological active compounds directly in tissues, to assure complementary and essential spatial data compared with those obtained by LC-ESI-MS/MS technique.     

Analysis of chloroquine and metabolites directly from whole‐body animal tissue sections by liquid extraction surface analysis (LESA) and tandem mass spectrometry

The rapid and direct analysis of the amount and spatial distribution of exogenous chloroquine (CHQ) and CHQ metabolites from tissue sections by liquid extraction surface sampling analysis coupled with tandem mass spectrometry (LESA‐MS/MS) was demonstrated. LESA‐MS/MS results compared well with previously published CHQ quantification data collected by organ excision, extraction and fluorescent detection. The ability to directly sample and analyze spatially resolved exogenous molecules from tissue sections with minimal sample preparation and analytical method development has the potential to facilitate the assessment of target tissue penetration of pharmaceutical compounds, to establish pharmacokinetic/pharmacodynamic relationships, and to complement established pharmacokinetic methods used in the drug discovery process during tissue distribution assessment. Copyright © 2012 John Wiley & Sons, Ltd.     

Detection of small molecule concentration gradients in ocular tissues and humours

The eye is an elegant organ consisting of a number of tissues and fluids with specialised functions that together allow it to effectively transmit and transduce light input to the brain for visual perception. One key determinant of this integrated function is the spatial relationship of ocular tissues. Biomolecular distributions within the main ocular tissues cornea, lens, and retina have been studied extensively in isolation, yet the potential for metabolic communication between ocular tissues via the ocular humours has been difficult to visualise. To address this limitation, the current study presents a method to map spatial distributions of metabolites and small molecules in whole eyes, including ocular humours. Using a tape‐transfer system and freeze‐drying, the spatial distribution of ocular small molecules was investigated in mouse, rat, fish (black bream), and rabbit eyes using negative ion mode MALDI imaging mass spectrometry. Full‐scan imaging was used for discovery experiments, while MS/MS imaging for identification and localisation was also demonstrated. In all eyes, metabolites such as glutathione and phospholipids were localised in the main ocular tissues. In addition, in rodent eyes, major metabolites were distributed relatively uniformly in ocular humours. In contrast, both uniform and spatially defined ocular metabolite distributions were observed in the black bream eye. Tissue and ocular humour distributions were reproducible, as demonstrated by the three‐dimensional analysis of a mouse eye, and able to be captured with high spatial resolution analysis. The presented method could be used to further investigate the role of inter‐tissue metabolism in ocular health, and to support the development of therapeutics to treat major ocular diseases.     

Imaging with mass spectrometry: Which ionization technique is best?

The use of mass spectrometry (MS) to acquire molecular images of biological tissues and other substrates has developed into an indispensable analytical tool over the past 25 years. Imaging mass spectrometry technologies are widely used today to study the in situ spatial distributions for a variety of analytes. Early MS images were acquired using secondary ion mass spectrometry and matrix-assisted laser desorption/ionization. Researchers have also designed and developed other ionization techniques in recent years to probe surfaces and generate MS images, including desorption electrospray ionization (DESI), nanoDESI, laser ablation electrospray ionization, and infrared matrix-assisted laser desorption electrospray ionization. Investigators now have a plethora of ionization techniques to select from when performing imaging mass spectrometry experiments. This brief perspective will highlight the utility and relative figures of merit of these techniques within the context of their use in imaging mass spectrometry.     

磷酸铵盐作为基质添加物促进磷酸化肽在MALDI-MS分析中的离子化效率

本文建立了以磷酸铵盐为添加剂的基质新系统,增强了磷酸化肽在MALDI正离子模式下的离子化。系统地考察了不同的磷酸盐以及不同的盐浓度对磷酸化肽离子化效率的影响。考察了两种适合于磷酸化肽离子化的基质类型2,5-二羟基苯甲酸和2,4,6-三羟基苯乙酮。用2,5-二羟基苯甲酸作为基质时,当加入10 mM 磷酸氢二铵时,磷酸化蛋白质β-casein的磷酸肽 48FQ[pS]EEQQQTEDELQDK63的离子化效率可以增强5-8倍,当加入10 mM磷酸二氢胺时,磷酸肽的离子化效率可以增强3-4倍。用2,4,6-三羟基苯乙酮作为基质时,当加入5mM磷酸氢二铵时,磷酸化肽的离子化效率比文献报道的最有利于磷酸化肽离子化的基质体系增强了2倍。并探讨了铵根离子和磷酸根离子促进磷酸化肽在MALDI的正离子模式下离子化效率的机理。     

