16 results on '"Kohlbacher O"'
Search Results
2. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data.
- Author
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Pfeuffer J, Bielow C, Wein S, Jeong K, Netz E, Walter A, Alka O, Nilse L, Colaianni PD, McCloskey D, Kim J, Rosenberger G, Bichmann L, Walzer M, Veit J, Boudaud B, Bernt M, Patikas N, Pilz M, Startek MP, Kutuzova S, Heumos L, Charkow J, Sing JC, Feroz A, Siraj A, Weisser H, Dijkstra TMH, Perez-Riverol Y, Röst H, Kohlbacher O, and Sachsenberg T
- Subjects
- Mass Spectrometry methods, Spectrum Analysis, Software
- Published
- 2024
- Full Text
- View/download PDF
3. Cross-linking of the endolysosomal system reveals potential flotillin structures and cargo.
- Author
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Singh J, Elhabashy H, Muthukottiappan P, Stepath M, Eisenacher M, Kohlbacher O, Gieselmann V, and Winter D
- Subjects
- Membrane Proteins metabolism, Hydrolases metabolism, Endosomes metabolism, Lysosomes metabolism
- Abstract
Lysosomes are well-established as the main cellular organelles for the degradation of macromolecules and emerging as regulatory centers of metabolism. They are of crucial importance for cellular homeostasis, which is exemplified by a plethora of disorders related to alterations in lysosomal function. In this context, protein complexes play a decisive role, regulating not only metabolic lysosomal processes but also lysosome biogenesis, transport, and interaction with other organelles. Using cross-linking mass spectrometry, we analyze lysosomes and early endosomes. Based on the identification of 5376 cross-links, we investigate protein-protein interactions and structures of lysosome- and endosome-related proteins. In particular, we present evidence for a tetrameric assembly of the lysosomal hydrolase PPT1 and a heterodimeric structure of FLOT1/FLOT2 at lysosomes and early endosomes. For FLOT1-/FLOT2-positive early endosomes, we identify >300 putative cargo proteins and confirm eleven substrates for flotillin-dependent endocytosis, including the latrophilin family of adhesion G protein-coupled receptors., (© 2022. The Author(s).)
- Published
- 2022
- Full Text
- View/download PDF
4. FLASHIda enables intelligent data acquisition for top-down proteomics to boost proteoform identification counts.
- Author
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Jeong K, Babović M, Gorshkov V, Kim J, Jensen ON, and Kohlbacher O
- Subjects
- DNA-Binding Proteins metabolism, Escherichia coli metabolism, Heart, Peptides, Protein Processing, Post-Translational, Proteome metabolism, Proteomics methods, Sarcoplasmic Reticulum Calcium-Transporting ATPases antagonists & inhibitors
- Abstract
The detailed analysis and structural characterization of proteoforms by top-down proteomics (TDP) has gained a lot of interest in biomedical research. Data-dependent acquisition (DDA) of intact proteins is non-trivial due to the diversity and complexity of proteoforms. Dedicated acquisition methods thus have the potential to greatly improve TDP. Here, we present FLASHIda, an intelligent online data acquisition algorithm for TDP that ensures the real-time selection of high-quality precursors of diverse proteoforms. FLASHIda combines fast charge deconvolution algorithms and machine learning-based quality assessment for optimal precursor selection. In an analysis of E. coli lysate, FLASHIda increases the number of unique proteoform level identifications from 800 to 1500 or generates a near-identical number of identifications in one third of the instrument time when compared to standard DDA mode. Furthermore, FLASHIda enables sensitive mapping of post-translational modifications and detection of chemical adducts. As a software extension module to the instrument, FLASHIda can be readily adopted for TDP studies of complex samples to enhance proteoform identification rates., (© 2022. The Author(s).)
- Published
- 2022
- Full Text
- View/download PDF
5. DIAMetAlyzer allows automated false-discovery rate-controlled analysis for data-independent acquisition in metabolomics.
