Own Research Interests:  

Mitochondrial proteomics/metabolomics

Quantitative mass spectrometry techniques are heavily used in my group, most of my research utilities is state-of-the-art infrastructure and located within the Max Planck Institute.

Mitochondria are organelles found in almost all eukaryotic cells. Important pathways are located within mitochondria, like oxidative phosphorylation, TCA cycle, fatty acid metabolism. Furthermore, they play a critical role in heat production, storage of calcium ions, apoptosis… . Many pathologies, including cancer, diabetes and aging have been reported to be associated with mitochondrial dysfunction.

Human mitochondrial dysfunctions will be investigated by a combination of proteomic and metabolomic tools. The aim is to gain quantitative information on the regulatory network and interplay of proteins and metabolites in mitochondrial disorders. Cells, featuring known mitochondrial dysfunctions will be analyzed by high resolution mass spectrometers with a special focus on post translational modifications. The identification of differentially expressed mitochondrial proteins in pathologies will help to further understand these diseases.

Mitochondrial proteomics can contribute deciphering molecular mechanisms and provides important information for discovering therapeutic targets for mitochondria-related diseases.

Mass spectrometry service:

If you want to analyze proteins, peptides or metabolites, please contact me in order to discuss details.

Phone: 1567; room T4/0.206

The following instruments are available for MS analysis:

QTrap from AB/Sciex:

This instrument is set up to detect known peptides or metabolites. For each peptide or metabolite, an individual method has to be established on the instrument. It is the most sensitive (low atto mol range) mass spectrometer in house, but you really need to know the exact mass you are looking for, otherwise you will not detect anything.

MALDI Ultraflex II / Bruker:

This instrument can be used for fast identification of simple protein/peptide mixtures and oligonucleotides.

Orbitrap XL from Thermo Fisher:

This instrument can be used in cooperation with Sascha Sauer. It is set up to quantitatively analyze peptides proteome wide. In contrast to the QTrap, you don’t need to know your proteins and PTM´s.

We developed a bunch of pipelines in order to decipher entire proteomes and post translational modifications, as well as single proteins, e.g. bands from SDS page gels.

We are able to detect more than 7000 proteins in a mammalian proteome and working on getting even more. As phosphorylations are of main interest, we can now detect more than 10.000 individual phosphorylation sites per proteome with our new enrichment method.

For relative quantification, we are using SILAC (stable isotope labeling by amino acids in cell culture) and dimethyl labeling routinely.

For data analysis, we have a Mascot server (search engine that uses mass spectrometry peptide data to identify proteins from primary sequence databases), which is accessible under http://mascot-srv/mascot/cgi/search_form.pl?FORMVER=2&SEARCH=MIS

For more complex and larger mass spectrometry files, we have a powerful Dell server with MaxQuant tools installed (a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets), to analyze the data for you.

As MS instruments are very sensitive and expensive, they don’t like to get any dirt inside. Some chemicals, like detergents, salts….. quench the ionization process or harm (oxidize) the instrument. If you have samples, you should ask first, how to prepare them. We can assist in sample preparation or do it for you, depending on availability of our MS technician and complexity of the samples.

Small and easy samples can be processed as a service, more complex and time intensive samples can be done in cooperation.

Your mass spec team

David

Contact:

David Meierhofer, PhD

Mass Spectrometry Facility
Max Planck Institute for Molecular Genetics
Ihnestrasse 63-73
14195 Berlin
GERMANY

email:        meierhof@molgen.mpg.de
Phone office: ++49-30-8413-1567
Phone lab:     ++49-30-8413-1568
Fax:               ++49-30-8413-1365

http://www.molgen.mpg.de/~mass_spectrometry/