The department of Proteomics and Signal Transduction is headed by Prof. Matthias Mann and was established in 2005. Matthias Mann is the highest cited German researcher by his h-index of more than 242 and over 280,000 citations ( google scholar). In addition to his group at the Max Planck Institute of Biochemistry, Matthias Mann is the director of the proteomics program at the Novo Nordisk Foundation Center for Protein Research (NNF-CPR) in Copenhagen where he also leads the Clinical Proteomics group ( clinical proteomics group). The Mann lab is a leader in the technology and application of mass spectrometry-based proteomics and has been at the forefront of the field for over two decades. The core research interests of the group are signal transduction, biomarker discovery and metabolic diseases. Another focus is the development of mass spectrometric and proteomic methods for application in biological and clinical contexts. The group is also developing computer algorithms for automated identification and quantification of peptides as well as systems biological and clinical knowledge mining. Ultimately, our vision is to transfer proteomics knowledge into clinics for predictive, diagnostic and preventive purposes. We are a highly collaborative team and involved in several networks including MICROB-PREDICT, Michael J. Fox Foundation for Parkinson’s Research projects, German-Israeli project (DIP), CLINSPECT-M, Munich Heart Alliance, and Digimed Bayern.


Data-independent acquisition method for ubiquitinome analysis reveals regulation of circadian biology
Fynn Hansen, […] Matthias Mann 

Nature Commununications, 11 January 2021 more
Ultra-high sensitivity mass spectrometry quantifies single-cell proteome changes upon perturbation
Andreas-David Brunner, […] Matthias Mann

BioRxiv, 22 December 2020 more
diaPASEF: parallel accumulation–serial fragmentation combined with data-independent acquisition
Florian Meier, Andreas-David Brunner, […]Ben C. Collins, Hannes L. Röst, Matthias Mann

Nature Methods, 30 November 2020 more
Splicing factor YBX1 mediates persistence of JAK2-mutated neoplasms
Ashok Kumar Jayavelu, Tina M. Schnöder, […]Matthias Mann, Florian H. Heidel

Nature, 25 November 2020 more
A beginner’s guide to mass spectrometry–based proteomics
Ankit Sinha and Matthias Mann

The Biochemist, 9 September 2020 more
The proteome landscape of the kingdoms of life
Johannes Müller, Philipp Geyer, […] Matthias Mann

Nature, 17 June 2020 more
12 March 2020

Matthias Mann gives a research lecture at the Nobel Forum at the Karolinska Institute

12 March 2020
Plasma Proteome Profiling Reveals Dynamics of Inflammatory and Lipid Homeostasis Markers after Roux-En-Y Gastric Bypass Surgery
Cell Systems 7, Open Access - Published: December 5, 2018 - DOI: 

Nicolai J. Wewer Albrechtsen, Philipp E. Geyer, Sophia Doll, Peter V. Treit, Kirstine N. Bojsen-Møller, Christoffer Martinussen, Nils B. Jørgensen, Signe S. Torekov, Florian Meier, Lili Niu, Alberto Santos, Eva C. Keilhauer, Jens J. Holst, Sten Madsbad, Matthias Mann more
Plasma proteome profiling to detect and avoid sample-related biases in biomarker studies
bioRxiv preprint first posted online Nov. 30, 2018; doi:

Philipp Emanuel Geyer, Eugenia Voytik, Peter V. Treit, Sophia Doll, Alisa Kleinhempel, Lili Niu, Johannes Bruno Mueller, Jakob Bader, Daniel Teupser, Lesca Miriam Holdt, Matthias Mann more
Proteomics in the Study of Liver Diseases
The Human Gut-Liver-Axis in Health and Disease pp 165-193
Niu L, Geyer P, Mann M more
Opinion: Advocating for science progress as a human right
PNAS October 23, 2018 115 (43) 10820-10823;

S. Porsdam Mann, Y. Donders, C. Mitchell, V. J. Bradley, M. F. Chou, M. Mann, G. Church, and H. Porsdam more
Organellar Proteomics and Phospho-Proteomics Reveal Subcellular Reorganization in Diet-Induced Hepatic Steatosis
Dev Cell. 2018 Oct 22;47(2):205-221.e7. doi: 10.1016/j.devcel.2018.09.017.

