Publications

Matthias Mann has authored and co-authored over 900 publications and is the highest cited German researcher with an h-index of 272 and over 350,000 total citations ( google scholar). His personal views and vision on proteomics are regularly tweeted on the Matthias Mann lab twitter account (Matthias Mann Lab (@labs_mann) / Twitter), which currently has over 10,000 followers.

Research highlights

BioRxiv

Deep Visual Proteomics advances human colon organoid models by revealing a switch to an in vivo-like phenotype upon xenotransplantation

Frederik Post, Annika Hausmann, Sonja Kabatnik, Sophia Steigerwald, Alexandra Brand, Ditte L. Clement, Jonathan Skov, Theresa L. Boye, Toshiro Sato, Casper Steenholdt, Andreas Mund, Ole H. Nielsen, Kim B. Jensen, Matthias Mann

bioRxiv 2024.05.13.593888; doi: https://doi.org/10.1101/2024.05.13.593888

Deep Visual Proteomics Unveils Precision Medicine Insights in Composite Small Lymphocytic and Classical Hodgkin Lymphoma

Xiang Zheng, Lars Møller Pedersen, Michael Bzorek, Andreas Mund, Lise Mette Rahbek Gjerdrum, Matthias Mann

bioRxiv 2024.06.12.598635; doi: https://doi.org/10.1101/2024.06.12.598635

Spatial proteo-transcriptomic profiling reveals the molecular landscape of borderline ovarian tumors and their invasive progression.

Schweizer L, Krishnan R, Shimizu A, Metousis A, Kenny H, Mendoza R, Nordmann TM, Rauch S, Kelliher L, Heide J, Rosenberger FA, Bilecz A, Borrego SN, Strauss MT, Thielert M, Rodriguez E, Müller-Reif JB, Chen M, Yamada SD, Mund A, Lastra RR, Mann M, Lengyel E.medRxiv [Preprint]. 2023 Nov 13:2023.11.13.23298409. doi: 10.1101/2023.11.13.23298409.

Publications

2025

Mass-spectrometry-based proteomics: from single cells to clinical applications.

Guo T, Steen JA, Mann M.Nature. 2025 Feb;638(8052):901-911. doi: 10.1038/s41586-025-08584-0. Epub 2025 Feb 26.

Plasma proteome variation and its genetic determinants in children and adolescents.

Niu L, Stinson SE, Holm LA, Lund MAV, Fonvig CE, Cobuccio L, Meisner J, Juel HB, Fadista J, Thiele M, Krag A, Holm JC, Rasmussen S, Hansen T, Mann M.Nat Genet. 2025 Feb 19. doi: 10.1038/s41588-025-02089-2. Online ahead of print.

Deep visual proteomics reveals DNA replication stress as a hallmark of signet ring cell carcinoma.

Kabatnik S, Zheng X, Pappas G, Steigerwald S, Padula MP, Mann M.NPJ Precis Oncol. 2025 Feb 5;9(1):37. doi: 10.1038/s41698-025-00819-7.

Deciphering functional tumor-immune crosstalk through highly multiplexed imaging and deep visual proteomics.

Zheng X, Mund A, Mann M.Mol Cell. 2025 Mar 6;85(5):1008-1023.e7. doi: 10.1016/j.molcel.2024.12.023. Epub 2025 Jan 14.

2024

A new understanding of tissue biology from MS-based proteomics at single-cell resolution.

Nordmann TM, Mund A, Mann M.Nat Methods. 2024 Dec;21(12):2220-2222. doi: 10.1038/s41592-024-02541-x.

Spatial proteomics identifies JAKi as treatment for a lethal skin disease.

Nordmann TM, Anderton H, Hasegawa A, Schweizer L, Zhang P, Stadler PC, Sinha A, Metousis A, Rosenberger FA, Zwiebel M, Satoh TK, Anzengruber F, Strauss MT, Tanzer MC, Saito Y, Gong T, Thielert M, Kimura H, Silke N, Rodriguez EH, Restivo G, Nguyen HH, Gross A, Feldmeyer L, Joerg L, Levesque MP, Murray PJ, Ingen-Housz-Oro S, Mund A, Abe R, Silke J, Ji C, French LE, Mann M.Nature. 2024 Nov;635(8040):1001-1009. doi: 10.1038/s41586-024-08061-0. Epub 2024 Oct 16.

Spatial characterization and stratification of colorectal adenomas by deep visual proteomics.

