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2023
- Toward an Integrated Machine Learning Model of a Proteomics Experiment. Journal of Proteome Research 22 (3), 2023, 681-696 more…
- Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification. Nature Communications 14 (1), 2023 more…
- Decrypting drug actions and protein modifications by dose- and time-resolved proteomics. Science 380 (6640), 2023, 93-101 more…
2022
- Prosit Transformer: A transformer for Prediction of MS2 Spectrum Intensities. Journal of Proteome Research 21 (5), 2022, 1359-1364 more…
- Predicting fragment intensities and retention time of iTRAQ‐ and TMTPro‐labeled peptides with Prosit‐TMT. PROTEOMICS, 2022, 2100257 more…
- Prosit-TMT: Deep Learning Boosts Identification of TMT-Labeled Peptides. Analytical Chemistry, 2022 more…
- Mass spectrometry-based draft of the mouse proteome. Nature Methods, 2022 more…
- SIMSI-Transfer: Software-assisted reduction of missing values in phosphoproteomic and proteomic isobaric labeling data using tandem mass spectrum clustering. Molecular & Cellular Proteomics, 2022, 100238 more…
- High temporal resolution proteome and phosphoproteome profiling of stem cell-derived hepatocyte development. Cell Reports 38 (13), 2022, 110604 more…
- ProteomicsDB: toward a FAIR open-source resource for life-science research. Nucleic Acids Research, 2022 more…
- Target deconvolution of HDAC pharmacopoeia reveals MBLAC2 as common off-target. Nature Chemical Biology, 2022 more…
- Interpretation of the DOME Recommendations for Machine Learning in Proteomics and Metabolomics. Journal of Proteome Research 21 (4), 2022, 1204-1207 more…
- Reanalysis of ProteomicsDB Using an Accurate, Sensitive, and Scalable False Discovery Rate Estimation Approach for Protein Groups. Molecular & Cellular Proteomics 21 (12), 2022, 100437 more…
- Linking post-translational modifications and protein turnover by site-resolved protein turnover profiling. Nature Communications 13 (1), 2022 more…
2021
- The emerging landscape of single-molecule protein sequencing technologies. Nature Methods 18 (6), 2021, 604-617 more…
- Identification of 7 000–9 000 Proteins from Cell Lines and Tissues by Single-Shot Microflow LC–MS/MS. Analytical Chemistry 93 (25), 2021, 8687-8692 more…
- A proteomics sample metadata representation for multiomics integration and big data analysis. Nature Communications 12 (1), 2021 more…
- Target deconvolution of HDAC pharmacopoeia highlights MBLAC2 as common off-target. 2021 more…
- Universal Spectrum Explorer: A Standalone (Web-)Application for Cross-Resource Spectrum Comparison. Journal of Proteome Research 20 (6), 2021, 3388-3394 more…
- Spectral Prediction Features as a Solution for the Search Space Size Problem in Proteogenomics. Molecular & Cellular Proteomics 20, 2021, 100076 more…
- Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics. Nature Communications 12 (1), 2021 more…
2020
- Proteome activity landscapes of tumor cell lines determine drug responses. Nature Communications 11 (1), 2020 more…
- Meltome atlas—thermal proteome stability across the tree of life. Nature Methods 17 (5), 2020, 495-503 more…
- Mass-spectrometry-based draft of the Arabidopsis proteome. Nature 579 (7799), 2020, 409-414 more…
- Proteomic and transcriptomic profiling of aerial organ development in Arabidopsis. Scientific Data 7 (1), 2020 more…
- Generating high quality libraries for DIA MS with empirically corrected peptide predictions. Nature Communications 11 (1), 2020 more…
- HPI Future SOC Lab – Proceedings 2017. Universitätsverlag Potsdam, 2020 more…
2019
- Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning. Nature Methods 16 (6), 2019, 509-518 more…
- Challenges in Clinical Metaproteomics Highlighted by the Analysis of Acute Leukemia Patients with Gut Colonization by Multidrug-Resistant Enterobacteriaceae. Proteomes 7 (1), 2019, 2 more…