Krahmer N, Najafi B, Schueder F, Quagliarini F, Steger M, Seitz S, Kasper R, Salinas F, Cox J, Uhlenhaut NH, Walther TC, Jungmann R, Zeigerer A, Borner GHH, Mann M.

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Multi-level Proteomics Identifies CT45 as a Chemosensitivity Mediator and Immunotherapy Target in Ovarian Cancer.
Cell. 2018 Sep 20;175(1):159-170.e16. doi: 10.1016/j.cell.2018.08.065.

Coscia F, Lengyel E, Duraiswamy J, Ashcroft B, Bassani-Sternberg M, Wierer M, Johnson A, Wroblewski K, Montag A, Yamada SD, López-Méndez B, Nilsson J, Mund A, Mann M, Curtis M. more
High-throughput and high-sensitivity phosphoproteomics with the EasyPhos platform
Nature Protocols | Published: 06 September 2018

Sean J. Humphrey, Ozge Karayel, David E. James and Matthias Mann more
In vivo brain GPCR signaling elucidated by phosphoproteomics

Science 22 Jun 2018: Vol. 360, Issue 6395, eaao4927,DOI: 10.1126/science.aao4927
[Full text]

Jeffrey J. Liu, Kirti Sharma, Luca Zangrandi, Chongguang Chen, Sean J. Humphrey, Yi-Ting Chiu, Mariana Spetea, Lee-Yuan Liu-Chen, Christoph Schwarzer, Matthias Mann 
Rapid proteomic analysis for solid tumors reveals LSD1 as a drug target in an end‐stage cancer patient
Sophia Doll, Maximilian C. Kriegmair, Alberto Santos, Michael Wierer, Fabian Coscia, Helen Michele Neil, Stefan Porubsky, Philipp E. Geyer, Andreas Mund, Philipp Nuhn, Matthias Mann more
Online parallel accumulation − serial fragmentation (PASEF) with a novel trapped ion mobility mass spectrometer
Molecular & Cellular Proteomics November 1, 2018, mcp.TIR118.000900;

Florian Meier, Andreas-David Brunner, Scarlet Koch, Heiner Koch, Markus Lubeck, Michael Krause, Niels Goedecke, Jens Decker, Thomas Kosinski, Melvin A Park, Nicolai Bache, Ole Hoerning, Juergen Cox, Oliver Raether, Matthias Mann
Nicolai Bache, Philipp E. Geyer, Dorte B. Bekker-Jensen, Ole Hoerning, Lasse Falkenby, Peter V. Treit, Sophia Doll, Igor Paron, Florian Meier, Jesper V. Olsen, Ole Vorm, Matthias Mann more
BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes
Nature Methods (2018) doi:10.1038/s41592-018-0003-5

Meier F, Geyer PE, Winter SV, Cox J & Mann M more
Systematic proteomic analysis of LRRK2-mediated Rab GTPase phosphorylation establishes a connection to ciliogenesis
Elife. 2017 Nov 10;6. pii: e31012. doi: 10.7554/eLife.31012.

Steger M, Diez F, Dhekne HS, Lis P, Nirujogi RS, Karayel O, Tonelli F, Martinez TN, Lorentzen E, Pfeffer SR, Alessi DR, Mann M.
Neuron Volume 96, Issue 3, 1 November 2017, Pages 558–571;

Fabian Hosp and Matthias Mann more

Matthias Mann talks about clinical proteomics in interview with Evosep Biosystems
Single Muscle Fiber Proteomics Reveals Fiber-Type-Specific Features of Human Muscle Aging
Cell Rep. 2017 Jun 13;19(11):2396-2409. doi: 10.1016/j.celrep.2017.05.054.

Murgia M, Toniolo L, Nagaraj N, Ciciliot S, Vindigni V, Schiaffino S, Reggiani C, Mann M.

