An optimized quantitative proteomics method establishes the cell type‐resolved mouse brain secretome
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Abstract
To understand how cells communicate in the nervous system, it is essential to define their secretome, which is challenging for primary cells because of large cell numbers being required. Here, we miniaturized secretome analysis by developing the “high‐performance secretome protein enrichment with click sugars” (hiSPECS) method. To demonstrate its broad utility, hiSPECS was used to identify the secretory response of brain slices upon LPS‐induced neuroinflammation and to establish the cell type‐resolved mouse brain secretome resource using primary astrocytes, microglia, neurons, and oligodendrocytes. This resource allowed mapping the cellular origin of CSF proteins and revealed that an unexpectedly high number of secreted proteins in vitro and in vivo are proteolytically cleaved membrane protein ectodomains. Two examples are neuronally secreted ADAM22 and CD200, which we identified as substrates of the Alzheimer‐linked protease BACE1. hiSPECS and the brain secretome resource can be widely exploited to systematically study protein secretion and brain function and to identify cell type‐specific biomarkers for CNS diseases.
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Self-citationADAM10-Mediated Ectodomain Shedding Is an Essential Driver of Podocyte Damage
Sachs, M., Wetzel, S., Reichelt, J., Sachs, W., Schebsdat, L., Zielinski, S., Seipold, L., Blume, L., Müller, S. A., Kretz, O., et al. (2021) · Journal of the American Society of Nephrology · doi:10.1681/asn.2020081213 · Cited by 25 · see citing works
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Tsumagari, K., Chang, C.-H., & Ishihama, Y. (2021) · iScience · doi:10.1016/j.isci.2021.102259 · Cited by 24 · see citing works
Signatures of glial activity can be detected in the CSF proteome
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Self-citationMass spectrometry methods for analysis of extracellular matrix components in neurological diseases
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Multifarious astrocyte–neuron dialog in shaping neural circuit architecture
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Systematic characterization of extracellular glycoproteins using mass spectrometry
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Activity-Driven Synaptic Translocation of LGI1 Controls Excitatory Neurotransmission
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Deciphering the Properties and Functions of Glycoproteins Using Quantitative Proteomics
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Neuroimmunomodulatory properties of polysialic acid
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Endo-lysosomal dysfunction and neuronal–glial crosstalk in Niemann–Pick type C disease
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The pseudoprotease iRhom1 controls ectodomain shedding of membrane proteins in the nervous system
Tüshaus, J., Müller, S. A., Shrouder, J. J., Arends, M., Simons, M., Plesnila, N., Blobel, C., & Lichtenthaler, S. F. (2021) · The FASEB Journal · doi:10.1096/fj.202100936r · Cited by 11 · see citing works
Self-citationA lightweight convolutional neural network for surface defect detection in strip steel
Yang, C., Lv, D., Tian, X., Wang, C., Yang, P., & Zhang, Y. (2025) · Measurement Science and Technology · doi:10.1088/1361-6501/adbc10 · Cited by 12 · see citing works
The β-Secretase Substrate Seizure 6–Like Protein (SEZ6L) Controls Motor Functions in Mice
Ong-Pålsson, E., Njavro, J. R., Wilson, Y. M., Pigoni, M., Schmidt, A., Müller, S. A., Meyer, M., Hartmann, J., Busche, M. A., Gunnersen, J. M., et al. (2021) · Molecular Neurobiology · doi:10.1007/s12035-021-02660-y · Cited by 12 · see citing works
Self-citationMolecular methods to study protein trafficking between organs
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Interval-Based Secretomics Unravels Acute-Phase Response in Hepatocyte Model Systems