- Author
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Alka O, Shanthamoorthy P, Witting M, Kleigrewe K, Kohlbacher O, and Röst HL
- Subjects
- Biomarkers, Mass Spectrometry, Workflow, Metabolomics methods
- Abstract
The extraction of meaningful biological knowledge from high-throughput mass spectrometry data relies on limiting false discoveries to a manageable amount. For targeted approaches in metabolomics a main challenge is the detection of false positive metabolic features in the low signal-to-noise ranges of data-independent acquisition results and their filtering. Another factor is that the creation of assay libraries for data-independent acquisition analysis and the processing of extracted ion chromatograms have not been automated in metabolomics. Here we present a fully automated open-source workflow for high-throughput metabolomics that combines data-dependent and data-independent acquisition for library generation, analysis, and statistical validation, with rigorous control of the false-discovery rate while matching manual analysis regarding quantification accuracy. Using an experimentally specific data-dependent acquisition library based on reference substances allows for accurate identification of compounds and markers from data-independent acquisition data in low concentrations, facilitating biomarker quantification., (© 2022. The Author(s).)
- Published
- 2022
- Full Text
- View/download PDF
6. A proteomics sample metadata representation for multiomics integration and big data analysis.
- Author
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Dai C, Füllgrabe A, Pfeuffer J, Solovyeva EM, Deng J, Moreno P, Kamatchinathan S, Kundu DJ, George N, Fexova S, Grüning B, Föll MC, Griss J, Vaudel M, Audain E, Locard-Paulet M, Turewicz M, Eisenacher M, Uszkoreit J, Van Den Bossche T, Schwämmle V, Webel H, Schulze S, Bouyssié D, Jayaram S, Duggineni VK, Samaras P, Wilhelm M, Choi M, Wang M, Kohlbacher O, Brazma A, Papatheodorou I, Bandeira N, Deutsch EW, Vizcaíno JA, Bai M, Sachsenberg T, Levitsky LI, and Perez-Riverol Y
- Subjects
- Big Data, Humans, Reproducibility of Results, Software, Transcriptome, Data Analysis, Databases, Protein, Metadata, Proteomics
- Abstract
The amount of public proteomics data is rapidly increasing but there is no standardized format to describe the sample metadata and their relationship with the dataset files in a way that fully supports their understanding or reanalysis. Here we propose to develop the transcriptomics data format MAGE-TAB into a standard representation for proteomics sample metadata. We implement MAGE-TAB-Proteomics in a crowdsourcing project to manually curate over 200 public datasets. We also describe tools and libraries to validate and submit sample metadata-related information to the PRIDE repository. We expect that these developments will improve the reproducibility and facilitate the reanalysis and integration of public proteomics datasets., (© 2021. The Author(s).)
- Published
- 2021
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- View/download PDF
7. Large-scale discovery of protein interactions at residue resolution using co-evolution calculated from genomic sequences.
- Author
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Green AG, Elhabashy H, Brock KP, Maddamsetti R, Kohlbacher O, and Marks DS
- Subjects
- Bacterial Proteins chemistry, Base Sequence, Escherichia coli genetics, Eukaryotic Cells metabolism, Membrane Proteins metabolism, Molecular Docking Simulation, Protein Binding, Proteome metabolism, Amino Acids genetics, Bacterial Proteins genetics, Bacterial Proteins metabolism, Evolution, Molecular, Genome, Bacterial, Protein Interaction Mapping
- Abstract
Increasing numbers of protein interactions have been identified in high-throughput experiments, but only a small proportion have solved structures. Recently, sequence coevolution-based approaches have led to a breakthrough in predicting monomer protein structures and protein interaction interfaces. Here, we address the challenges of large-scale interaction prediction at residue resolution with a fast alignment concatenation method and a probabilistic score for the interaction of residues. Importantly, this method (EVcomplex2) is able to assess the likelihood of a protein interaction, as we show here applied to large-scale experimental datasets where the pairwise interactions are unknown. We predict 504 interactions de novo in the E. coli membrane proteome, including 243 that are newly discovered. While EVcomplex2 does not require available structures, coevolving residue pairs can be used to produce structural models of protein interactions, as done here for membrane complexes including the Flagellar Hook-Filament Junction and the Tol/Pal complex.
