Proteomics

The Proteomics and Membrane mass spectrometry group comprises a shared lab by the Max Planck Institutes for Brain Research and Biophysics. Here we provide customized tools, develop mass spectrometry-based methods for and work on specific research projects. By combining the resources of both MPIs, we are able to provide a wide range of MS methods including analyses of specific membrane components and full length proteins, PTM and functional studies, targeted analyses of enriched sub-proteomes, and qualitative and quantitative assays of whole cell or tissue lysates (Biophysics-related methods on this page).

Our instrumentation includes analytical (Dionex U3000) and nano UPLCs (Dionex U3000, Bruker nanoAdvance and Proxeon easy-nLC-1200), spotting robots (Bruker Proteineer fc), chip-based (Advion Triversa NanoMate) nano ESI-sources and the following mass spectrometers:

Thermo FusionLumos, Q Exactive Plus, Orbitrap Elite

Bruker Rapiflex TOF/TOF prototype, Impact-II, maXis and Autoflex III Smartbeam

Waters Synapt G2-Si HDMS ETD with HDX-2 Automation

We also collaborate with Bruker, Thermo and Waters for method and instrument development, and engage in multiple national and international collaborations with academia and industry.

Recent research highlights:

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 also 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.


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

Direct sequencing to identify novel subunits of membrane protein complexes.
Membrane proteins represent challenging targets for bottom-up proteomics. In particular small proteins lack proteolytic cleavage sites or don’t 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 that could not be identified previously (Kohlstädt et al., mBio, 2015; Safarian et al., Science, 2016; Bausewein et al., Cell, 2017, Murphy and Klusch, Science, 2019; Hahn and Safarian, Science, 2019).

Head of the Proteomics Lab:
Dr. Julian D. Langer Pubmed
T: +49 69 850033 2500 (office)
T: +49 69 850033 2501 (lab)

Interactive

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