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Yang, S., Yi, L., Xia, X., Chen, X., Hou, X., Zhang, L., Yang, F. Y., Liao, J., Han, Z., & Fu, Y. (2023) · Journal of Affective Disorders · doi:10.1016/j.jad.2023.04.074 · Cited by 9 · see citing works
Hu, X., Wang, Y., Chai, C., & Han, S. (2025) · Measurement Science and Technology · doi:10.1088/1361-6501/ae214a · Cited by 7 · see citing works
Hsia, H., Tüshaus, J., Feng, X. M., Hofmann, L. I., Wefers, B., Marciano, D. K., Wurst, W., & Lichtenthaler, S. F. (2021) · The FASEB Journal · doi:10.1096/fj.202100475r · Cited by 7 · see citing works
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Deuterium labeling enables proteome-wide turnover kinetics analysis in cell culture
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Self-citationThe late-onset Alzheimer’s disease risk factor RHBDF2 is a modifier of microglial TREM2 proteolysis
Jocher, G., Müller, S. A., Hsia, H., Osua, M. L., Özcelik, G., Hofmann, L. I., Aßfalg, M., Dinkel, L., Feng, X. M., Schlepckow, K., et al. (2025) · Life Science Alliance · doi:10.26508/lsa.202403080 · Cited by 6 · see citing works
Self-citationYang, C., Bonelli, S., Calligaris, M., Carreca, A. P., Müller, S. A., Lichtenthaler, S. F., Troeberg, L., & Scilabra, S. D. (2022) · Membranes · doi:10.3390/membranes12060578 · Cited by 5 · see citing works
Self-citationKojima, R., Pasławski, W., Lyu, G., Arenas, E., Zhang, X., & Svenningsson, P. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25010683 · Cited by 5 · see citing works
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Lourbopoulos, A. I., Müller, S. A., Jocher, G., Wick, M. W., Plesnila, N., & Lichtenthaler, S. F. (2025) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2025.100958 · Cited by 5 · see citing works
Self-citationDegradomics for large‐scale mechanistic insights on proteases and proteolysis in human health
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Voukali, E., & Vinkler, M. (2022) · Neural Regeneration Research · doi:10.4103/1673-5374.329002 · Cited by 3 · see citing works
Bhattacharya, D., da Silva‐Buttkus, P., Nalbach, K., Cheng, L., Garrett, L., Irmler, M., Kislinger, G., Werner, G., Rodde, R., Lengger, C., et al. (2025) · Cell Death and Disease · doi:10.1038/s41419-025-08168-w · Cited by 2 · see citing works
Self-citationBACE1 regulates sleep–wake cycle through both enzymatic and non–enzymatic actions
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Self-citationRen, K., Chen, R., Zhang, H., Cui, K., Wu, Q., Dong, J., Liang, L., & Liu, L. (2025) · Measurement Science and Technology · doi:10.1088/1361-6501/ae2b22 · Cited by 2 · see citing works
Spatially Resolved Tagging of Proteolytic Neo-N termini with Subtiligase-TM
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Proteomics applications in next generation induced pluripotent stem cell models
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A methodology to globally assess ectodomain shedding using soluble fractions from the mouse brain
Lobete, M., Salinas, T., Izquierdo-Bermejo, S., Socas, S., Oset‐Gasque, M. J., & Martin‐de‐Saavedra, M. D. (2024) · Frontiers in Psychiatry · doi:10.3389/fpsyt.2024.1367526 · Cited by 2 · see citing works
Mass spectrometry-based candidate substrate and site identification of PTM enzymes
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Pesämaa, I., Müller, S. A., Robinson, S., Darcher, A., Paquet, D., Zetterberg, H., Lichtenthaler, S. F., & Haass, C. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.06.15.545187 · Cited by 2 · see citing works
Self-citationYOLO-PTSW: an improved YOLOv8n-based algorithm for small target defect detection on swash plates
Shen, Z., Lv, Y., Ni, Y., & Wang, P. (2026) · Measurement Science and Technology · doi:10.1088/1361-6501/ae3792 · Cited by 1 · see citing works
Özata, G., Wise, R. M., Cardona-Alberich, A., Mayeen, N. F., Müller, S. A., Lichtenthaler, S. F., Zecca, L., & Burbulla, L. F. (2026) · Scientific Reports · doi:10.1038/s41598-026-55648-w · Cited by 1 · see citing works
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Merighi, A., & Lossi, L. (2022) · F1000Research · doi:10.12688/f1000research.126787.1