Kabatnik S, Post F, Drici L, Bartels AS, Strauss MT, Zheng X, Madsen GI, Mund A, Rosenberger FA, Moreira J, Mann M.iScience. 2024 Jul 31;27(9):110620. doi: 10.1016/j.isci.2024.110620. eCollection 2024 Sep 20.

AlphaPept: a modern and open framework for MS-based proteomics.

Strauss MT, Bludau I, Zeng WF, Voytik E, Ammar C, Schessner JP, Ilango R, Gill M, Meier F, Willems S, Mann M.Nat Commun. 2024 Mar 9;15(1):2168. doi: 10.1038/s41467-024-46485-4.

2023

The social and structural architecture of the yeast protein interactome.

Michaelis AC, Brunner AD, Zwiebel M, Meier F, Strauss MT, Bludau I, Mann M.Nature. 2023 Dec;624(7990):192-200. doi: 10.1038/s41586-023-06739-5. Epub 2023 Nov 15.

A Standardized and Reproducible Workflow for Membrane Glass Slides in Routine Histology and Spatial Proteomics.

Nordmann TM, Schweizer L, Metousis A, Thielert M, Rodriguez E, Rahbek-Gjerdrum LM, Stadler PC, Bzorek M, Mund A, Rosenberger FA, Mann M.Mol Cell Proteomics. 2023 Oct;22(10):100643. doi: 10.1016/j.mcpro.2023.100643. Epub 2023 Sep 7.

Spatial single-cell mass spectrometry defines zonation of the hepatocyte proteome.

Rosenberger FA, Thielert M, Strauss MT, Schweizer L, Ammar C, Mädler SC, Metousis A, Skowronek P, Wahle M, Madden K, Gote-Schniering J, Semenova A, Schiller HB, Rodriguez E, Nordmann TM, Mund A, Mann M.Nat Methods. 2023 Oct;20(10):1530-1536. doi: 10.1038/s41592-023-02007-6. Epub 2023 Oct 2.

Robust dimethyl-based multiplex-DIA doubles single-cell proteome depth via a reference channel.

Thielert M, Itang EC, Ammar C, Rosenberger FA, Bludau I, Schweizer L, Nordmann TM, Skowronek P, Wahle M, Zeng WF, Zhou XX, Brunner AD, Richter S, Levesque MP, Theis FJ, Steger M, Mann M.

Accurate Label-Free Quantification by directLFQ to Compare Unlimited Numbers of Proteomes.

Ammar C, Schessner JP, Willems S, Michaelis AC, Mann M.Mol Cell Proteomics. 2023 Jul;22(7):100581. doi: 10.1016/j.mcpro.2023.100581. Epub 2023 May 22.

Proteomics separates adult-type diffuse high-grade gliomas in metabolic subgroups independent of 1p/19q codeletion and across IDH mutational status.

Bader JM, Deigendesch N, Misch M, Mann M, Koch A, Meissner F.Cell Rep Med. 2023 Jan 17;4(1):100877. doi: 10.1016/j.xcrm.2022.100877. Epub 2022 Dec 29.

2022

Spatial proteomics in three-dimensional intact specimens.

Bhatia HS, Brunner AD, Öztürk F, Kapoor S, Rong Z, Mai H, Thielert M, Ali M, Al-Maskari R, Paetzold JC, Kofler F, Todorov MI, Molbay M, Kolabas ZI, Negwer M, Hoeher L, Steinke H, Dima A, Gupta B, Kaltenecker D, Caliskan ÖS, Brandt D, Krahmer N, Müller S, Lichtenthaler SF, Hellal F, Bechmann I, Menze B, Theis F, Mann M, Ertürk A.Cell. 2022 Dec 22;185(26):5040-5058.e19. doi: 10.1016/j.cell.2022.11.021.

Synchro-PASEF Allows Precursor-Specific Fragment Ion Extraction and Interference Removal in Data-Independent Acquisition.

Skowronek P, Krohs F, Lubeck M, Wallmann G, Itang ECM, Koval P, Wahle M, Thielert M, Meier F, Willems S, Raether O, Mann M.Mol Cell Proteomics. 2022 Dec 22;22(2):100489. doi: 10.1016/j.mcpro.2022.100489.

AlphaPeptDeep: a modular deep learning framework to predict peptide properties for proteomics.

Zeng WF, Zhou XX, Willems S, Ammar C, Wahle M, Bludau I, Voytik E, Strauss MT, Mann M.Nat Commun. 2022 Nov 24;13(1):7238. doi: 10.1038/s41467-022-34904-3.

