Antigen retrieval prior to on-tissue digestion of formalin-fixed paraffin-embedded tumour tissue sections yields oxidation of proline residues

MALDI-mass spectrometry imaging (MALDI-MSI) has been shown to allow the study of protein distribution and identification directly within formalin-fixed paraffin-embedded (FFPE) tissue sections. However, direct protein identification from tissue sections remains challenging due to signal interferences and/or existing post-translational or other chemical modifications. The use of antigen retrieval (AR) has been demonstrated for unlocking proteins prior to in situ enzymatic digestion and MALDI-MSI analysis of FFPE tissue sections. In the work reported here, the identification of proline oxidation, which may occur when performing the AR protocol, is described. This facilitated and considerably increased the number of identified peptides when adding proline oxidation as a variable modification to the MASCOT search criteria. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.

MALDI-MSI for the analysis of a 3D tissue-engineered psoriatic skin model

MALDI-MS Imaging is a novel label-free technique that can be used to visualize the changes in multiple mass responses following treatment. Following treatment with proinflammatory cytokine interleukin-22 (IL-22), the epidermal differentiation of Labskin, a living skin equivalent (LSE), successfully modeled psoriasis in vitro. Masson's trichrome staining enabled visualization and quantification of epidermal differentiation between the untreated and IL-22 treated psoriatic LSEs. Matrix-assisted laser desorption ionization mass spectrometry imaging was used to observe the spatial location of the psoriatic therapy drug acetretin following 48 h treatments within both psoriatic and normal LSEs. After 24 h, the drug was primarily located in the epidermal regions of both the psoriatic and nonpsoriatic LSE models whereas after 48 h it was detectible in the dermis.

MALDI MSI analysis of lipid changes in living skin equivalents in response to emollient creams containing palmitoylethanolamide

Mass spectrometry imaging (MSI) is a powerful tool for the study of intact tissue sections. The use of matrix-assisted laser desorption/ionisation (MALDI) MSI for the study of the distribution and effect of emollient treatment on sections of reconstructed living skin equivalents during their development and maturation is described. Living skin equivalent (LSE) samples were obtained at 14days development, re-suspended in maintenance medium and incubated for 24h after delivery. The medium was changed, the LSE treated with either Physiogel A.I.® or Oilatum Junior® emollients and then re-incubated and samples taken at 4, 6 and 24h time points. Mass spectra and mass spectral images were recorded from 12μm sections of the LSE taken at each time point for comparison using MALDI mass spectrometry (MS). It was possible to detect ions characteristic of each emollient in the LSE. In addition a number of lipid species previously reported as being significant in the maturation of the LSE were observable. At the 24h time point, the images revealed what appeared to be differences in the organisation of the skin cells observed across the Physiogel A.I.® treatment group tissue sections when directly compared to the untreated tissue group.

Mapping drug distribution in brain tissue using liquid extraction surface analysis mass spectrometry imaging

Liquid extraction surface analysis mass spectrometry (LESA-MS) is a surface sampling technique that incorporates liquid extraction from the surface of tissue sections with nanoelectrospray mass spectrometry. Traditional tissue analysis techniques usually require homogenization of the sample prior to analysis via high-performance liquid chromatography mass spectrometry (HPLC-MS), but an intrinsic weakness of this is a loss of all spatial information and the inability of the technique to distinguish between actual tissue penetration and response caused by residual blood contamination. LESA-MS, in contrast, has the ability to spatially resolve drug distributions and has historically been used to profile discrete spots on the surface of tissue sections. Here, we use the technique as a mass spectrometry imaging (MSI) tool, extracting points at 1 mm spatial resolution across tissue sections to build an image of xenobiotic and endogenous compound distribution to assess drug blood-brain barrier penetration into brain tissue. A selection of penetrant and "nonpenetrant" drugs were dosed to rats via oral and intravenous administration. Whole brains were snap-frozen at necropsy and were subsequently sectioned prior to analysis by matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) and LESA-MSI. MALDI-MSI, as expected, was shown to effectively map the distribution of brain penetrative compounds but lacked sufficient sensitivity when compounds were marginally penetrative. LESA-MSI was used to effectively map the distribution of these poorly penetrative compounds, highlighting its value as a complementary technique to MALDI-MSI. The technique also showed benefits when compared to traditional homogenization, particularly for drugs that were considered nonpenetrant by homogenization but were shown to have a measurable penetration using LESA-MSI.

