Supportive Activities & Events

We continuously supported biological research at the EMBL and outside according to our capacity.
In 2001 we spent a considerable amount of time to establish the
proteomics visitor laboratory sponsored by Waters and Biorad.
Two spin-off companies are directly related to main projects of our group, Protana, which later split off
Proxeon, and CellZome.

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Functional Proteomics

One of the early important decisions in 1999 was to dedicate all available resources to the support of the “Tandem Affinity Purification” (TAP) method [1]. The TAP method had been developed in Bertrand Seraphin’s group. It was a tag based, gentle, specific and in-vivo protein complex purification method established in yeast cells (slide 2, 3). This technology could evolve together with mass spectrometry based protein identification into a key component of an organism wide functional proteomics projects - a systematic effort to place proteins into their functional cellular context (slide 4, 6) [2].
Later we demonstrated how the TAP method could be used with cells from higher eukaryotes, the iTAP project (slide 7, 8, 9) [3].

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Mass Spectrometric Methods Development

In 1998 Matthias Mann took up a professorship in Odense, Denmark and Matthias Wilm became group leader at the EMBL. Being an instrumentation group we continued to develop methods to improve protein characterization by mass spectrometry.

Method development:

  • Noise filtering technique to improve peptide detection

  • Data processing to improve automated peptide identification

  • Differential scanning to improve de-novo sequencing

  • Parallel fragmentation of peptides to improve specific detection of secondary modifications

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Learning How to Identify & Sequence Proteins by Mass Spectrometry

In 1992 a mass spectrometry group was established under the leadership of Matthias Mann. In the following years we explored how to sequence peptides and identify proteins using mass spectrometers in the most sensitive way. There were three important components to this
  • the nano-electrospray ion source (figure 1 - 4)

  • the sequence tag based protein identification algorithm (slide 5)

  • protocols for gel staining, in-gel digestion and sample preparation for the analysis with mass spectrometry

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