- Published
- 2021
- Full Text
- View/download PDF
8. Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry.
- Author
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Stützer A, Welp LM, Raabe M, Sachsenberg T, Kappert C, Wulf A, Lau AM, David SS, Chernev A, Kramer K, Politis A, Kohlbacher O, Fischle W, and Urlaub H
- Subjects
- Chromatin chemistry, Chromatin genetics, DNA chemistry, DNA genetics, Humans, Mass Spectrometry, Nucleosomes chemistry, Nucleosomes genetics, Nucleosomes metabolism, Polycomb-Group Proteins chemistry, Polycomb-Group Proteins genetics, Polycomb-Group Proteins metabolism, Polycomb-Group Proteins radiation effects, Protein Binding radiation effects, Proteins chemistry, Proteins genetics, Proteins radiation effects, Ultraviolet Rays, Chromatin metabolism, DNA metabolism, DNA radiation effects, Proteins metabolism
- Abstract
Protein-DNA interactions are key to the functionality and stability of the genome. Identification and mapping of protein-DNA interaction interfaces and sites is crucial for understanding DNA-dependent processes. Here, we present a workflow that allows mass spectrometric (MS) identification of proteins in direct contact with DNA in reconstituted and native chromatin after cross-linking by ultraviolet (UV) light. Our approach enables the determination of contact interfaces at amino-acid level. With the example of chromatin-associated protein SCML2 we show that our technique allows differentiation of nucleosome-binding interfaces in distinct states. By UV cross-linking of isolated nuclei we determined the cross-linking sites of several factors including chromatin-modifying enzymes, demonstrating that our workflow is not restricted to reconstituted materials. As our approach can distinguish between protein-RNA and DNA interactions in one single experiment, we project that it will be possible to obtain insights into chromatin and its regulation in the future.
- Published
- 2020
- Full Text
- View/download PDF
9. Feature-based molecular networking in the GNPS analysis environment.
- Author
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Nothias LF, Petras D, Schmid R, Dührkop K, Rainer J, Sarvepalli A, Protsyuk I, Ernst M, Tsugawa H, Fleischauer M, Aicheler F, Aksenov AA, Alka O, Allard PM, Barsch A, Cachet X, Caraballo-Rodriguez AM, Da Silva RR, Dang T, Garg N, Gauglitz JM, Gurevich A, Isaac G, Jarmusch AK, Kameník Z, Kang KB, Kessler N, Koester I, Korf A, Le Gouellec A, Ludwig M, Martin H C, McCall LI, McSayles J, Meyer SW, Mohimani H, Morsy M, Moyne O, Neumann S, Neuweger H, Nguyen NH, Nothias-Esposito M, Paolini J, Phelan VV, Pluskal T, Quinn RA, Rogers S, Shrestha B, Tripathi A, van der Hooft JJJ, Vargas F, Weldon KC, Witting M, Yang H, Zhang Z, Zubeil F, Kohlbacher O, Böcker S, Alexandrov T, Bandeira N, Wang M, and Dorrestein PC
- Subjects
- Computational Biology methods, Databases, Factual, Metabolomics methods, Software, Biological Products chemistry, Mass Spectrometry
- Abstract
Molecular networking has become a key method to visualize and annotate the chemical space in non-targeted mass spectrometry data. We present feature-based molecular networking (FBMN) as an analysis method in the Global Natural Products Social Molecular Networking (GNPS) infrastructure that builds on chromatographic feature detection and alignment tools. FBMN enables quantitative analysis and resolution of isomers, including from ion mobility spectrometry.
