Herbert Thiele - Academia.edu (original) (raw)

Papers by Herbert Thiele

Research paper thumbnail of Benchmark datasets for 3D MALDI- and DESI-imaging mass spectrometry

GigaScience, 2015

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Research paper thumbnail of Hochdurchsatz Analyse in den Biowissenschaften durch die Nutzung von Service Oriented Clustering (Proliferating High Throughput Analysis in Life Science by using Service Oriented Clustering)

it - Information Technology, 2005

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Research paper thumbnail of Towards data management of the HUPO Human Brain Proteome Project pilot phase

Proteomics, 2004

The pilot phase of the Human Brain Proteome Project as a part of the Human Proteome Organisation ... more The pilot phase of the Human Brain Proteome Project as a part of the Human Proteome Organisation has just been started. In two pilot studies, 18 different laboratories are analyzing mouse brains of three age stages and human brain autopsy versus biopsy material, respectively. The overall aim is to elucidate the portfolio of available techniques as well as to elaborate common standards. As a first step, it was decided to use the common bioinformatics platform ProteinScape that was introduced to the participating groups in a two day course in Bochum, Germany.

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Research paper thumbnail of Sparse Deconvolution for Peak Picking and Ion Charge Estimation in Mass Spectrometry

In this paper we propose a new procedure for peak detection in mass-spectrometry data using spars... more In this paper we propose a new procedure for peak detection in mass-spectrometry data using sparse deconvolution. We apply the procedure for estimation of the ion charges for isotopic patterns of overlapping peaks. The evaluation is performed on the thymosin β4 16-38 fragment measurements. Moreover, a comparison with the Mexican hat based algorithm of peak picking is provided.

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Research paper thumbnail of Comparison of protein expression lists from mass spectrometry of human blood fluids using exact peptide sequences versus BLAST

Clinical Proteomics, 2006

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Research paper thumbnail of Multiscale Approximation

During the last two decades wavelet methods have developed into powerful tools for a wide range o... more During the last two decades wavelet methods have developed into powerful tools for a wide range of applications in signal and image processing. The success of wavelet methods is based on their potential for resolving local properties and to analyze non-stationary structures. This is achieved by multiscale decompositions, e.g., a signal or image is mapped to a phase space parametrized

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Research paper thumbnail of On the importance of mathematical methods for analysis of MALDI-imaging mass spectrometry data

In the last decade, matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry... more In the last decade, matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS), also called as MALDI-imaging, has proven its potential in proteomics and was successfully applied to various types of biomedical problems, in particular to histopathological label-free analysis of tissue sections. In histopathology, MALDI-imaging is used as a general analytic tool revealing the functional proteomic structure of tissue sections, and as a discovery tool for detecting new biomarkers discriminating a region annotated by an experienced histologist, in particular, for cancer studies. A typical MALDI-imaging data set contains 10⁸ to 10⁹ intensity values occupying more than 1 GB. Analysis and interpretation of such huge amount of data is a mathematically, statistically and computationally challenging problem. In this paper we overview some computational methods for analysis of MALDI-imaging data sets. We discuss the importance of data preprocessing, which typically includes normalization, baseline removal and peak picking, and hightlight the importance of image denoising when visualizing IMS data.

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Research paper thumbnail of MALDI imaging mass spectrometry: Discrimination of pathophysiological regions in traumatized skeletal muscle by characteristic peptide signatures

Due to formation of fibrosis and the loss of contractile muscle tissue, severe muscle injuries of... more Due to formation of fibrosis and the loss of contractile muscle tissue, severe muscle injuries often result in insufficient healing marked by a significant reduction of muscle force and motor activity. Our previous studies demonstrated that the local transplantation of mesenchymal stromal cells into an injured skeletal muscle of the rat improves the functional outcome of the healing process. Since, due to the lack of sufficient markers, the accurate discrimination of pathophysiological regions in injured skeletal muscle is inadequate, underlying mechanisms of the beneficial effects of mesenchymal stromal cell transplantation on primary trauma and trauma adjacent muscle area remain elusive. For discrimination of these pathophysiological regions, formalin-fixed injured skeletal muscle tissue was analyzed by MALDI imaging MS. By using two computational evaluation strategies, a supervised approach (ClinProTools) and unsupervised segmentation (SCiLS Lab), characteristic m/z species could be assigned to primary trauma and trauma adjacent muscle regions. Using "bottom-up" MS for protein identification and validation of results by immunohistochemistry, we could identify two proteins, skeletal muscle alpha actin and carbonic anhydrase III, which discriminate between the secondary damage on adjacent tissue and the primary traumatized muscle area. Our results underscore the high potential of MALDI imaging MS to describe the spatial characteristics of pathophysiological changes in muscle.