Decellularization of intact tissue enables MALDI imaging mass spectrometry analysis of the extracellular matrix

Matrix‐assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) is a powerful molecular mapping technology that offers unbiased visualization of the spatial arrangement of biomolecules in tissue. Although there has been a significant increase in the number of applications employing this technology, the extracellular matrix (ECM) has received little attention, likely because ECM proteins are mostly large, insoluble and heavily cross‐linked. We have developed a new sample preparation approach to enable MALDI IMS analysis of ECM proteins in tissue. Prior to freezing and sectioning, intact tissues are decellularized by incubation in sodium dodecyl sulfate. Decellularization removes the highly abundant, soluble species that dominate a MALDI IMS spectrum while preserving the structural integrity of the ECM. In situ tryptic hydrolysis and imaging of tryptic peptides are then carried out to accommodate the large sizes of ECM proteins. This new approach allows the use of MALDI IMS for identification of spatially specific changes in ECM protein expression and modification in tissue. Copyright © 2015 John Wiley & Sons, Ltd.     

A concise review of mass spectrometry imaging

Mass spectrometric imaging allows the investigation of the spatial distribution of molecules at complex surfaces. The combination of molecular speciation with local analysis renders a chemical microscope that can be used for the direct biomolecular characterization of histological tissue surfaces. MS based imaging advantageously allows label-free detection and mapping of a wide-range of biological compounds whose presence or absence can be the direct result of disease pathology. Successful detection of the analytes of interest at the desired spatial resolution requires careful attention to several steps in the mass spectrometry imaging protocol. This review will describe and discuss a selected number of crucial developments in ionization, instrumentation, and application of this innovative technology. The focus of this review is on the latest developments in imaging MS. Selected biological applications are employed to illustrate some of the novel features discussed. Two commonly used MS imaging techniques, secondary ion mass spectrometric (SIMS) imaging and matrix-assisted laser desorption ionization (MALDI) mass spectrometric imaging, center this review. New instrumental developments are discussed that extend spatial resolution, mass resolving power, mass accuracy, tandem-MS capabilities, and offer new gas-phase separation capabilities for both imaging techniques. It will be shown how the success of MS imaging is crucially dependent on sample preparation protocols as they dictate the nature and mass range of detected biomolecules that can be imaged. Finally, developments in data analysis strategies for large imaging datasets will be briefly discussed.     

Structural characterization of chelator-terminated dendrimers and their synthetic intermediates by mass spectrometry

Herein, we report the structural analysis of a novel family of iron-chelating dendrimers and their synthetic intermediates utilizing matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and electrospray ionization ion trap (ESI IT) MS. These dendrimers share a benzene tricarbonyl core moiety attached to three tripodal branching units, each linking to three terminal groups, ranging from carboxyl, catechol and 3-hydroxy-6-methyl-pyran-4-one moieties and their protected analogs. In order to monitor the progression of dendrimer synthesis, all intermediates and final products were mass analyzed by conventional MALDI-TOF MS with and without alkali metal spiking. For structural characterization, interpretable post-source decay (PSD) and electrospray ionization ion trap MS/MS spectra were obtained from proton, sodium and potassium adducts of the dendrimers. One major route of dendrimer fragmentation was at or adjacent to the amide bonds either of the terminal chelating groups or near the core moiety. Fragmentation in the latter case was primarily at the N-terminal side of the amide bond and was directed by the proximity of a tertiary carbon of the branching unit. Furthermore, it was found that terminal ester, ether and amide linkages to the protecting and chelating groups could be sequentially broken in a single MS/MS spectrum through multiple cleavages resulting in product ions of decreasing intensity. Moreover, such cleavages could also be induced in a stepwise manner in a multistage ion trap MS(n) experiment.     