- Published
- 2020
- Full Text
- View/download PDF
10. A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry.
- Author
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Wein S, Andrews B, Sachsenberg T, Santos-Rosa H, Kohlbacher O, Kouzarides T, Garcia BA, and Weisser H
- Subjects
- Base Sequence genetics, Databases, Factual statistics & numerical data, Datasets as Topic, Humans, Oligonucleotides chemistry, Oligonucleotides genetics, Oligonucleotides metabolism, RNA, Transfer chemistry, RNA, Transfer genetics, RNA, Transfer metabolism, Reproducibility of Results, Epigenomics methods, High-Throughput Screening Assays methods, RNA Processing, Post-Transcriptional genetics, Search Engine, Tandem Mass Spectrometry methods
- Abstract
The field of epitranscriptomics continues to reveal how post-transcriptional modification of RNA affects a wide variety of biological phenomena. A pivotal challenge in this area is the identification of modified RNA residues within their sequence contexts. Mass spectrometry (MS) offers a comprehensive solution by using analogous approaches to shotgun proteomics. However, software support for the analysis of RNA MS data is inadequate at present and does not allow high-throughput processing. Existing software solutions lack the raw performance and statistical grounding to efficiently handle the numerous modifications found on RNA. We present a free and open-source database search engine for RNA MS data, called NucleicAcidSearchEngine (NASE), that addresses these shortcomings. We demonstrate the capability of NASE to reliably identify a wide range of modified RNA sequences in four original datasets of varying complexity. In human tRNA, we characterize over 20 different modification types simultaneously and find many cases of incomplete modification.
- Published
- 2020
- Full Text
- View/download PDF
11. Induction of neoantigen-reactive T cells from healthy donors.
- Author
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Ali M, Foldvari Z, Giannakopoulou E, Böschen ML, Strønen E, Yang W, Toebes M, Schubert B, Kohlbacher O, Schumacher TN, and Olweus J
- Subjects
- Cells, Cultured, Dendritic Cells metabolism, Electroporation methods, Epitopes genetics, Humans, Immunotherapy methods, Neoplasms therapy, RNA, Messenger genetics, Receptors, Antigen, T-Cell analysis, Receptors, Antigen, T-Cell immunology, Transfection methods, CD8-Positive T-Lymphocytes immunology, Dendritic Cells immunology, Epitopes immunology, Neoplasms immunology
- Abstract
The identification of immunogenic neoantigens and their cognate T cells represents the most crucial and rate-limiting steps in the development of personalized cancer immunotherapies that are based on vaccination or on infusion of T cell receptor (TCR)-engineered T cells. Recent advances in deep-sequencing technologies and in silico prediction algorithms have allowed rapid identification of candidate neoepitopes. However, large-scale validation of putative neoepitopes and the isolation of reactive T cells are challenging because of the limited availablity of patient material and the low frequencies of neoepitope-specific T cells. Here we describe a standardized protocol for the induction of neoepitope-reactive T cells from healthy donor T cell repertoires, unaffected by the potentially immunosuppressive environment of the tumor-bearing host. Monocyte-derived dendritic cells (DCs) transfected with mRNA encoding candidate neoepitopes are used to prime autologous naive CD8
+ T cells. Antigen-specific T cells that recognize endogenously processed and presented epitopes are detected using peptide-MHC (pMHC) multimers. Single multimer-positive T cells are sorted for the identification of TCR sequences, after an optional step that includes clonal expansion and functional characterization. The time required to identify neoepitope-specific T cells is 15 d, with an additional 2-4 weeks required for clonal expansion and downstream functional characterization. Identified neoepitopes and corresponding TCRs provide candidates for use in vaccination and TCR-based cancer immunotherapies, and datasets generated by this technology should be useful for improving algorithms to predict immunogenic neoantigens.- Published