•Single-fiber proteomic analysis of human muscle aging
•Oxidative phosphorylation decreases similarly in slow and fast fibers
•Enzymes of carbohydrate metabolism increase in slow and decrease in fast aging fibers
•Proteomics elucidates why fast fibers age more rapidly than slow ones
Novo Nordisk Foundation Center for Protein Research   Olsen Group defines the HeLa cell proteome
Bekker-Jensen et al. show that proteomics can now provide an essentially complete HeLa proteome. They provide measurements acquired simultaneously for more than 12,200 protein-coding genes, 10,000 phosphorylation sites, and 7,000 N-acetylation sites. Their approach is fast, accessible, and requires modest amounts of starting material, making it easily extendable to other human cell lines and patient samples. - Bekker-Jensen et al., 2017, Cell Systems 4, 1–13 June 28, 2017
EMBL Alumni Award 2017  Matthias Mann winner of Lennart Philipson Award
“Matthias Mann, former Group Leader in EMBL’s Instrumentation Programme (1992-1998), has been selected as the 2017 Lennart Philipson Award winner for his pioneering work in the field of mass spectrometry-based proteomics.

Matthias has contributed breakthroughs that have revolutionised proteomics techniques in biomedical laboratories around the world. His contributions include the “peptide sequence tag” approach which allows proteins to be computationally identified by the fragment spectra; nanoelectrospray which allows minute quantities of protein to be tested; and methods for analysing proteins after extracting them from gels."
Social network architecture of human immune cells unveiled by quantitative proteomics
Jan C Rieckmann, Roger Geiger, Daniel Hornburg, Tobias Wolf, Ksenya Kveler, David Jarrossay, Federica Sallusto, Shai S Shen-Orr, Antonio Lanzavecchia, Matthias Mann & Felix Meissner

Immune cells give rise to the most interconnected system in the body. Here, we perform comprehensive proteomics and secretomics ( to describe in detail the 'social network' of human immune cells and throw light on novel cell connectivities
Phosphorylation Is a Central Mechanism for Circadian Control of Metabolism and Physiology
Cell Metabolism 25, 1–10January 10, 2017 ª 2016 Elsevier Inc.

Robles MS, Humphrey SJ, Mann M.
Ruedi Aebersold & Matthias Mann

Nature 537, 347–355 (15 September 2016) doi:10.1038/nature19949
Received 11 January 2016 Accepted 15 July 2016 Published online 14 September 2016
Integrative proteomic profiling of ovarian cancer cell lines reveals precursor cell associated proteins and functional status
Nat Commun. 2016 Aug 26;7:12645. doi: 10.1038/ncomms12645.

Coscia F, Watters KM, Curtis M, Eckert MA, Chiang CY, Tyanova S, Montag A, Lastra RR, Lengyel E, Mann M.
Circadian control of oscillations in mitochondrial rate-limiting enzymes and nutrient utilization by PERIOD proteins
Proc Natl Acad Sci U S A. 2016 Mar 22;113(12):E1673-82. doi: 10.1073/pnas.1519650113. Epub 2016 Feb 9.

Neufeld-Cohen A, Robles MS, Aviram R, Manella G, Adamovich Y, Ladeuix B, Nir D, Rousso-Noori L, Kuperman Y, Golik M, Mann M, Asher G

Highlighted at
Cell Systems: featured articlePlasma Proteome Profiling to Assess Human Health and Disease
cell systems, Volume 2, Issue 3, p185–195, 23 March 2016
Geyer et al.

Breakthrough in Parkinson’s Research
Identification of bona fide and verifiable substrates of the Parkinson’s disease kinase LRRK2 has eluded researchers for over ten years and was considered as one of the greatest challenges in the field. Using phosphoproteomics, we identified and validated Rab GTPases as key physiological LRRK2 substrates.

Phosphoproteomics reveals that Parkinson’s disease kinase LRRK2 regulates a subset of Rab GTPases

eLife, January 28, 2016

Steger, M et al.

Press Release
Dispatch in Current Biology
Comment in Movement Disorders
Matthias Mann receives The Order of Dannebrog Knights Cross
Her Majesty the Queen of Denmark recognizes Matthias for his outstanding contribution to mankind in general, and science in particular. more
the Medal is a biennial award recognizing an individual who has significantly contributed to the development of new bioanalytical methods. more
Cell type– and brain region–resolved mouse brain proteome
Nat Neurosci. 2015 Nov 2. doi: 10.1038/nn.4160

Sharma K, Schmitt S, Bergner CG, Tyanova S, Kannaiyan N, Manrique-Hoyos N, Kongi K, Cantuti L, Hanisch UK, Philips MA, Rossner MJ, Mann M, Simons M
  Press Release
A Human Interactome in Three Quantitative Dimensions Organized by Stoichiometries and Abundances
Cell 163(3):712-23 (2015). doi: 10.1016/j.cell.2015.09.053

Marco Y. Hein, Nina C. Hubner, Ina Poser, Jürgen Cox, Nagarjuna Nagaraj, Yusuke Toyoda, Igor A. Gak, Ina Weisswange, Jörg Mansfeld, Frank Buchholz, Anthony A. Hyman & Matthias Mann   Press Release Research Highlight in Nature Reviews Molecular Cell Biology
High-throughput phosphoproteomics reveals in vivo insulin signaling dynamics
Nat Biotechnol. 2015 Aug 17. doi: 10.1038/nbt.3327.