Ion mobility‐mass spectrometry for the separation and analysis of procyanidins

Procyanidins are polymeric flavan‐3‐ones occurring in many plants with antioxidant and other beneficial bioactivities. They are composed of catechin and epicatechin monomeric units connected by single carbon‐carbon B‐type linkages or A‐type linkages containing both carbon‐carbon and carbon‐oxygen‐carbon bonds. Their polymeric structure makes analysis of procyanidin mixtures always difficult. Evaluation of procyanidins according to degree of polymerization (DP) using high‐performance liquid chromatography (HPLC) is time‐consuming and at best has resolved polymeric families up to DP‐17. To expedite studies of procyanidins, the utility of positive ion electrospray ion mobility‐mass spectrometry (IM‐MS) was investigated for the rapid separation and characterization of procyanidins in mixtures. Applying IM‐MS to analyse structurally defined standards containing up to five subunits, procyanidins could be resolved in less than 6 ms not only by degree of polymerization but also by linkage type. A‐type procyanidins could be resolved from B‐type and both could be at least partially resolved from mixed‐type procyanidins of the same DP. IM‐MS separated higher order procyanidins with DP of at least 24 from extracts of cranberry. As DP increased, the abundances of multiply‐charged procyanidins also increased. During IM‐MS of ions of similar m/z, the ion drift times decreased inversely with increasing charge state. Therefore, IM‐MS was shown to separate mixtures of procyanidins containing at least 24 interconnected subunits in less than 16 ms, not only according to DP, but also according to linkage type between subunits and charge state.     

Imaging of peptides in the rat brain using MALDI-FTICR mass spectrometry

Analytical methods are pursued to measure the identity and location of biomolecules down to the subcellular (microm) level. Available mass spectrometric imaging methods either compromise localization accuracy or identification accuracy in their analysis of surface biomolecules. In this study, imaging FTICR-MS is applied for the spatially resolved mass analysis of rat brain tissue with the aim to optimize protein identification by the high mass accuracy and online MS/MS capabilities of the technique. Mass accuracies up to 6 ppm were obtained in the direct MALDI-analysis of the tissue together with a spatial resolution of 200 microm. The spatial distributions of biomolecules differing in mass by less than 0.1 Da could be resolved, and are shown to differ significantly. Online MS/MS analysis of selected ions was demonstrated. A comparison of the FTICR-MS imaging results with stigmatic TOF imaging on the same sample is presented. To reduce the extended measuring times involved, it is recommended to restrict the FTICR-MS analyses to areas of interest as can be preselected by other, faster imaging methods.     

In situ isobaric lipid mapping by MALDI–ion mobility separation–mass spectrometry imaging

The highly diverse chemical structures of lipids make their analysis directly from biological tissue sections extremely challenging. Here, we report the in situ mapping and identification of lipids in a freshwater crustacean Gammarus fossarum using matrix‐assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) in combination with an additional separation dimension using ion mobility spectrometry (IMS). The high‐resolution trapped ion mobility spectrometry (TIMS) allowed efficient separation of isobaric/isomeric lipids showing distinct spatial distributions. The structures of the lipids were further characterized by MS/MS analysis. It is demonstrated that MALDI MSI with mobility separation is a powerful tool for distinguishing and localizing isobaric/isomeric lipids.     

Development of a matrix-assisted laser desorption ionization mass spectrometric method for rapid process-monitoring of phthalocyanine compounds

Phthalocyanines (PCs), an important class of chemicals widely used in many industrial sectors, are macrocyclic compounds possessing a heteroaromatic π-electron system with optical properties influenced by chemical structures and impurities or by-products introduced during the synthesis process. Analytical tools allowing for rapid monitoring of the synthesis processes are of significance for the development of new PCs with improved performance in many application areas. In this work, we report a matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry (TOFMS) method for rapid and convenient monitoring of PC synthesis reactions. For this class of compounds, intact molecular ions could be detected by MALDI using retinoic acid as matrix. It was shown that relative quantification results of two PC compounds could be generated by MALDI MS. This method was applied to monitor the bromination reactions of nickel- and copper-containing PCs. It was demonstrated that, compared to the traditional UV–visible method, the MALDI MS method offers the advantage of higher sensitivity while providing chemical species and relative quantification information on the reactants and products, which are crucial to process monitoring.     

Spectroscopic characterization of a microplasma used as ionization source for ion mobility spectrometry

We report a miniaturized excitation source for soft ionization of molecules based on a dielectric barrier discharge. An atmospheric plasma is established at the end of a 500 μm diameter capillary using He as buffer gas. The plasma jet which comes out of the capillary is dependent on the gas flow rate. The mechanism of the production of N₂⁺ outside the capillary, which is relevant for the protonation of molecules and sustains the production of primary ions, is investigated by spatially resolved spectroscopic measurements throughout the plasma. Possible application of such miniaturized plasmas is the ionization of gaseous compounds under atmospheric pressure as an alternative to traditional APCI (atmospheric pressure chemical ionization). The miniaturized plasma was applied as ionization source for ion mobility spectrometry where the common sources are radioactive, thus limiting the place of installation. First measurements of gaseous compounds with such a plasma ion mobility spectrometer with promising results showed detection limits comparable or even better than those obtained using common radioactive ionization sources.     

