36 research outputs found
MALDI-MS tissue imaging identification of biliverdin reductase B overexpression in prostate cancer
No full textAbstract not availableJohannes Dominikus Pallua, Georg Schaefer, Christof Seifarth, Michael Becker, Stephan Meding, Sandra Rauser, Axel Walch, Michael Handler, Michael Netzer, Marina Popovscaia, Melanie Osl, Christian Baumgartner, Herbert Lindner, Leopold Kremser, Bettina Sarg, Georg Bartsch, Christian W. Huck, Günther K. Bonn, Helmut Klocke
Matrix-assisted laser desorption/ionization imaging protocol for in situ characterization of tryptic peptide identity and distribution in formalin-fixed tissue
No full textLink to a related website: https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/rcm.6488, Open Access via UnpaywallRATIONALE: Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry provides the means tomap the in situ distribution of tryptic peptides in formalin-fixed clinical tissue samples. The ability to analyze clinicalsamples is of great importance to further developments in the imaging field. However, there is a requirement in this fieldof research for additional methods describing the characterization of tryptic peptides by MALDI imaging.
METHODS AND RESULTS: This protocol gives highly detailed instructions, with examples, for (1) successfully performingtryptic peptide MALDI imaging on formalin-fixed cancer tissue using a MALDI-TOF/TOF MS instrument, (2) tentativelygenerating identifications through nLC/MS/MS, and (3) validating these identifications by in situ MS/MS of peptides ofinterest.
CONCLUSIONS: This protocol provides a detailed and straightforward description of the methods required for groupsnew to MALDI imaging to begin analysis of formalin-fixed clinical samples.Ove J. R. Gustafsson, James S. Eddes, Stephan Meding, Shaun R. McColl, Martin K. Oehler and Peter Hoffman
Internal calibrants allow high accuracy peptide matching between MALDI imaging MS and LC-MS/MS
No full textOne of the important challenges for MALDI imaging mass spectrometry (MALDI-IMS) is theunambiguous identification of measured analytes. One way to do this is to match trypticpeptide MALDI-IMS m/z values with LC-MS/MS identified m/z values. Matching using currentMALDI-TOF/TOF MS instruments is difficult due to the variability of in situ time-of-flight (TOF)m/z measurements. This variability is currently addressed using external calibration, whichlimits achievable mass accuracy for MALDI-IMS and makes it difficult to match these data todownstream LC-MS/MS results. To overcome this challenge, the work presented here details amethod for internally calibrating data sets generated from tryptic peptide MALDI-IMS onformalin-fixed paraffin-embedded sections of ovarian cancer. By calibrating all spectra tointernal peak features the m/z error for matches made between MALDI-IMS m/z values and LCMS/MSidentified peptide m/z values was significantly reduced. This improvement wasconfirmed by follow up matching of LC-MS/MS spectra to in situ MS/MS spectra from the samem/z peak features. The sum of the data presented here indicates that internal calibrantsshould be a standard component of tryptic peptide MALDI-IMS experiments.This article is part of a Special Issue entitled: Imaging Mass Spectrometry: A User’s Guide toa New Technique for Biological and Biomedical Research.Johan O.R. Gustafsson, James S. Eddes, Stephan Meding, Tomas Koudelka, Martin K. Oehler, Shaun R. McColl and Peter Hoffman
Feature extraction for proteomics imaging mass spectrometry data
No full textImaging mass spectrometry (IMS) has transformed proteomics by providing an avenue for collecting spatially distributed molecular data. Mass spectrometry data acquired with matrix assisted laser desorption ionization (MALDI) IMS consist of tens of thousands of spectra, measured at regular grid points across the surface of a tissue section. Unlike the more standard liquid chromatography mass spectrometry, MALDI-IMS preserves the spatial information inherent in the tissue. Motivated by the need to differentiate cell populations and tissue types in MALDI-IMS data accurately and efficiently, we propose an integrated cluster and feature extraction approach for such data. We work with the derived binary data representing presence/absence of ions, as this is the essential information in the data. Our approach takes advantage of the spatial structure of the data in a noise removal and initial dimension reduction step and applies k -means clustering with the cosine distance to the high-dimensional binary data. The combined smoothing-clustering yields spatially localized clusters that clearly show the correspondence with cancer and various noncancerous tissue types. Feature extraction of the high-dimensional binary data is accomplished with our difference in proportions of occurrence (DIPPS) approach which ranks the variables and selects a set of variables in a data-driven manner. We summarize the best variables in a single image that has a natural interpretation. Application of our method to data from patients with ovarian cancer shows good separation of tissue types and close agreement of our results with tissue types identified by pathologists.Lyron J. Winderbaum, Inge Koch, Ove J. R. Gustafsson, Stephan Meding and Peter Hoffman
Identifikation klinischer Marker im Kolonkarzinom durch gewebsbasierte <i>in situ</i> Proteomik
No full textColon cancer is one of the most frequent cancers. In this thesis, human primary tumour tissues were analysed by MALDI Imaging, label-free quantitative proteomics, and immunohistochemical tissue staining. The clinical aspects of regional lymph node metastasis, tumour recurrence and correct classification of primary tumours were of central interest. Novel proteomic markers for regional lymph node metastasis and tumour recurrence were identified. Additionally, primary tumours could be classified with high accuracy. These results could support new, personalised approaches in diagnostics and therapy.Darmkrebs ist eine der häufigsten Krebserkrankungen. In dieser Arbeit wurden humane Primärtumoren des Kolonkarzinoms mittels bildgebender Massenspektrometrie (MALDI Imaging), markierungsfreier quantitativer Massenspektrometrie und immunhistochemischer Gewebsfärbung untersucht. Dabei standen die klinischen Fragestellungen der lokoregionäre Lymphknotenmetastasierung, der Rezidivbildung und der korrekten Primärtumorklassifikation im Mittelpunkt. Es konnten neue, proteomische Marker für die lokoregionäre Lymphknotenmetastasierung und Rezidivbildung identifiziert werden. Zudem konnte gezeigt werden, dass Primärtumoren mit hoher Genauigkeit klassifiziert werden können. Diese Ergebnisse könnten neue, personalisierte Ansätze in Diagnostik und Therapie ermöglichen