- 2019
- Full Text
- View/download PDF
12. OpenMS: a flexible open-source software platform for mass spectrometry data analysis.
- Author
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Röst HL, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, Andreotti S, Ehrlich HC, Gutenbrunner P, Kenar E, Liang X, Nahnsen S, Nilse L, Pfeuffer J, Rosenberger G, Rurik M, Schmitt U, Veit J, Walzer M, Wojnar D, Wolski WE, Schilling O, Choudhary JS, Malmström L, Aebersold R, Reinert K, and Kohlbacher O
- Subjects
- Aging blood, Blood Proteins chemistry, Humans, Molecular Sequence Annotation, Proteogenomics methods, Workflow, Computational Biology methods, Electronic Data Processing, Mass Spectrometry methods, Proteomics methods, Software
- Abstract
High-resolution mass spectrometry (MS) has become an important tool in the life sciences, contributing to the diagnosis and understanding of human diseases, elucidating biomolecular structural information and characterizing cellular signaling networks. However, the rapid growth in the volume and complexity of MS data makes transparent, accurate and reproducible analysis difficult. We present OpenMS 2.0 (http://www.openms.de), a robust, open-source, cross-platform software specifically designed for the flexible and reproducible analysis of high-throughput MS data. The extensible OpenMS software implements common mass spectrometric data processing tasks through a well-defined application programming interface in C++ and Python and through standardized open data formats. OpenMS additionally provides a set of 185 tools and ready-made workflows for common mass spectrometric data processing tasks, which enable users to perform complex quantitative mass spectrometric analyses with ease.
- Published
- 2016
- Full Text
- View/download PDF
13. Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets.
- Author
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Griss J, Perez-Riverol Y, Lewis S, Tabb DL, Dianes JA, Del-Toro N, Rurik M, Walzer MW, Kohlbacher O, Hermjakob H, Wang R, and Vizcaíno JA
- Abstract
Mass spectrometry (MS) is the main technology used in proteomics approaches. However, on average 75% of spectra analysed in an MS experiment remain unidentified. We propose to use spectrum clustering at a large-scale to shed a light on these unidentified spectra. PRoteomics IDEntifications database (PRIDE) Archive is one of the largest MS proteomics public data repositories worldwide. By clustering all tandem MS spectra publicly available in PRIDE Archive, coming from hundreds of datasets, we were able to consistently characterize three distinct groups of spectra: 1) incorrectly identified spectra, 2) spectra correctly identified but below the set scoring threshold, and 3) truly unidentified spectra. Using a multitude of complementary analysis approaches, we were able to identify less than 20% of the consistently unidentified spectra. The complete spectrum clustering results are available through the new version of the PRIDE Cluster resource (http://www.ebi.ac.uk/pride/cluster). This resource is intended, among other aims, to encourage and simplify further investigation into these unidentified spectra., Competing Interests: The authors declare no competing financial interests.
- Published
- 2016
- Full Text
- View/download PDF
14. Carfilzomib alters the HLA-presented peptidome of myeloma cells and impairs presentation of peptides with aromatic C-termini.