Spatially Resolved Quantification of Gadolinium(III)‐Based Magnetic Resonance Agents in Tissue by MALDI Imaging Mass Spectrometry after In Vivo MRI

Gadolinium(III)‐based contrast agents improve the sensitivity and specificity of magnetic resonance imaging (MRI), especially when targeted contrast agents are applied. Because of nonlinear correlation between the contrast agent concentration in tissue and the MRI signal obtained in vivo, quantification of certain biological or pathophysiological processes by MRI remains a challenge. Up to now, no technology has been able to provide a spatially resolved quantification of MRI agents directly within the tissue, which would allow a more precise verification of in vivo imaging results. MALDI imaging mass spectrometry for spatially resolved in situ quantification of gadolinium(III) agents, in correlation to in vivo MRI, were evaluated. Enhanced kinetics of Gadofluorine M were determined dynamically over time in a mouse model of myocardial infarction. MALDI imaging was able to corroborate the in vivo imaging MRI signals and enabled in situ quantification of the gadolinium probe with high spatial resolution.     

Inkjet printing of gold nanoparticles onto a biologically relevant matrix to create quantitative test materials for time-of-flight secondary ion mass spectrometry

This study describes the use of inkjet printing for the preparation of test materials containing gold nanoparticles (AuNPs) on a biologically relevant matrix and discusses the methods of using time-of-flight secondary ion mass spectrometry (ToF-SIMS) for their spatially resolved quantification. Evaluation of test materials containing AuNPs with nominal diameters of (30, 80, 100, and 150) nm deposited onto gelatin with loadings ranging from 34 fg up to 67 000 fg per spot suggests that ToF-SIMS has the sensitivity and the dynamic range to quantify NP deposits in a biological matrix at toxicologically relevant concentrations, although it was not capable of reliably determining the size of the AuNPs from the intensity data. Regardless, the ability to extract intensity data from individual regions of interest (ROIs) showed that spatially resolved quantification is possible, even when multiple features exist in a single image and in a single depth profile. The argon gas cluster source used for sputtering led to a matrix removal effect where the matrix surrounding the AuNPs became negligible, which may facilitate the preparation of quantitative test materials.     

An Inexpensive,simple calibration method for MALDI TOF/TOF systems

The array of analytes that can be measured by MADLI MS has created an equally vast range of calibration mixtures. The inherent problem with this is that acquiring all of them at commercial rates can be prohibitively expensive. With this in mind, we have created a low‐cost alternative to the most commonly used peptide calibrants. We were able to achieve an overall 78 ppm mass accuracy across a mass range of 900 to 2500 Da which was comparable to the mass accuracy achievable with commercial peptide mixes and hence has become a viable alternative.     

ESI,APCI, and MALDI tandem mass spectrometry of poly(methyl acrylate)s: A comparison study for the structural characterization of polymers synthesized via CRP techniques and the software application to analyze MS/MS data

Research in polymer science and engineering is moving from classical methodologies to advanced analytical strategies in which mass spectrometry (MS)‐based techniques play a crucial role. The molecular complexity of polymers requires new characterization tools and approaches to elucidate the detailed structural information. In this contribution, a comparison study of poly(methyl acrylate)s (PMA) using different tandem mass spectrometry techniques (ESI, APCI, and MALDI MS/MS) is reported to provide insights into the macromolecular structure with the aid of a special MS/MS data interpretation software. Collision‐induced dissociation (CID) was utilized to examine the fragmentation pathways of PMAs synthesized via various controlled radical polymerization techniques. All three mass spectrometry techniques are used to analyze structural details of PMAs and the labile end‐groups are determined based on the fragmentation behavior in CID. Fragmentation products were identified which are characteristics for the cleavage between the polymer chain and the end‐group. The application of a tailor‐made software is shown to analyze complex MS/MS data, and it is proven that this kind of software will be helpful for polymer scientists to identify fragmentation products obtained by tandem mass spectrometry similar to the fields of proteomics, metabolomics, genomics, and glycomics. © 2013 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2013     

正负离子切换扫描质谱成像分析方法及其整体动物体内代谢应用研究

基于质谱成像(MSI)技术的空间分辨代谢组学方法已经成为生物组织学、肿瘤分子病理诊断和新药药效毒理研究的有力工具.该研究采用敞开式空气动力辅助解吸电喷雾离子化(AFADESI)技术,开发了一种正负离子切换扫描的质谱成像方法.该方法在离子化过程中无需施加高电压,既提高了敞开式离子化质谱成像的操作安全性,还可将生物组织切片...