Communication of medical images to diverse audiences using multimodal imaging

A study has been completed examining design issues concerning the interpretation of and dissemination of multimodal medical imaging data sets to diverse audiences. To create a model data set mouse fibrosarcoma tissue was visualised via magnetic resonance imaging (MRI), Matrix-Assisted Laser Desorption/Ionisation-Mass Spectrometry (MALDI-MSI) and histology. MRI images were acquired using the 0.25T Esaote GScan; MALDI images were acquired using a Q-Star Pulsar I mass spectrometer. Histological staining of the same tissue sections used for MALDI-MSI was then carried out. Areas assigned to hemosiderin deposits due to haemorrhaging could be visualised via MRI. In the MALDI-MSI data obtained the distribution sphingomyelin species could be used to identify regions of viable tumour. Mathematical ‘up sampling’ using hierarchical clustering-based segmentation provided a sophisticated image enhancement tool for both MRI and MALDI-MS and assisted in the correlation of images.

Mass spectrometry imaging tools in oncology

MS imaging allows profiling and imaging of compounds directly from tumor tissue, tissue microarrays and tissue-engineered models of tumors. Methodologies for the quantitative analysis of localized/colocalized ion signals from a single cancer cell would be a major advance. Alternative methods of generating ions to matrix-assisted laser desorption ionization are increasingly employed. Desorption electrospray ionization has been used for the intraoperative diagnosis of human brain tumors and secondary ion MS imaging with cluster primary ion sources has been used for high spatial resolution imaging tumor sections. Extensive validation of the technique for the analysis of disease biomarkers is required, if imaging MS is to have a future role in the clinic.

Lipid changes within the epidermis of living skin equivalents observed across a time-course by MALDI-MS imaging and profiling

Background

Mass spectrometry imaging (MSI) is a powerful tool for the study of intact tissue sections. Here, its application to the study of the distribution of lipids in sections of reconstructed living skin equivalents during their development and maturation is described.

Methods

Living skin equivalent (LSE) samples were obtained at 14 days development, re-suspended in maintenance medium and incubated for 24 h after delivery. The medium was then changed, the LSE re-incubated and samples taken at 4, 6 and 24 h time points. Mass spectra and mass spectral images were recorded from 12 μm sections of the LSE taken at each time point for comparison using matrix assisted laser desorption ionisation mass spectrometry.

Results

A large number of lipid species were identified in the LSE via accurate mass-measurement MS and MSMS experiments carried out directly on the tissue sections. MS images acquired at a spatial resolution of 50 μm × 50 μm showed the distribution of identified lipids within the developing LSE and changes in their distribution with time. In particular development of an epidermal layer was observable as a compaction of the distribution of phosphatidylcholine species.

Conclusions

MSI can be used to study changes in lipid composition in LSE. Determination of the changes in lipid distribution during the maturation of the LSE will assist in the identification of treatment responses in future investigations.

Electronic supplementary material

The online version of this article (doi:10.1186/s12944-015-0089-z) contains supplementary material, which is available to authorized users.

Thin-layer chromatography/matrix-assisted laser desorption/ionisation mass spectrometry and matrix-assisted laser desorption/ionisation mass spectrometry imaging for the analysis of phospholipids in LS174T colorectal adenocarcinoma xenografts treated with the vascular disrupting agent DMXAA

RATIONALE

5,6-Dimethylxanthenone-4-acetic acid (DMXAA) is a low molecular weight drug of the flavonoid group, which has an anti-vascular effect in tumours causing endothelial cell apoptosis and activation of cytokines. Flavonoid-based compounds have been reported to lead to an upregulation in the expression of lysophosphatidylcholines (LPC)-type lipids in solid tumours. A study employing TLC/MALDI-MS and MALDI-MS imaging to examine LS174T colorectal adenocarcinoma xenografts following administration of DMXAA has been conducted into this effect.

METHODS

LS174T colorectal adenocarcinoma xenografts grown in male immune-deficient mice were treated with 27.5 mg/kg DMXAA. The control (before treatment) and 4 h and 24 h post-treatment tumours were excised and divided into two. MALDI-MS imaging experiments were carried out on 12 µm cryosections sections taken from one half of the tumours and from the other half the lipids were extracted and analysed by TLC/MALDI-MS. These experiments were carried out in triplicate.