Comprehensive identification of proteins from MALDI imaging
No full textMatrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) is a powerful tool for the visualization of proteins in tissues and has demonstrated considerable diagnostic and prognostic value. One main challenge is that the molecular identity of such potential biomarkers mostly remains unknown. We introduce a generic method that removes this issue by systematically identifying the proteins embedded in the MALDI matrix using a combination of bottom-up and top-down proteomics. The analyses of ten human tissues lead to the identification of 1400 abundant and soluble proteins constituting the set of proteins detectable by MALDI IMS including >90% of all IMS biomarkers reported in the literature. Top-down analysis of the matrix proteome identified 124 mostly N- and C-terminally fragmented proteins indicating considerable protein processing activity in tissues. All protein identification data from this study as well as the IMS literature has been deposited into MaTisse, a new publically available database, which we anticipate will become a valuable resource for the IMS community.Stefan K. Maier, Hannes Hahne, Amin Moghaddas Gholami, Benjamin Balluff, Stephan Meding, Cedrik Schoene, Axel K. Walch, and Bernhard Kuste
High-resolution metabolite imaging of light and dark treated retina using MALDI-FTICR mass spectrometry
No full textMS imaging (MSI) is a valuable tool for diagnostics and systems biology studies, being a highly sensitive, label-free technique capable of providing comprehensive spatial distribution of different classes of biomolecules. The application of MSI to the study of endogenous compounds has received considerable attention because metabolites are the result of the interactions of a biosystem with its environment. MSI can therefore enhance understanding of disease mechanisms and elucidate mechanisms for biological variation. We present the in situ comparative metabolomics imaging data for analyses of light- and dark-treated retina using MALDI-FTICR. A wide variety of tissue metabolites were imaged at a high spatial resolution. These include nucleotides, central carbon metabolism pathway intermediates, 2-oxocarboxylic acid metabolism, oxidative phosphorylation, glycerophospholipid metabolism, and cysteine and methionine metabolites. The high lateral resolution enabled the differentiation of retinal layers, allowing determination of the spatial distributions of different endogenous compounds. A number of metabolites demonstrated differences between light and dark conditions. These findings add to the understanding of metabolic activity in the retina.Na Sun, Alice Ly, Stephan Meding, Michael Witting, Stefanie M. Hauck, Marius Ueffing, Philippe Schmitt-Kopplin, Michaela Aichler, and Axel Walc
High-resolution MALDI mass spectrometric imaging of lipids in the mammalian retina
No full textFirst online: 23 December 2014Matrix-assisted laser desorption/ionization mass spectrometric imaging (MALDI-MSI) is emerging as a powerful tool for the analysis of molecular distributions in biological samples in situ. When compared to classical histology, the major benefit of this method is the ability to identify and localize many molecules in a single tissue sample. MALDI-MSI spatial resolution currently falls short of traditional microscopic methods as it is limited by instrumentation and sample preparation. Tissue preparation steps, such as matrix deposition, are critical when considering strategies to further enhance the spatial resolution. The mammalian retina was selected as the tissue of choice for method development; its stratified anatomy renders it an ideal tissue to test high-resolution MALDI-MSI as the different layers correspond to specific neuronal classes and cellular structures. We compared alcohol-fixed, paraffin-embedded retina to fresh-frozen samples and matrix that had been deposited by spray or by sublimation. We present a lipid imaging method based on MALDI-MSI of frozen retinal sections with sublimated 2,5-dihydroxybenzoic acid matrix, which results in a highly advanced resolution compared to previous established methods. Hierarchical clustering of the primary data allows robust detection and differentiation of molecular distributions at a spatial resolution between 10 and 20 μm, thus approaching single-cell resolution.Alice Ly, Cédrik Schöne, Michael Becker, Janine Rattke, Stephan Meding, Michaela Aichler, Detlev Suckau, Axel Walch, Stefanie M. Hauck, Marius Ueffin
Lake Pleasant striped bass
No full textabstract: Lake Pleasant has historically been regarded as one of the premier largemouth bass (Micropteus
salmoides) fisheries in Arizona. However, the quality of the largemouth bass fishery has decreased, resulting in low angler satisfaction and a general concern for the health of the fishery. The leading
hypothesis for the cause of this decline is the recent invasion of striped bass (Morone saxatilis), which may be responsible, in part, for the shift in largemouth bass size structure through competition for resources and predation.Technical guidance bulletin ; no. 11Includes bibliographical references (p. 33-35)
MALDI imaging mass spectrometry for direct tissue analysis.
No full textMALDI (Matrix-Assisted Laser Desorption/Ionization) Imaging mass spectrometry is a powerful new method for analyzing the spatial distribution of molecules in tissues. Several different classes of cellular constituents such as proteins, peptides, lipids, and small molecules can be analyzed in situ while maintaining the morphological integrity of the tissue. This allows a correlation of the morphology with the previously acquired molecular patterns. By this, specific molecules can be clearly assigned to their cellular origin. Here, we will present a protocol for the analysis of proteins in tissues which are either native or alcohol-fixed and paraffin-embedded