Humphrey SJ, Azimifar SB, Mann M.
  Press Release Nature Biotechnology | NEWS AND VIEWS
The Impact II, a Very High-Resolution Quadrupole Time-of-Flight Instrument (QTOF) for Deep Shotgun Proteomics
Mol Cell Proteomics. 2015 Jul;14(7):2014-29. doi: 10.1074/mcp.M114.047407.

Beck S, Michalski A, Raether O, Lubeck M, Kaspar S, Goedecke N, Baessmann C, Hornburg D, Meier F, Paron I, Kulak NA, Cox J, Mann M
Time- and compartment-resolved proteome profiling of the extracellular niche in lung injury and repair
Molecular Systems Biology, July 6, 2015

H.B. Schiller, I.E. Fernandez, G. Burgstaller, C. Schaab, R.A. Scheltema, T. Schwarzmayr, T.M. Strom, O. Eickelberg and M. Mann more
A double-barrel LC-MS/MS system to quantify 96 interactomes per day
Mol Cell Proteomics. 2015 Apr 17.

Hosp F, Scheltema RA, Eberl C, Kulak NA, Keilhauer EC, Mayr K, Mann M. more
Widespread Proteome Remodeling and Aggregation in Aging C. elegans
Cell, May 7, 2015 DOI: 10.1016/j.cell.2015.03.032

Walther DM, Kasturi P, Zheng M, Pinkert S, Vecchi G, Ciryam P, Morimoto RI, Dobson CM, Vendruscolo M, Mann M, Hartl FU.
Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links
Science 1 May 2015

Räschle M, Smeenk G, Hansen RK, Temu T, Oka Y, Hein MY, Nagaraj N, Long DT, Walter JC, Hofmann K, Storchova Z, Cox J, Bekker-Jensen S, Mailand N, Mann M
Single muscle fiber proteomics reveals unexpected mitochondrial specialization
EMBO Rep. 2015 Feb 2

Murgia M, Nagaraj N, Deshmukh AS, Zeiler M, Cancellara P, Moretti I, Reggiani C, Schiaffino S, Mann M
Mass spectrometry of HLA-I peptidomes reveals strong effects of protein abundance and turnover on antigen presentation
Mol Cell Proteomics (2015)

Bassani-Sternberg M, Pletscher-Frankild S, Jensen LJ, Mann M



Cell-Type-Resolved Quantitative Proteomics of Murine Liver

Cell Metabolism

S. Babak Azimifar, Nagarjuna Nagaraj, Juergen Cox, Matthias Mann

Image: Max Iglesias

Structural Model of a CRISPR RNA-Silencing Complex Reveals the RNA-Target Cleavage Activity in Cmr4
Molecular Cell (2014)

Christian Benda, Judith Ebert, Richard A. Scheltema, Herbert B. Schiller, Marc Baumgärtner, Fabien Bonneau, Matthias Mann, Elena Conti

The Q Exactive HF, a Benchtop Mass Spectrometer with a Pre-filter, High Performance Quadrupole and an Ultra-High Field Orbitrap Analyzer
MCP (2014)
Richard Alexander Scheltema,  Jan-Peter Hauschild, Oliver Lange, Daniel Hornburg, Eduard Denisov, Eugen Damoc, Andreas Kuehn, Alexander Makarov and Matthias Mann   more
Ultradeep Human Phosphoproteome Reveals a Distinct Regulatory Nature of Tyr and Ser/Thr-Based Signaling
Cell Reports (2014)

Kirti Sharma, Rochelle C.J. D’Souza, Stefka Tyanova, Christoph Schaab, Jacek R. Wisniewski, Juergen Cox and Matthias Mann

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