RESULTS

Statistical analysis of the MALDI-MS imaging data set indicated an increased amount of LPC in the 24 h post-treated sample and a decreased amount of PC in the 24 h post-treated sample, compared with the 4 h post-treated sample and the control. These effects were confirmed by the TLC/MALDI-MS data. The lipid extracts were separated into six spots on the TLC plate. These were identified as arising from different lipids classes, i.e. LPC, sphingomyelins (SM), phosphatidylcholines (PC) and phosphatidylethanolamines (PE). The TLC/MALDI-MS data indicated that LPC were highly expressed in the 4 h and 24 h post-treated tumour samples compared with the control. Examination of the mass spectrometric images confirms this increase and demonstrates additionally that the increase in the signals arising from LPC appears to be localised primarily within the central areas of the xenograft.

CONCLUSIONS

An increase in expression of LPC lipids in solid tumours treated with DMXAA has been demonstrated and shown to be localised in the central area of the tumour.

Alternative surfactants for improved efficiency of in situ tryptic proteolysis of fingermarks

Despite recent improvements to in situ proteolysis strategies, a higher efficiency is still needed to increase both the number of peptides detected and the associated ion intensity, leading to a complete and reliable set of biomarkers for diagnostic or prognostic purposes. In the study presented here, an extract of a systematic study is illustrated investigating a range of surfactants assisting trypsin proteolytic activity. Method development was trialled on fingermarks; this specimen results from a transfer of sweat from an individual's fingertip to a surface upon contact. As sweat carries a plethora of biomolecules, including peptides and proteins, fingermarks are, potentially, a very valuable specimen for non-invasive prognostic or diagnostic screening. A recent study has demonstrated the opportunity to quickly detect peptides and small proteins in fingermarks using Matrix Assisted Laser Desorption Ionization Mass Spectrometry Profiling (MALDI MSP). However, intact detection bears low sensitivity and does not allow species identification; therefore, a shotgun proteomic approach was employed involving in situ proteolysis. Data demonstrate that in fingermarks, further improvements to the existing method can be achieved using MEGA-8 as surfactant in higher percentages as well as combinations of different detergents. Also, for the first time, Rapigest SF, normally used in solution digestions, has been shown to successfully work also for in situ proteolysis.

Mass spectrometry imaging for the proteomic study of clinical tissue

Over the last decade, MALDI-MS imaging has been used by researchers to explore areas of proteomics, lipidomics and metabolomics in samples of clinical origin for both targeted and global biomarker analysis. Numerous technological advancements in MS and clinical tissue MS imaging have been accomplished; hence, in this article we aim to critically discuss whether MS imaging has now in fact become a true champion of the 'Omics Era'. In order to assess the potential for it to be routinely used in the clinical setting, it is pertinent to discuss some of its limitations, and to examine how these have been addressed by researchers. The key limitations of the technique we will discuss in this viewpoint article are as follows: sample throughput; relevance to patients, the availability of validated/standardised techniques; and integration with conventional pathology and other medical imaging techniques. Good progress has been made over the last 5 years in overcoming these limitations that had previously restricted the use of this technology in the clinical setting.

The use of hydrazine-based derivatization reagents for improved sensitivity and detection of carbonyl containing compounds using MALDI-MSI

Hydrazine-based derivatization reagents have been used to detect the presence of the carbonyl containing glucocorticoid fluticasone proprionate in rat lung tissue by MALDI-MSI. Such reagents also act as a matrix for analysis by MALDI-MS and have been termed "reactive matrices". Cryosections of rat lung tissue (12 μm), spotted with a range of concentrations of fluticasone proprionate, were derivatized in situ with 2,4-dinitrophenylhydrazine (DNPH) and 4-dimethylamino-6-(4-methoxy-1-naphthyl)-1,3,5-triazine-2-hydrazine (DMNTH) by the use of an acoustic reagent spotter. It has been demonstrated that DMNTH gave superior results compared to DNPH and that analysis of samples immediately after application of DMNTH resulted in the detection of the protonated hydrazone derivative ([MD + H](+)) of fluticasone propionate at a concentration of 500 ng/μL. It has been further shown that a prolonged reaction time (~48 h) improves the detection limit of the protonated hydrazone derivative to 50 ng/μL and that improvements in sensitivity and limits of detection are obtained when a conventional MALDI matrix CHCA is employed in conjunction with the DNPH/DMNTH reactive matrix.