- Kinobeads: A Chemical Proteomic Approach for Kinase Inhibitor Selectivity Profiling and Target Discovery – 4. In: Target Discovery and Validation. John Wiley & Sons, Ltd, 2019, 97-130 more…
- Chemoproteomic Selectivity Profiling of PIKK and PI3K Kinase Inhibitors. ACS Chemical Biology 14 (4), 2019, 655-664 more…
- ProteomicsDB: a multi-omics and multi-organism resource for life science research. Nucleic Acids Research, 2019 more…
- CiRCus: A Framework to Enable Classification of Complex High-Throughput Experiments. Journal of Proteome Research 18 (4), 2019, 1486-1493 more…
- PROTEOFORMER 2.0: Further Developments in the Ribosome Profiling-assisted Proteogenomic Hunt for New Proteoforms. Molecular & Cellular Proteomics 18 (8), 2019, S126-S140 more…
- A deep proteome and transcriptome abundance atlas of 29 healthy human tissues. Molecular Systems Biology 15 (2), 2019 more…
2018
- Expanding the Use of Spectral Libraries in Proteomics. Journal of Proteome Research 17 (12), 2018, 4051-4060 more…
- Mining the Human Tissue Proteome for Protein Citrullination. Molecular & Cellular Proteomics 17 (7), 2018, 1378-1391 more…
- Peptide Level Turnover Measurements Enable the Study of Proteoform Dynamics. Molecular & Cellular Proteomics 17 (5), 2018, 974-992 more…
- ProteomeTools: Systematic Characterization of 21 Post-translational Protein Modifications by Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) Using Synthetic Peptides. Molecular & Cellular Proteomics 17 (9), 2018, 1850-1863 more…
2017
- Pharmacoproteomic characterisation of human colon and rectal cancer. Molecular Systems Biology 13 (11), 2017, 951 more…
- The target landscape of clinical kinase drugs. Science 358 (6367), 2017, eaan4368 more…
- ProteomicsDB. Nucleic Acids Research 46 (D1), 2017, D1271-D1281 more…
- Trimodal Mixed Mode Chromatography That Enables Efficient Offline Two-Dimensional Peptide Fractionation for Proteome Analysis. Analytical Chemistry 89 (17), 2017, 8884-8891 more…
- Building ProteomeTools based on a complete synthetic human proteome. Nature Methods 14 (3), 2017, 259-262 more…
- PROCAL: A Set of 40 Peptide Standards for Retention Time Indexing, Column Performance Monitoring, and Collision Energy Calibration. PROTEOMICS 17 (21), 2017, 1700263 more…
2016
- Chemical Proteomics and Structural Biology Define EPHA2 Inhibition by Clinical Kinase Drugs. ACS Chemical Biology 11 (12), 2016, 3400-3411 more…
- Phosphoproteome Profiling Reveals Molecular Mechanisms of Growth-Factor-Mediated Kinase Inhibitor Resistance in EGFR-Overexpressing Cancer Cells. Journal of Proteome Research 15 (12), 2016, 4490-4504 more…
- Ethylene glycol improves electrospray ionization efficiency in bottom-up proteomics. Analytical and Bioanalytical Chemistry 409 (4), 2016, 1049-1057 more…
2015
- Semi-supervised Learning Predicts Approximately One Third of the Alternative Splicing Isoforms as Functional Proteins. Cell Reports 12 (2), 2015, 183-189 more…
- Optimized Chemical Proteomics Assay for Kinase Inhibitor Profiling. Journal of Proteome Research 14 (3), 2015, 1574-1586 more…
- A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets. Molecular & Cellular Proteomics 14 (9), 2015, 2394-2404 more…
2014
2013
- A Classifier Based on Accurate Mass Measurements to Aid Large Scale, Unbiased Glycoproteomics. Molecular & Cellular Proteomics 12 (4), 2013, 1017-1025 more…
- Global Proteome Analysis of the NCI-60 Cell Line Panel. Cell Reports 4 (3), 2013, 609-620 more…
- BiPACE 2D—graph-based multiple alignment for comprehensive 2D gas chromatography-mass spectrometry. Bioinformatics 30 (7), 2013, 988-995 more…
2012
- Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets. BMC Bioinformatics 13 (1), 2012 more…
- mz5: Space- and Time-efficient Storage of Mass Spectrometry Data Sets. Molecular & Cellular Proteomics 11 (1), 2012, O111.011379 more…