Rapid and in-depth coverage of the (phospho-)proteome with deep libraries and optimal window design for dia-PASEF

Skowronek P, Thielert M, Voytik E, Tanzer MC, Hansen FM, Willems S, Karayel O, Brunner AD, Meier F, Mann M.Mol Cell Proteomics. 2022 Aug 6;21(9):100279. doi: 10.1016/j.mcpro.2022.100279. Online ahead of print.PMID: 35944843

Noninvasive proteomic biomarkers for alcohol-related liver disease.

Niu L, Thiele M, Geyer PE, Rasmussen DN, Webel HE, Santos A, Gupta R, Meier F, Strauss M, Kjaergaard M, Lindvig K, Jacobsen S, Rasmussen S, Hansen T, Krag A, Mann M.Nat Med. 2022 Jun;28(6):1277-1287. doi: 10.1038/s41591-022-01850-y. Epub 2022 Jun 2.PMID: 35654907 Free PMC article.

Unbiased spatial proteomics with single-cell resolution in tissues.

Mund A, Brunner AD, Mann M.Mol Cell. 2022 Jun 16;82(12):2335-2349. doi: 10.1016/j.molcel.2022.05.022.PMID: 35714588 Review.

Proteome profiling of cerebrospinal fluid reveals biomarker candidates for Parkinson's disease.

Karayel O, Virreira Winter S, Padmanabhan S, Kuras YI, Vu DT, Tuncali I, Merchant K, Wills AM, Scherzer CR, Mann M. Cell Rep Med. 2022 Jun 21;3(6):100661. doi: 10.1016/j.xcrm.2022.100661.PMID: 35732154

Deep Visual Proteomics defines single-cell identity and heterogeneity.

Mund A, Coscia F, Kriston A, Hollandi R, Kovács F, Brunner AD, Migh E, Schweizer L, Santos A, Bzorek M, Naimy S, Rahbek-Gjerdrum LM, Dyring-Andersen B, Bulkescher J, Lukas C, Eckert MA, Lengyel E, Gnann C, Lundberg E, Horvath P, Mann M.Nat Biotechnol. 2022 May 19. doi: 10.1038/s41587-022-01302-5. Online ahead of print.PMID: 35590073

 The structural context of posttranslational modifications at a proteome-wide scale.

Bludau I, Willems S, Zeng WF, Strauss MT, Hansen FM, Tanzer MC, Karayel O, Schulman BA, Mann M.PLoS Biol. 2022 May 16;20(5):e3001636. doi: 10.1371/journal.pbio.3001636. Online ahead of print.PMID: 35576205 

Dynamic human liver proteome atlas reveals functional insights into disease pathways.

Niu L, Geyer PE, Gupta R, Santos A, Meier F, Doll S, Wewer Albrechtsen NJ, Klein S, Ortiz C, Uschner FE, Schierwagen R, Trebicka J, Mann M.Mol Syst Biol. 2022 May;18(5):e10947. doi: 10.15252/msb.202210947.PMID: 35579278

A GID E3 ligase assembly ubiquitinates an Rsp5 E3 adaptor and regulates plasma membrane transporters.

Langlois CR, Beier V, Karayel O, Chrustowicz J, Sherpa D, Mann M, Schulman BA.EMBO Rep. 2022 Apr 19:e53835. doi: 10.15252/embr.202153835. Online ahead of print.PMID: 35437932

The emerging role of mass spectrometry-based proteomics in drug discovery.

Meissner F, Geddes-McAlister J, Mann M, Bantscheff M.Nat Rev Drug Discov. 2022 Mar 29. doi: 10.1038/s41573-022-00409-3. Online ahead of print.PMID: 35351998 

OpenCell: Endogenous tagging for the cartography of human cellular organization.

Cho NH, Cheveralls KC, Brunner AD, Kim K, Michaelis AC, Raghavan P, Kobayashi H, Savy L, Li JY, Canaj H, Kim JYS, Stewart EM, Gnann C, McCarthy F, Cabrera JP, Brunetti RM, Chhun BB, Dingle G, Hein MY, Huang B, Mehta SB, Weissman JS, Gómez-Sjöberg R, Itzhak DN, Royer LA, Mann M, Leonetti MD.

Science. 2022 Mar 11;375(6585):eabi6983. doi: 10.1126/science.abi6983. Epub 2022 Mar 11.PMID: 35271311

The proteogenomic subtypes of acute myeloid leukemia.