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Research paper thumbnail of Gaining knowledge from previously unexplained spectra-application of the PTM-Explorer software to detect PTM in HUPO BPP MS/MS data

PROTEOMICS, 2006

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Research paper thumbnail of Protein Information and Knowledge Extractor: Discovering biological information from proteomics data

PROTEOMICS, 2010

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Research paper thumbnail of Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase

PROTEOMICS, 2006

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Research paper thumbnail of HUPO Brain Proteome Project: Summary of the pilot phase and introduction of a comprehensive data reprocessing strategy

PROTEOMICS, 2006

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Research paper thumbnail of Getting a grip on proteomics data - Proteomics Data Collection (ProDaC)

PROTEOMICS, 2009

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Research paper thumbnail of 5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK - Setting the Analysis Frame

PROTEOMICS, 2005

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Research paper thumbnail of Application of Slicing of One-Dimensional Gels with Subsequent Slice-by-Slice Mass Spectrometry for the Proteomic Profiling of Human Liver Cytochromes P450

Journal of Proteome Research, 2010

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Research paper thumbnail of New Analysis Workflow for MALDI Imaging Mass Spectrometry: Application to the Discovery and Identification of Potential Markers of Childhood Absence Epilepsy

Journal of Proteome Research, 2012

Childhood absence epilepsy is a prototypic form of generalized nonconvulsive epilepsy characteriz... more Childhood absence epilepsy is a prototypic form of generalized nonconvulsive epilepsy characterized by short impairments of consciousness concomitant with synchronous and bilateral spike-and-wave discharges in the electroencephalogram. For scientists in this field, the BS/Orl and BR/Orl mouse lines, derived from a genetic selection, constitute an original mouse model "in mirror" of absence epilepsy. The potential of MALDI imaging mass spectrometry (IMS) for the discovery of potential biomarkers is increasingly recognized. Interestingly, statistical analysis tools specifically adapted to IMS data sets and methods for the identification of detected proteins play an essential role. In this study, a new cross-classification comparative design using a combined discrete wavelet transformation-support vector machine classification was developed to discriminate spectra of brain sections of BS/Orl and BR/Orl mice. Nineteen m/z ratios were thus highlighted as potential markers with very high recognition rates (87-99%). Seven of these potential markers were identified using a top-down approach, in particular a fragment of Synapsin-I. This protein is yet suspected to be involved in epilepsy. Immunohistochemistry and Western Blot experiments confirmed the differential expression of Synapsin-I observed by IMS, thus tending to validate our approach. Functional assays are being performed to confirm the involvement of Synapsin-I in the mechanisms underlying childhood absence epilepsy.

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Research paper thumbnail of Uranium secondary phase formation during anoxic hydrothermal leaching processes of UO2 nuclear fuel

Journal of Nuclear Materials, 2005

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Research paper thumbnail of Even-electron ions: a systematic study of the neutral species lost in the dissociation of quasi-molecular ions

Journal of Mass Spectrometry, 2007

The collision-induced dissociations of the even-electron [M + H](+) and/or [M - H](-) ions of 121... more The collision-induced dissociations of the even-electron [M + H](+) and/or [M - H](-) ions of 121 model compounds (mainly small aromatic compounds with one to three functional groups) ionized by electrospray ionization (ESI) or atmospheric pressure chemical ionization (APCI) have been studied using an ion trap instrument, and the results are compared with the literature data. While some functional groups (such as COOH, COOCH(3), SO(3)H in the negative ion mode, or NO(2) in both the positive and negative ion modes) generally promote the loss of neutrals that are characteristic as well as specific, other functional groups (such as COOH in the positive ion mode) give rise to the loss of neutrals that are characteristic, but not specific. Finally, functional groups such as OH and NH(2) in aromatic compounds do not lead to the loss of a neutral that reflects the presence of these substituents. In general, the dissociation of [M + H](+) and [M - H](-) ions generated from aliphatic compounds or compounds containing an aliphatic moiety obeys the even-electron rule (loss of a molecule), but deviations from this rule (loss of a radical) are sometimes observed for aromatic compounds, in particular for nitroaromatic compounds. Thermochemical data and ab initio calculations at the CBS-QB3 level of theory provide an explanation for these exceptions. When comparing the dissociation behaviour of the even-electron [M + H](+) and/or [M - H](-) ions (generated by ESI or APCI) with that of the corresponding odd-electron [M](+) ions (generated by electron ionization, EI), three cases may be distinguished: (1) the dissociation of the two ionic species differs completely; (2) the dissociation involves the loss of a common neutral, yielding product ions differing in mass by one Da, or (3) the dissociations lead to a common product ion.

