Proteomics Core Facility

Proteomics Core Facility

Dr. Julian Langer

The “Proteomics and membrane mass spectrometry” lab is funded by the MPIs for Biophysics and Brain Research. We specialize in the development of workflows, methods and – in collaboration with instrument vendors – mass spectrometers to address specific questions in structural, molecular and neuro-biology. 

Our Methods

Direct
Direct, digest free sequencing of membrane protein complexes
Functional assays on membrane protein complexes
Hydrogen-Deuterium-eXchange mass spectrometry (HDX-MS)
Single-crystal mass spectrometry
Shotgun proteomics of complex biological samples
Targeted proteomics of sub-proteomes (newly-synthesized and cell-type specific)
Proteome turnover studies
Post-Translational modifications
MS Imaging
Neuroproteomics

We also engage in external collaborations and are currently a member of SPP 2002 (Small proteins in prokaryotes) by the DFG and the MOEL-SOEL-program by the BMBF.

Recent research highlights

Direct sequencing to identify novel subunits of membrane protein complexes.

Membrane protein complexes represent challenging targets for bottom-up proteomics. In particular small membrane-embedded subunits often lack proteolytic cleavage sites or do not ionize efficiently in ESI. Together with Bruker Daltonics, we’ve modified a rapifleX MALDI-TOF/TOF mass spectrometer that now allows acquisition of information-rich PSD MS/MS spectra up to m/z 9000. We’ve successfully used this technique to identify multiple new subunits in membrane protein complexes (Kohlstädt et al., mBio, 2015; Safarian et al., Science, 2016; Bausewein et al., Cell, 2017; Murphy et al., Science, 2019; Hahn and Safarian et al., Science, 2019).

HDX-MS of membrane protein complexes.

We successfully characterized ligand binding sites and activity-associated conformational dynamics in multiple membrane protein complexes, including a sodium:proton antiporter (Eisinger et al., PNAS, 2017), a MATE transporter (Eisinger et al., JMB, 2018) and a Molybdate-storage protein (Brünle et al., PNAS, 2019). We currently extend this technique to large membrane protein complexes.

Proteome profiling.

We successfully characterized the proteome remodeling in homeostatic synaptic plasticity in primary hippocampal neurons, making use of the BONCAT technology (Schanzenbächer et al., Neuron, 2016; Schanzenbächer et al., eLife, 2018). We also monitored proteome turnover in this system (Dörrbaum et al., eLife, 2018), and currently investigate its role in homeostatic scaling.

We established a workflow allowing analysis of cell-type specific proteomes from living animals, and investigated proteome dynamics in animals exposed to an enriched environment (Alvarez-Castelao et al., Nature Biotechnology, 2017). A detailed description of the method is available at Alvarez-Castelao et al., Nature Protocols, 2019. Recently, we’ve successfully investigated protein synthesis in neuronal processes (Biever and Glock et al., Science, 2020).

MS Imaging.

We successfully characterized the molecular components in Sepia chromatophores, that play a key role in their camouflage syste,. Using a combination of UPLC-UV-ESI-MS/MS, MS Imaging and direct infusion UHR-MS, we identified Xanthomatin in these chromatophores, a redox-switchable molecule that had previously been described to play a role in dragonfly maturation and coloration (Reiter et al., Nature, 2018).

Instruments

We operate eight instruments from Bruker, Thermo and Waters, including...

Orbitrap Fusion Lumos
Q Exactive Plus
Impact-II
rapifleX
Synapt G2-Si HDMS
Orbitrap Elite
maXis Autoflex
Autoflex III

The systems are coupled to nano-UPLCs (Thermo/Dionex Ultimate3000 and easy-1200; Bruker nanoElute) and analytical UPLCs (Thermo/Dionex Ultimate3000; Waters Acquity).


Recent Publications

1.
Biever A, Glock C, Tushev G, Ciirdaeva E, Dalmay T, Langer JD, Schuman EM.
Monosomes actively translate synaptic mRNAs in neuronal processes.
Science. 2020 Jan 31;367(6477). pii: eaay4991.
2.
Brünle S, Eisinger ML, Poppe J, Mills DJ, Langer JD, Vonck J, Ermler U.
Molybdate pumping into the molybdenum storage protein via an ATP-powered piercing mechanism.
Proc Natl Acad Sci U S A. 2019 Dec 6. pii: 201913031.
3.
Wang X, You X, Langer JD, Hou J, Rupprecht F, Vlatkovic I, Quedenau C, Tushev  G, Epstein I, Schaefke B, Sun W, Fang L, Li G, Hu Y, Schuman EM, Chen W.
Full-length transcriptome reconstruction reveals a large diversity of RNA and protein isoforms in rat hippocampus.
Nat Commun. 2019 Nov 1;10(1):5009.
4.
Safarian S, Hahn A, Mills DJ, Radloff M, Eisinger ML, Nikolaev A, Meier-Credo J, Melin F, Miyoshi H, Gennis RB, Sakamoto J, Langer JD, Hellwig P, Kühlbrandt W, Michel H. 
Active site rearrangement and structural divergence in prokaryotic respiratory oxidases.
Science. 2019 Oct 4;366(6461):100-104.

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