"Afterlife experiment": use of MALDI-MS and SIMS imaging for the study of the nitrogen cycle within plants

As part of a project to demonstrate the science of decay, a series of mass spectrometry imaging experiments were performed. The aim was to demonstrate that decay and decomposition are only part of the story and to show pictorially that atoms and molecules from dead plants and animals are incorporated into new life. Radish plants (Raphanus sativus) were grown hydroponically using a nutrient system containing (15)N KNO3 (98% labeled) as the only source of nitrogen. Plants were cropped and left to ferment in water for 2 weeks to create a radish "tea", which was used as a source of nitrogen for radish grown in a second hydroponics experiment. After 5 weeks of growth, the radish plants were harvested and cryosectioned, and sections were imaged by positive-ion MALDI and SIMS mass spectrometry imaging. The presence of labeled species in the plants grown using (15)N KNO3 as nutrient and those grown from the radish "tea" was readily discernible. The uptake of (15)N into a number of identifiable metabolites has been studied by MALDI-MS and SIMS imaging.

Recombinant " IMS TAG" proteins--a new method for validating bottom-up matrix-assisted laser desorption/ionisation ion mobility separation mass spectrometry imaging

RATIONALE

Matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) provides a methodology to map the distribution of peptides generated by in situ tryptic digestion of biological tissue. It is challenging to correlate these peptides to the proteins from which they arise because of the many potentially overlapping and hence interfering peptide signals generated.

METHODS

A recombinant protein has been synthesised that when cleaved with trypsin yields a range of peptide standards for use as identification and quantification markers for multiple proteins in one MALDI-IMS-MSI experiment. Mass spectrometry images of the distribution of proteins in fresh frozen and formalin-fixed paraffin-embedded tissue samples following in situ tryptic digestion were generated by isolating signals on the basis of their m/z value and ion mobility drift time, which were correlated to matching peptides in the recombinant standard.

RESULTS

Tryptic digestion of the IMS-TAG protein and MALDI-MS analysis yielded m/z values and ion mobility drift time for the signature peptides included in it. MALDI-IMS-MSI images for the distribution of the proteins HSP90 and vimentin, in FFPE EMT6 mouse tumours, and HSP90 and plectin in a fresh frozen mouse fibrosarcoma, were generated by extracting ion images at the corresponding m/z value and drift time from the tissue samples.

CONCLUSIONS

The IMS-TAG approach provides a new means to confirm the identity of peptides generated by in situ digestion of biological tissue.

Metabolomics in toxicology and preclinical research

Metabolomics, the comprehensive analysis of metabolites in a biological system, provides detailed information about the biochemical/physiological status of a biological system, and about the changes caused by chemicals. Metabolomics analysis is used in many fields, ranging from the analysis of the physiological status of genetically modified organisms in safety science to the evaluation of human health conditions. In toxicology, metabolomics is the -omics discipline that is most closely related to classical knowledge of disturbed biochemical pathways. It allows rapid identification of the potential targets of a hazardous compound. It can give information on target organs and often can help to improve our understanding regarding the mode-of-action of a given compound. Such insights aid the discovery of biomarkers that either indicate pathophysiological conditions or help the monitoring of the efficacy of drug therapies. The first toxicological applications of metabolomics were for mechanistic research, but different ways to use the technology in a regulatory context are being explored. Ideally, further progress in that direction will position the metabolomics approach to address the challenges of toxicology of the 21st century. To address these issues, scientists from academia, industry, and regulatory bodies came together in a workshop to discuss the current status of applied metabolomics and its potential in the safety assessment of compounds. We report here on the conclusions of three working groups addressing questions regarding 1) metabolomics for in vitro studies 2) the appropriate use of metabolomics in systems toxicology, and 3) use of metabolomics in a regulatory context.

Efficiency of the dry-wet method for the MALDI-MSI analysis of latent fingermarks

Matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) has proven to be a powerful analytical tool to investigate problems in several fields of life science. A novel application is in the field of forensics, particularly in the analysis of latent fingermarks. This technology enables images of the fingermark ridge detail and additional intelligence to be simultaneously obtained. Although several methods are available to deposit the MALDI matrix, to make the technology forensically operational, another deposition approach was devised and reported, namely the 'dry-wet' method. In the present study, the efficiency of the dry-wet method was evaluated and compared with the conventional spray coat methodology. Results indicate that the dry-wet method is superior for all the donors' typologies in terms of ion signal intensity and clarity of the ridge details. To underpin the reasons of this efficiency, scanning electron microscopy analyses were carried out in parallel to MALDI-MSI experiments using matrices of different particle size. Results have confirmed that the particle size plays an important role in the efficiency of the method as higher quality images and higher intensity spectra are produced as the matrix particle size decreases.