- Author
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Kowalewski DJ, Walz S, Backert L, Schuster H, Kohlbacher O, Weisel K, Rittig SM, Kanz L, Salih HR, Rammensee HG, Stevanović S, and Stickel JS
- Subjects
- Biomarkers, Cell Line, Tumor, Cell Membrane metabolism, Epitopes chemistry, Epitopes metabolism, Epitopes, T-Lymphocyte immunology, Epitopes, T-Lymphocyte metabolism, HLA Antigens metabolism, Histocompatibility Antigens Class I immunology, Histocompatibility Antigens Class I metabolism, Humans, Immunophenotyping, Ligands, Mass Spectrometry, Multiple Myeloma metabolism, Multiple Myeloma pathology, Multiple Myeloma therapy, Peptides chemistry, Peptides metabolism, Proteasome Inhibitors pharmacology, Proteasome Inhibitors therapeutic use, Antigen Presentation drug effects, Antigen Presentation immunology, Epitopes immunology, HLA Antigens immunology, Multiple Myeloma immunology, Oligopeptides pharmacology, Peptides immunology
- Abstract
Recent studies suggest that multiple myeloma is an immunogenic disease, which might be effectively targeted by antigen-specific T-cell immunotherapy. As standard of care in myeloma includes proteasome inhibitor therapy, it is of great importance to characterize the effects of this treatment on HLA-restricted antigen presentation and implement only robustly presented targets for immunotherapeutic intervention. Here, we present a study that longitudinally and semi-quantitatively maps the effects of the proteasome inhibitor carfilzomib on HLA-restricted antigen presentation. The relative presentation levels of 4780 different HLA ligands were quantified in an in vitro model employing carfilzomib treatment of MM.1S and U266 myeloma cells, which revealed significant modulation of a substantial fraction of the HLA-presented peptidome. Strikingly, we detected selective down-modulation of HLA ligands with aromatic C-terminal anchor amino acids. This particularly manifested as a marked reduction in the presentation of HLA ligands through the HLA allotypes A*23:01 and A*24:02 on MM.1S cells. These findings implicate that carfilzomib mediates a direct, peptide motif-specific inhibitory effect on HLA ligand processing and presentation. As a substantial proportion of HLA allotypes present peptides with aromatic C-termini, our results may have broad implications for the implementation of antigen-specific treatment approaches in patients undergoing carfilzomib treatment.
- Published
- 2016
- Full Text
- View/download PDF
15. Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins.
- Author
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Kramer K, Sachsenberg T, Beckmann BM, Qamar S, Boon KL, Hentze MW, Kohlbacher O, and Urlaub H
- Subjects
- Amino Acids chemistry, Automation, Binding Sites, Computer Simulation, Cross-Linking Reagents chemistry, Fungal Proteins chemistry, Humans, Oligonucleotides chemistry, Peptides chemistry, Proteome, Proteomics methods, Software, Mass Spectrometry methods, RNA chemistry, RNA-Binding Proteins chemistry
- Abstract
RNA-protein complexes play pivotal roles in many central biological processes. Although methods based on high-throughput sequencing have advanced our ability to identify the specific RNAs bound by a particular protein, there is a need for precise and systematic ways to identify RNA interaction sites on proteins. We have developed an experimental and computational workflow combining photo-induced cross-linking, high-resolution mass spectrometry and automated analysis of the resulting mass spectra for the identification of cross-linked peptides, cross-linking sites and the cross-linked RNA oligonucleotide moieties of such RNA-binding proteins. The workflow can be applied to any RNA-protein complex of interest or to whole proteomes. We applied the approach to human and yeast mRNA-protein complexes in vitro and in vivo, demonstrating its powerful utility by identifying 257 cross-linking sites on 124 distinct RNA-binding proteins. The open-source software pipeline developed for this purpose, RNP(xl), is available as part of the OpenMS project.
- Published
- 2014
- Full Text
- View/download PDF
16. Visualization of omics data for systems biology.
- Author
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Gehlenborg N, O'Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, Kitano H, Kohlbacher O, Neuweger H, Schneider R, Tenenbaum D, and Gavin AC
- Subjects
- Mass Spectrometry, Nuclear Magnetic Resonance, Biomolecular, Protein Binding, Genomics, Image Processing, Computer-Assisted, Metabolomics, Proteomics, Systems Biology
- Abstract
High-throughput studies of biological systems are rapidly accumulating a wealth of 'omics'-scale data. Visualization is a key aspect of both the analysis and understanding of these data, and users now have many visualization methods and tools to choose from. The challenge is to create clear, meaningful and integrated visualizations that give biological insight, without being overwhelmed by the intrinsic complexity of the data. In this review, we discuss how visualization tools are being used to help interpret protein interaction, gene expression and metabolic profile data, and we highlight emerging new directions.
- Published
- 2010
- Full Text
- View/download PDF
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