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Research paper thumbnail of Structure elucidation of phase II metabolites by tandem mass spectrometry: an overview

Journal of Chromatography A, 2005

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Research paper thumbnail of Shrinkage versus deconvolution

Inverse Problems, 2007

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Research paper thumbnail of Benchmark datasets for 3D MALDI- and DESI-imaging mass spectrometry

GigaScience, 2015

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Research paper thumbnail of Hochdurchsatz Analyse in den Biowissenschaften durch die Nutzung von Service Oriented Clustering (Proliferating High Throughput Analysis in Life Science by using Service Oriented Clustering)

it - Information Technology, 2005

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Towards data management of the HUPO Human Brain Proteome Project pilot phase

Proteomics, 2004

The pilot phase of the Human Brain Proteome Project as a part of the Human Proteome Organisation ... more The pilot phase of the Human Brain Proteome Project as a part of the Human Proteome Organisation has just been started. In two pilot studies, 18 different laboratories are analyzing mouse brains of three age stages and human brain autopsy versus biopsy material, respectively. The overall aim is to elucidate the portfolio of available techniques as well as to elaborate common standards. As a first step, it was decided to use the common bioinformatics platform ProteinScape that was introduced to the participating groups in a two day course in Bochum, Germany.

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Sparse Deconvolution for Peak Picking and Ion Charge Estimation in Mass Spectrometry

In this paper we propose a new procedure for peak detection in mass-spectrometry data using spars... more In this paper we propose a new procedure for peak detection in mass-spectrometry data using sparse deconvolution. We apply the procedure for estimation of the ion charges for isotopic patterns of overlapping peaks. The evaluation is performed on the thymosin β4 16-38 fragment measurements. Moreover, a comparison with the Mexican hat based algorithm of peak picking is provided.

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Comparison of protein expression lists from mass spectrometry of human blood fluids using exact peptide sequences versus BLAST

Clinical Proteomics, 2006

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Multiscale Approximation

During the last two decades wavelet methods have developed into powerful tools for a wide range o... more During the last two decades wavelet methods have developed into powerful tools for a wide range of applications in signal and image processing. The success of wavelet methods is based on their potential for resolving local properties and to analyze non-stationary structures. This is achieved by multiscale decompositions, e.g., a signal or image is mapped to a phase space parametrized

Bookmarks Related papers MentionsView impact

Research paper thumbnail of On the importance of mathematical methods for analysis of MALDI-imaging mass spectrometry data

In the last decade, matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry... more In the last decade, matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS), also called as MALDI-imaging, has proven its potential in proteomics and was successfully applied to various types of biomedical problems, in particular to histopathological label-free analysis of tissue sections. In histopathology, MALDI-imaging is used as a general analytic tool revealing the functional proteomic structure of tissue sections, and as a discovery tool for detecting new biomarkers discriminating a region annotated by an experienced histologist, in particular, for cancer studies. A typical MALDI-imaging data set contains 10⁸ to 10⁹ intensity values occupying more than 1 GB. Analysis and interpretation of such huge amount of data is a mathematically, statistically and computationally challenging problem. In this paper we overview some computational methods for analysis of MALDI-imaging data sets. We discuss the importance of data preprocessing, which typically includes normalization, baseline removal and peak picking, and hightlight the importance of image denoising when visualizing IMS data.

Bookmarks Related papers MentionsView impact

Research paper thumbnail of MALDI imaging mass spectrometry: Discrimination of pathophysiological regions in traumatized skeletal muscle by characteristic peptide signatures

Due to formation of fibrosis and the loss of contractile muscle tissue, severe muscle injuries of... more Due to formation of fibrosis and the loss of contractile muscle tissue, severe muscle injuries often result in insufficient healing marked by a significant reduction of muscle force and motor activity. Our previous studies demonstrated that the local transplantation of mesenchymal stromal cells into an injured skeletal muscle of the rat improves the functional outcome of the healing process. Since, due to the lack of sufficient markers, the accurate discrimination of pathophysiological regions in injured skeletal muscle is inadequate, underlying mechanisms of the beneficial effects of mesenchymal stromal cell transplantation on primary trauma and trauma adjacent muscle area remain elusive. For discrimination of these pathophysiological regions, formalin-fixed injured skeletal muscle tissue was analyzed by MALDI imaging MS. By using two computational evaluation strategies, a supervised approach (ClinProTools) and unsupervised segmentation (SCiLS Lab), characteristic m/z species could be assigned to primary trauma and trauma adjacent muscle regions. Using "bottom-up" MS for protein identification and validation of results by immunohistochemistry, we could identify two proteins, skeletal muscle alpha actin and carbonic anhydrase III, which discriminate between the secondary damage on adjacent tissue and the primary traumatized muscle area. Our results underscore the high potential of MALDI imaging MS to describe the spatial characteristics of pathophysiological changes in muscle.

