Researcher Portfolio
Zhou, Xie-Xuan
Mann, Matthias / Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Max Planck Society
Researcher Profile
Position: Mann, Matthias / Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Max Planck Society
Researcher ID: https://pure.mpg.de/cone/persons/resource/persons284698
Publications
: Strauss, M. T., Bludau, I., Zeng, W.-F., Voytik, E., Ammar, C., Schessner, J. P., Ilango, R., Gill, M., Meier, F., Willems, S., & Mann, M. (2024). AlphaPept: A modern and open framework for MS-based proteomics. Nature Communications, 15(1): 2168. doi:10.1038/s41467-024-46485-4. [PubMan] : Michaelis, A. C., Brunner, A.-D., Zwiebel, M., Meier, F., Strauss, M. T., Bludau, I., & Mann, M. (2023). The social and structural architecture of the yeast protein interactome. Nature, 624(7990), 192-200. doi:10.1038/s41586-023-06739-5. [PubMan] : Thielert, M., Itang, E. C. M., Ammar, C., Rosenberger, F. A., Bludau, I., Schweizer, L., Nordmann, T. M., Skowronek, P., Wahle, M., Zeng, W.-F., Zhou, X.-X., Brunner, A.-D., Richter, S., Levesque, M. P., Theis, F. J., Steger, M., & Mann, M. (2023). Robust dimethyl-based multiplex-DIA doubles single-cell proteome depth via a reference channel. Molecular Systems Biology, 19(9): e1150. doi:10.15252/msb.202211503. [PubMan] : Krismer, E., Bludau, I., Strauss, M. T., & Mann, M. (2023). AlphaPeptStats: An open-source Python package for automated and scalable statistical analysis of mass spectrometry-based proteomics. Bioinformatics, 39(8): btad461. doi:10.1093/bioinformatics/btad461. [PubMan] : Bludau, I., Nicod, C., Martelli, C., Xue, P., Heusel, M., Fossati, A., Uliana, F., Frommelt, F., Aebersold, R., & Collins, B. C. (2023). Rapid profiling of protein complex reorganization in perturbed systems. Journal of Proteome Research, 22(5), 1520-1536. doi:10.1021/acs.jproteome.3c00125. [PubMan] : Neely, B. A., Dorfer, V., Martens, L., Bludau, I., Bouwmeester, R., Degroeve, S., Deutsch, E. W., Gessulat, S., Kaell, L., Palczynski, P., Payne, S. H., Rehfeldt, T. G., Schmidt, T., Schwaemmle, V., Uszkoreit, J., Vizcaino, J. A., Wilhelm, M., & Palmblad, M. (2023). Toward an integrated machine learning model of a proteomics experiment. Journal of Proteome Research, 22(3), 681-696. doi:10.1021/acs.jproteome.2c00711. [PubMan] : Samant, R. S., Batista, S., Larance, M., Ozer, B., Milton, C. I., Bludau, I., Wu, E., Biggins, L., Andrews, S., Hervieu, A., Johnston, H. E., Al-Lazikhani, B., Lamond, A. I., Clarke, P. A., & Workman, P. (2023). Native size-exclusion chromatography-based mass spectrometry reveals new components of the early heat shock protein 90 inhibition response among limited global changes. Molecular & Cellular Proteomics, 22(2): 100485. doi:10.1016/j.mcpro.2022.100485. [PubMan] : Zeng, W.-F., Zhou, X.-X., Willems, S., Ammar, C., Wahle, M., Bludau, I., Voytik, E., Strauss, M. T., & Mann, M. (2022). AlphaPeptDeep: A modular deep learning framework to predict peptide properties for proteomics. Nature Communications, 13(1): 7238. doi:10.1038/s41467-022-34904-3. [PubMan] : Bludau, I., Willems, S., Zeng, W.-F., Strauss, M. T., Hansen, F. M., Tanzer, M. C., Karayel, O., Schulman, B. A., & Mann, M. (2022). The structural context of posttranslational modifications at a proteome-wide scale. PLoS Biology, 20(5): e3001636. doi:10.1371/journal.pbio.3001636. [PubMan] : Schessner, J. P., Voytik, E., & Bludau, I. (2022). A practical guide to interpreting and generating bottom-up proteomics data visualizations. Proteomics, 22(8): e2100103. doi:10.1002/pmic.202100103. [PubMan] : Voytik, E., Bludau, I., Willems, S., Hansen, F. M., Brunner, A.