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Bremen, Germany

Alexandrov T.,University of Bremen | Alexandrov T.,Steinbeis Innovation Center i Research | Alexandrov T.,SCiLS GmbH | Alexandrov T.,University of California at San Diego | Bartels A.,University of Bremen
Bioinformatics | Year: 2013

Motivation: Imaging mass spectrometry has emerged in the past decade as a label-free, spatially resolved and multi-purpose bioanalytical technique for direct analysis of biological samples. However, solving two everyday data analysis problems still requires expert judgment: (i) the detection of unknown molecules and (ii) the testing for presence of known molecules.Results: We developed a measure of spatial chaos of a molecular image corresponding to a mass-to-charge value, which is a proxy for the molecular presence, and developed methods solving considered problems. The statistical evaluation was performed on a dataset from a rat brain section with test sets of molecular images selected by an expert. The measure of spatial chaos has shown high agreement with expert judges. The method for detection of unknown molecules allowed us to find structured molecular images corresponding to spectral peaks of any low intensity. The test for presence applied to a list of endogenous peptides ranked them according to the proposed measure of their presence in the sample. © The Author 2013.


Diehl H.C.,Ruhr University Bochum | Beine B.,Ruhr University Bochum | Beine B.,Leibniz Institute for Analytical Sciences | Elm J.,Ruhr University Bochum | And 7 more authors.
Analytical and Bioanalytical Chemistry | Year: 2015

Mass spectrometry imaging (MSI) has become a powerful and successful tool in the context of biomarker detection especially in recent years. This emerging technique is based on the combination of histological information of a tissue and its corresponding spatial resolved mass spectrometric information. The identification of differentially expressed protein peaks between samples is still the method’s bottleneck. Therefore, peptide MSI compared to protein MSI is closer to the final goal of identification since peptides are easier to measure than proteins. Nevertheless, the processing of peptide imaging samples is challenging due to experimental complexity. To address this issue, a method development study for peptide MSI using cryoconserved and formalin-fixed paraffin-embedded (FFPE) rat brain tissue is provided. Different digestion times, matrices, and proteases were tested to define an optimal workflow for peptide MSI. All practical experiments were done in triplicates and analyzed by the SCiLS Lab software, using structures derived from myelin basic protein (MBP) peaks, principal component analysis (PCA) and probabilistic latent semantic analysis (pLSA) to rate the experiments’ quality. Blinded experimental evaluation in case of defining countable structures in the datasets was performed by three individuals. Such an extensive method development for peptide matrix-assisted laser desorption/ionization (MALDI) imaging experiments has not been performed so far, and the resulting problems and consequences were analyzed and discussed.[Figure not available: see fulltext.] © 2015 Springer-Verlag Berlin Heidelberg


Laouirem S.,University Paris Diderot | Le Faouder J.,University Paris Diderot | Alexandrov T.,University of Bremen | Alexandrov T.,Steinbeis Innovation Center i Research | And 9 more authors.
Journal of Pathology | Year: 2014

Cirrhosis is a lesion at risk of hepatocellular carcinoma (HCC). Identifying mechanisms associated with the transition from cirrhosis to HCC and characterizing biomarkers of cirrhosis at high risk of developing into cancer are crucial for improving early diagnosis and prognosis of HCC. We used MALDI imaging to compare mass spectra obtained from tissue sections of cirrhosis without HCC, cirrhosis with HCC, and HCC, and a top-down proteomics approach to characterize differential biomarkers. We identified a truncated form of monomeric ubiquitin lacking the two C-terminal glycine residues, Ubi(1-74), the level of which increased progressively, from cirrhosis without HCC to cirrhosis with HCC to HCC. We showed that kallikrein-related peptidase 6 (KLK6) catalysed the production of Ubi(1-74) from monomeric ubiquitin. Furthermore, we demonstrated that KLK6 was induced de novo in cirrhosis and increased in HCC in parallel with accumulation of Ubi(1-74). We investigated in vitro the possible consequences of Ubi(1-74) accumulation and demonstrated that Ubi(1-74) interferes with the normal ubiquitination machinery in what is likely to be a kinetic process. Our data suggest that de novo KLK6 expression during early liver carcinogenesis may induce production of Ubi(1-74) by post-translational modification of ubiquitin. Given the deleterious effect of Ubi(1-74) on protein ubiquitination and the major role of ubiquitin machinery in maintenance of cell homeostasis, Ubi(1-74) might severely impact a number of critical cellular functions during transition from cirrhosis to cancer. Ubi(1-74) and KLK6 may serve as markers of cancer risk in patients with cirrhosis. Copyright © 2014 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.


Le Faouder J.,University Paris Diderot | Laouirem S.,University Paris Diderot | Alexandrov T.,University of Bremen | Alexandrov T.,Steinbeis Innovation Center i Research | And 7 more authors.
Proteomics | Year: 2014

Cholangiocarcinoma (CC) is the second most common primary malignancy of the liver. Although all CC derive from biliary epithelial cells, two main subtypes, hilar (H), and peripheral (P) CC are described. The objective of the study was to compare, using MALDI imaging mass spectrometry (MALDI IMS), in situ proteomic profiles of H- and P-CC in order to assess whether these subtypes may express different markers and to describe their respective localizations. Twenty-seven CC (16 P-CC and 11 H-CC) were subjected to MALDI IMS. Proteomic data were submitted to a dedicated cross-classification comparative design, enabling comparison of the entire generated spectra. Immunohistochemistry was performed for validation. Comparative analysis yielded a list of 19 differential protein peaks for the two subtypes, 14 of which were overexpressed in H-CC and five in P-CC. Among H-CC protein markers, most discriminant were human neutrophil peptides 1-3 that were expressed mainly by tumor cells and S100 proteins (A6 and A11) that were restricted to the stromal area. In P-CC, thymosin β4 was diffusely overexpressed. These results highlight the potential of MALDI IMS to discover new relevant biomarkers of CC and to characterize the heterogeneity of the two different subtypes. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Palmer A.D.,European Molecular Biology Laboratory | Palmer A.D.,University of Bremen | Alexandrov T.,European Molecular Biology Laboratory | Alexandrov T.,University of Bremen | And 2 more authors.
Analytical Chemistry | Year: 2015

Since biology is by and large a 3-dimensional phenomenon, it is hardly surprising that 3D imaging has had a significant impact on many challenges in the life sciences. Imaging mass spectrometry (MS) is a spatially resolved label-free analytical technique that recently maturated into a powerful tool for in situ localization of hundreds of molecular species. Serial 3D imaging MS reconstructs 3D molecular images from serial sections imaged with mass spectrometry. As such, it provides a novel 3D imaging modality inheriting the advantages of imaging MS. Serial 3D imaging MS has been steadily developing over the past decade, and many of the technical challenges have been met. Essential tools and protocols were developed, in particular to improve the reproducibility of sample preparation, speed up data acquisition, and enable computationally intensive analysis of the big data generated. As a result, experimental data is starting to emerge that takes advantage of the extra spatial dimension that 3D imaging MS offers. Most studies still focus on method development rather than on exploring specific biological problems. The future success of 3D imaging MS requires it to find its own niche alongside existing 3D imaging modalities through finding applications that benefit from 3D imaging and at the same time utilize the unique chemical sensitivity of imaging mass spectrometry. This perspective critically reviews the challenges encountered during the development of serial-sectioning 3D imaging MS and discusses the steps needed to tip it from being an academic curiosity into a tool of choice for answering biological and medical questions. © 2015 American Chemical Society.

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