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Gaining knowledge from previously unexplained spectra-application of the PTM-Explorer software to detect PTM in HUPO BPP MS/MS data

PROTEOMICS, 2006

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Protein Information and Knowledge Extractor: Discovering biological information from proteomics data

PROTEOMICS, 2010

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase

PROTEOMICS, 2006

Bookmarks Related papers MentionsView impact

Research paper thumbnail of HUPO Brain Proteome Project: Summary of the pilot phase and introduction of a comprehensive data reprocessing strategy

PROTEOMICS, 2006

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Getting a grip on proteomics data - Proteomics Data Collection (ProDaC)

PROTEOMICS, 2009

Bookmarks Related papers MentionsView impact

Research paper thumbnail of 5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK - Setting the Analysis Frame

PROTEOMICS, 2005

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Application of Slicing of One-Dimensional Gels with Subsequent Slice-by-Slice Mass Spectrometry for the Proteomic Profiling of Human Liver Cytochromes P450

Journal of Proteome Research, 2010

Bookmarks Related papers MentionsView impact

Research paper thumbnail of New Analysis Workflow for MALDI Imaging Mass Spectrometry: Application to the Discovery and Identification of Potential Markers of Childhood Absence Epilepsy

Journal of Proteome Research, 2012

Childhood absence epilepsy is a prototypic form of generalized nonconvulsive epilepsy characteriz... more Childhood absence epilepsy is a prototypic form of generalized nonconvulsive epilepsy characterized by short impairments of consciousness concomitant with synchronous and bilateral spike-and-wave discharges in the electroencephalogram. For scientists in this field, the BS/Orl and BR/Orl mouse lines, derived from a genetic selection, constitute an original mouse model "in mirror" of absence epilepsy. The potential of MALDI imaging mass spectrometry (IMS) for the discovery of potential biomarkers is increasingly recognized. Interestingly, statistical analysis tools specifically adapted to IMS data sets and methods for the identification of detected proteins play an essential role. In this study, a new cross-classification comparative design using a combined discrete wavelet transformation-support vector machine classification was developed to discriminate spectra of brain sections of BS/Orl and BR/Orl mice. Nineteen m/z ratios were thus highlighted as potential markers with very high recognition rates (87-99%). Seven of these potential markers were identified using a top-down approach, in particular a fragment of Synapsin-I. This protein is yet suspected to be involved in epilepsy. Immunohistochemistry and Western Blot experiments confirmed the differential expression of Synapsin-I observed by IMS, thus tending to validate our approach. Functional assays are being performed to confirm the involvement of Synapsin-I in the mechanisms underlying childhood absence epilepsy.

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Uranium secondary phase formation during anoxic hydrothermal leaching processes of UO2 nuclear fuel

Journal of Nuclear Materials, 2005

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Even-electron ions: a systematic study of the neutral species lost in the dissociation of quasi-molecular ions

Journal of Mass Spectrometry, 2007

The collision-induced dissociations of the even-electron [M + H](+) and/or [M - H](-) ions of 121... more The collision-induced dissociations of the even-electron [M + H](+) and/or [M - H](-) ions of 121 model compounds (mainly small aromatic compounds with one to three functional groups) ionized by electrospray ionization (ESI) or atmospheric pressure chemical ionization (APCI) have been studied using an ion trap instrument, and the results are compared with the literature data. While some functional groups (such as COOH, COOCH(3), SO(3)H in the negative ion mode, or NO(2) in both the positive and negative ion modes) generally promote the loss of neutrals that are characteristic as well as specific, other functional groups (such as COOH in the positive ion mode) give rise to the loss of neutrals that are characteristic, but not specific. Finally, functional groups such as OH and NH(2) in aromatic compounds do not lead to the loss of a neutral that reflects the presence of these substituents. In general, the dissociation of [M + H](+) and [M - H](-) ions generated from aliphatic compounds or compounds containing an aliphatic moiety obeys the even-electron rule (loss of a molecule), but deviations from this rule (loss of a radical) are sometimes observed for aromatic compounds, in particular for nitroaromatic compounds. Thermochemical data and ab initio calculations at the CBS-QB3 level of theory provide an explanation for these exceptions. When comparing the dissociation behaviour of the even-electron [M + H](+) and/or [M - H](-) ions (generated by ESI or APCI) with that of the corresponding odd-electron [M](+) ions (generated by electron ionization, EI), three cases may be distinguished: (1) the dissociation of the two ionic species differs completely; (2) the dissociation involves the loss of a common neutral, yielding product ions differing in mass by one Da, or (3) the dissociations lead to a common product ion.

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Structure elucidation of phase II metabolites by tandem mass spectrometry: an overview

Journal of Chromatography A, 2005

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Shrinkage versus deconvolution

Inverse Problems, 2007

Bookmarks Related papers MentionsView impact