-D., Strauss, M. T., & Mann, M. (2022). AlphaMap: An open-source Python package for the visual annotation of proteomics data with sequence-specific knowledge. Bioinformatics, 38(3), 849-852. doi:10.1093/bioinformatics/btab674. [PubMan] : Grossbach, J., Gillet, L., Clement-Ziza, M., Schmalohr, C. L., Schubert, O. T., Schuetter, M., Mawer, J. S. P., Barnes, C. A., Bludau, I., Weith, M., Tessarz, P., Graef, M., Aebersold, R., & Beyer, A. (2022). The impact of genomic variation on protein phosphorylation states and regulatory networks. Molecular Systems Biology, 18(5): e10712. doi:10.15252/msb.202110712. [PubMan] : Bludau, I. (2021). Discovery-versus hypothesis-driven detection of protein-protein interactions and complexes. International Journal of Molecular Sciences, 22(9): 4450. doi:10.3390/ijms22094450. [PubMan] : Fossati, A., Li, C., Uliana, F., Wendt, F., Frommelt, F., Sykacek, P., Heusel, M., Hallal, M., Bludau, I., Capraz, T., Xue, P., Song, J., Wollscheid, B., Purcell, A. W., Gstaiger, M., & Aebersold, R. (2021). PCprophet: a framework for protein complex prediction and differential analysis using proteomic data. Nature Methods, 18(5), 520-527. doi:10.1038/s41592-021-01107-5. [PubMan] : Bludau, I., Frank, M., Doerig, C., Cai, Y., Heusel, M., Rosenberger, G., Picotti, P., Collins, B. C., Rost, H., & Aebersold, R. (2021). Systematic detection of functional proteoform groups from bottom-up proteomic datasets. Nature Communications, 12(1): 3810. doi:10.1038/s41467-021-24030-x. [PubMan] : Tanzer, M. C., Bludau, I., Stafford, C. A., Hornung, V., & Mann, M. (2021). Phosphoproteome profiling uncovers a key role for CDKs in TNF signaling. Nature Communications, 12(1): 6053. doi:10.1038/s41467-021-26289-6. [PubMan] : Hansen, F. M., Tanzer, M. C., Brüning, F., Bludau, I., Stafford, C., Schulman, B. A., Robles, M. S., Karayel, O., & Mann, M. (2021). Data-independent acquisition method for ubiquitinome analysis reveals regulation of circadian biology. Nature Communications, 12(1): 254. doi:10.1038/s41467-020-20509-1. [PubMan] : Bludau, I., & Aebersold, R. (2020). Proteomic and interactomic insights into the molecular basis of cell functional diversity. Nature Reviews Molecular Cell Biology, 21(6), 327-340. doi:10.1038/s41580-020-0231-2. [PubMan] : Karayel, Ö., Xu, P., Bludau, I., Velan Bhoopalan, S., Yao, Y., Ana Rita, F., Santos, A., Schulman, B. A., Alpi, A. F., Weiss, M., & Mann, M. (2020). Integrative proteomics reveals principles of dynamic phosphosignaling networks in human erythropoiesis. Molecular Systems Biology, 16(12): e9813. doi:10.15252/msb.20209813. [PubMan] : Bludau, I., Heusel, M., Frank, M., Rosenberger, G., Hafen, R., Banaei-Esfahani, A., van Drogen, A., Collins, B. C., Gstaiger, M., & Aebersold, R. (2020). Complex-centric proteome profiling by SEC-SWATH-MS for the parallel detection of hundreds of protein complexes. Nature Protocols, 15(8), 2341-2386. doi:10.1038/s41596-020-0332-6. [PubMan] : Meier, F., Brunner, A.-D., Frank, M., Ha, A., Bludau, I., Voytik, E., Kaspar-Schoenefeld, S., Lubeck, M., Raether, O., Bache, N., Aebersold, R., Collins, B., Röst, H., & Mann, M. (2020). diaPASEF: parallel accumulation–serial fragmentation combined with data-independent acquisition. Nature Methods, 17(12), 1229-1236. doi:10.1038/s41592-020-00998-0. [PubMan]