Jayavelu AK, Wolf S, Buettner F, Alexe G, Häupl B, Comoglio F, Schneider C, Doebele C, Fuhrmann DC, Wagner S, Donato E, Andresen C, Wilke AC, Zindel A, Jahn D, Splettstoesser B, Plessmann U, Münch S, Abou-El-Ardat K, Makowka P, Acker F, Enssle JC, Cremer A, Schnütgen F, Kurrle N, Chapuy B, Löber J, Hartmann S, Wild PJ, Wittig I, Hübschmann D, Kaderali L, Cox J, Brüne B, Röllig C, Thiede C, Steffen B, Bornhäuser M, Trumpp A, Urlaub H, Stegmaier K, Serve H, Mann M, Oellerich T.

Cancer Cell. 2022 Feb 28:S1535-6108(22)00058-7. doi: 10.1016/j.ccell.2022.02.006. Online ahead of print.PMID: 35245447

Ultra-high sensitivity mass spectrometry quantifies single-cell proteome changes upon perturbation.

Brunner AD, Thielert M, Vasilopoulou C, Ammar C, Coscia F, Mund A, Hoerning OB, Bache N, Apalategui A, Lubeck M, Richter S, Fischer DS, Raether O, Park MA, Meier F, Theis FJ, Mann M.

Mol Syst Biol. 2022 Mar;18(3):e10798. doi: 10.15252/msb.202110798.PMID: 35226415

A knowledge graph to interpret clinical proteomics data.

Santos A, Colaço AR, Nielsen AB, Niu L, Strauss M, Geyer PE, Coscia F, Albrechtsen NJW, Mundt F, Jensen LJ, Mann M.

Nat Biotechnol. 2022 Jan 31. doi: 10.1038/s41587-021-01145-6. Online ahead of print.PMID: 35102292

2021

Defining NASH from a Multi-Omics Systems Biology Perspective.

Niu L, Sulek K, Vasilopoulou CG, Santos A, Wewer Albrechtsen NJ, Rasmussen S, Meier F, Mann M.

J Clin Med. 2021 Oct 12;10(20):4673. doi: 10.3390/jcm10204673.PMID: 34682795 

Phosphoproteome profiling uncovers a key role for CDKs in TNF signaling.

Tanzer MC, Bludau I, Stafford CA, Hornung V, Mann M.

Nat Commun. 2021 Oct 18;12(1):6053. doi: 10.1038/s41467-021-26289-6.PMID: 34663829

AlphaMap: an open-source python package for the visual annotation of proteomics data with sequence specific knowledge.

Voytik E, Bludau I, Willems S, Hansen FM, Brunner AD, Strauss MT, Mann M.

Bioinformatics. 2021 Sep 29:btab674. doi: 10.1093/bioinformatics/btab674. Online ahead of print.PMID: 34586352

AlphaTims: Indexing trapped ion mobility spectrometry - time of flight data for fast and easy accession and visualization.

Willems S, Voytik E, Skowronek P, Strauss MT, Mann M.

Mol Cell Proteomics. 2021 Sep 17:100149. doi: 10.1016/j.mcpro.2021.100149. Online ahead of print.PMID: 34543758

SnapShot: Clinical proteomics.

Zhu Y, Aebersold R, Mann M, Guo T.

Cell. 2021 Sep 2;184(18):4840-4840.e1. doi: 10.1016/j.cell.2021.08.015.PMID: 34478659

Trapped Ion Mobility Spectrometry (TIMS) and Parallel Accumulation - Serial Fragmentation (PASEF) in Proteomics.

Meier F, Park MA, Mann M.

Mol Cell Proteomics. 2021 Aug 17:100138. doi: 10.1016/j.mcpro.2021.100138. Online ahead of print.PMID: 34416385

Artificial intelligence for proteomics and biomarker discovery.

Mann M, Kumar C, Zeng WF, Strauss MT.

Cell Syst. 2021 Aug 18;12(8):759-770. doi: 10.1016/j.cels.2021.06.006.PMID: 34411543

Identification of the transcription factor MAZ as a regulator of erythropoiesis.

Deen D, Butter F, Daniels DE, Ferrer-Vicens I, Ferguson DCJ, Holland ML, Samara V, Sloane-Stanley JA, Ayyub H, Mann M, Frayne J, Garrick D, Vernimmen D.

Blood Adv. 2021 Aug 10;5(15):3002-3015. doi: 10.1182/bloodadvances.2021004609.PMID: 34351390 

Identification of covalent modifications regulating immune signaling complex composition and phenotype.

Frauenstein A, Ebner S, Hansen FM, Sinha A, Phulphagar K, Swatek K, Hornburg D, Mann M, Meissner F.

