Quantitative Proteomics

Mass spectrometry is a powerful tool that can be used to study thousands of proteins in an unbiased and systematic manner in a single experiment. This allows us to answer biological questions at unprecedented speeds and with increased comprehension. Our laboratory focuses on quantitative approaches, such as the metabolic labelling of cells and organisms with stable isotopes, chemical labelling strategies and quantitation based on peptide intensities by computational algorithms.

We apply these techniques to answer questions of fundamental importance in transcriptional and translational gene regulation, epigenomics, genome stability and evolution. Currently, we apply our techniques in different model organisms to uncover previously uncharacterised telomere-binding proteins. Additionally, we pioneered the application of quantitative proteomics to map RNA-protein interactions.

Research website

Positions held

  • Since 2013: Group Leader, Institute of Molecular Biology (IMB), Mainz
  • 2010 - 2013: Postdoctoral Researcher, Max Planck Institute for Biochemistry, Martinsried


  • 2010: PhD in Biochemistry, Ludwig Maximilian University, Munich
  • 2006: Diploma in Biochemistry, University of Leipzig

Selected publications by Falk Butter

Pérez-Martínez L, Öztürk M, Butter F# and Luke B# (2020) Npl3 stabilizes R-loops at telomeres to prevent accelerated replicative senescenceEMBO Rep, doi: 10.15252/embr.201949087 (#indicates joint correspondance) Link

Bluhm A, Viceconte N, Li F, Rane G, Ritz S, Wang S, Levin M, Shi Y, Kappei D and Butter F (2019) ZBTB10 binds the telomeric variant repeat TTGGGG and interacts with TRF2Nucleic Acids Res, 47:1896–1907 Link

Goos C, Dejung M, Wehman AM, M-Natus E, Schmidt J, Sunter J, Engstler M, Butter F# and Kramer S# (2019) Trypanosomes can initiate nuclear export co-transcriptionallyNucleic Acids Res, 47:266–282 (#indicates joint correspondence) Link

Becker K, Bluhm A*, Casas-Vila N*, Dinges N*, Dejung M, Sayols S, Kreutz C, Roignant J-Y, Butter F# and Legewie S# (2018) Quantifying post-transcriptional regulation in the development of Drosophila melanogasterNat Commun, 9:4970 (*indicates joint contribution, #indicates joint correspondence) Link

Harris CJ*, Scheibe M*, Wongpalee SP, Liu W, Cornett EM, Vaughan RM, Li X, Chen W, Xue Y, Zhong Z, Yen L, Barshop WD, Rayatpisheh S, Gallego-Bartolome J, Groth M, Wang Z, Wohlschlegel JA, Du J, Rothbart SB, Butter F# and Jacobsen SE# (2018) A DNA methylation reader complex that enhances gene transcriptionScience, 362:1182–1186 (*indicates joint contribution, #indicates joint correspondence) Link