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Lourbopoulos, A. I., Müller, S. A., Jocher, G., Wick, M. W., Plesnila, N., & Lichtenthaler, S. F. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.06.18.599559 · Cited by 1 · see citing works
Self-citationSemaphorin 4B is an ADAM17-cleaved inhibitor of adipocyte thermogenesisPreprint
Amin, A., Badenes, M., Tüshaus, J., de Carvalho, É., Burbridge, E., Faísca, P., Trávníčková, K., Barros, A., Carobbio, S., Domingos, P. M. D. N., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.10.11.511765
Self-citationSpildrejorde, M., SAMARA, A. A., Sharma, A., Leithaug, M., Falck, M., Modafferi, S., Sundaram, A. Y. M., Acharya, G., Nordeng, H., Eskeland, R., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.12.08.519620
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The omics techniques used in perineuronal nets research
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Self-citationPesämaa, I., Müller, S. A., Robinson, S., Darcher, A., Paquet, D., Zetterberg, H., Lichtenthaler, S. F., & Haass, C. (2024) · Figshare · doi:10.6084/m9.figshare.24223891
Self-citationMSCA-RTDETR: multi-scale context-aligned real-time DETR for fabric defect detection
Li, R., Zhou, G., & Xiang, Z. (2025) · Measurement Science and Technology · doi:10.1088/1361-6501/ae2e1e
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SCA-YOLO: an improved YOLO algorithm for road object detection in autonomous driving
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Came-yolov11: a lightweight multi-scale surface defect detection method for ceramic insulators
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Microglia Ablation and Downstream Effects in the Cerebrospinal Fluid Proteome
Buchner, S., Song, S., Müller, S. A., Chen, Y., Parhizkar, S., Lichtenthaler, S. F., Holtzman, D. M., Jucker, M., & Kaeser, S. A. (2026) · PROTEOMICS · doi:10.1002/pmic.70178
Self-citation
- Authors
- Tüshaus, J., Müller, S. A., Kataka, E. S., Zaucha, J., Sebastian Monasor, L., Su, M., Güner, G., Jocher, G., Tahirovic, S., Frishman, D., Simons, M., & Lichtenthaler, S. F.
- Affiliations
- German Center for Neurodegenerative Diseases (DE)
- Technical University of Munich (DE)
- Corresponding author
- Lichtenthaler, Stefan F
- ORCID
- Venue
- The EMBO Journal
- Published
- 2020-09-21
- Volume
- 39
- Issue
- 20
- Pages
- e105693-e105693
- ISSN
- 0261-4189 (ISSN-L)
- 1460-2075
- PMC
- PMC7560198
- OpenAlex
- W3087614358
- Cited by
- 88
- References
- 64
- Citations by year
- 2026: 11 · 2025: 17 · 2024: 11 · 2023: 14 · 2022: 18 · 2021: 13 · 2020: 4
- FWCI
- 4.68
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- The EMBO Journal (publishedVersion, other-oa)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Open access LMU (Ludwid Maxmilian's Universitat Munchen) (submittedVersion, cc-by)
- mediaTUM (Technical University of Munich) (submittedVersion, other-oa)
- mediaTUM – the media and publications repository of the Technical University Munich (Technical University Munich) (submittedVersion)
- DZNE Pub (submittedVersion, cc-by)
- Funders
- Deutsche Forschungsgemeinschaft (EXC 2145 SyNergy project ID 390857198)
- Bundesministerium für Bildung und Forschung (CLINSPECT‐M and JPND PMG‐AD)
- Alzheimer Forschung Initiative (18014)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Neuroscience › Neurology › Neuroinflammation and Neurodegeneration Mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced Biosensing Techniques and Applications
- Keywords
- mouse brain, primary astrocytes, microglia, neurons, oligodendrocytes, LPS-induced neuroinflammation, cerebrospinal fluid protein, proteolytic cleavage, ADAM22, CD200, BACE1, Alzheimer's disease
- MeSH terms
- Animals, Astrocytes, Brain, Cells, Cultured, Cerebrospinal Fluid Proteins, Chromatography, Liquid, Lipopolysaccharides, Mice, Inbred C57BL, Nerve Tissue Proteins, Neurons, Oligodendroglia, Software, Antigens, CD, Aspartic Acid Endopeptidases, Microglia, Proteome, Principal Component Analysis, Proteomics, Mice, ADAM Proteins, Tandem Mass Spectrometry, Amyloid Precursor Protein Secretases, Gene Ontology
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