Mol Syst Biol. 2021 Jul;17(7):e10125. doi: 10.15252/msb.202010125.PMID: 34318608 

High-resolution serum proteome trajectories in COVID-19 reveal patient-specific seroconversion.

Geyer PE, Arend FM, Doll S, Louiset ML, Virreira Winter S, Müller-Reif JB, Torun FM, Weigand M, Eichhorn P, Bruegel M, Strauss MT, Holdt LM, Mann M, Teupser D.

EMBO Mol Med. 2021 Aug 9;13(8):e14167. doi: 10.15252/emmm.202114167. Epub 2021 Jul 7.PMID: 34232570

Multi-omics profiling of living human pancreatic islet donors reveals heterogeneous beta cell trajectories towards type 2 diabetes.

Wigger L, Barovic M, Brunner AD, Marzetta F, Schöniger E, Mehl F, Kipke N, Friedland D, Burdet F, Kessler C, Lesche M, Thorens B, Bonifacio E, Legido-Quigley C, Barbier Saint Hilaire P, Delerive P, Dahl A, Klose C, Gerl MJ, Simons K, Aust D, Weitz J, Distler M, Schulte AM, Mann M, Ibberson M, Solimena M.

Nat Metab. 2021 Jul;3(7):1017-1031. doi: 10.1038/s42255-021-00420-9. Epub 2021 Jun 28.PMID: 34183850

A New Parallel High-Pressure Packing System Enables Rapid Multiplexed Production of Capillary Columns.

Müller-Reif JB, Hansen FM, Schweizer L, Treit PV, Geyer PE, Mann M.

Mol Cell Proteomics. 2021 Apr 20;20:100082. doi: 10.1016/j.mcpro.2021.100082. Online ahead of print.PMID: 33887488 

Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV.

Stukalov A, Girault V, Grass V, Karayel O, Bergant V, Urban C, Haas DA, Huang Y, Oubraham L, Wang A, Hamad MS, Piras A, Hansen FM, Tanzer MC, Paron I, Zinzula L, Engleitner T, Reinecke M, Lavacca TM, Ehmann R, Wölfel R, Jores J, Kuster B, Protzer U, Rad R, Ziebuhr J, Thiel V, Scaturro P, Mann M, Pichlmair A.

Nature. 2021 Jun;594(7862):246-252. doi: 10.1038/s41586-021-03493-4. Epub 2021 Apr 12.PMID: 33845483

 Deep learning the collisional cross sections of the peptide universe from a million experimental values.

Meier F, Köhler ND, Brunner AD, Wanka JH, Voytik E, Strauss MT, Theis FJ, Mann M.

Nat Commun. 2021 Feb 19;12(1):1185. doi: 10.1038/s41467-021-21352-8.PMID: 33608539 

Urinary proteome profiling for stratifying patients with familial Parkinson's disease.

Virreira Winter S, Karayel O, Strauss MT, Padmanabhan S, Surface M, Merchant K, Alcalay RN, Mann M.

EMBO Mol Med. 2021 Mar 5;13(3):e13257. doi: 10.15252/emmm.202013257. Epub 2021 Jan 22.PMID: 33481347 

 Ethical Principles, Constraints and Opportunities in Clinical Proteomics.

Mann SP, Treit PV, Geyer PE, Omenn GS, Mann M.

Mol Cell Proteomics. 2021 Jan 14;20:100046. doi: 10.1016/j.mcpro.2021.100046. Online ahead of print.PMID: 33453411 

 Plasma proteomes can be re-identifiable and potentially contain personally sensitive and incidental findings.

Geyer PE, Mann SP, Treit PV, Mann M.

Mol Cell Proteomics. 2021 Jan 11;20:100035. doi: 10.1074/mcp.RA120.002359. Online ahead of print.PMID: 33444735

Data-independent acquisition method for ubiquitinome analysis reveals regulation of circadian biology.

Hansen FM, Tanzer MC, Brüning F, Bludau I, Stafford C, Schulman BA, Robles MS, Karayel O, Mann M.

Nat Commun. 2021 Jan 11;12(1):254. doi: 10.1038/s41467-020-20509-1.PMID: 33431886

Ethical principles, opportunities and constraints in clinical proteomics.

Porsdam Mann S, Treit PV, Geyer PE, Omenn GS, Mann M.

Mol Cell Proteomics. 2021 Jan 4:mcp.RA120.002435. doi: 10.1074/mcp.RA120.002435. Online ahead of print.PMID: 33397710

 

Complete Publication list

https://pubmed.ncbi.nlm.nih.gov/?term=matthias+mann&sort=date