Protein & Peptide Identification

At the FGCZ, we identify proteins in complex mixtures usually by mass spectrometry, which is described here.

Purified proteins can also be identified by protein sequencing (see Support Modes > Protein Service > Protein/Peptide Sequence Analysis).

Mass-Spectrometry Based Identification

The the proteins in a sample are cleaved by a protease into peptides which are then measured by a mass spectrometer. From the peptide masses the protein identity is inferred by comparison to reference databases.

Typical biological samples contain a complex mixture of different proteins with very different concentrations and have to be fractionated before they can be analyzed by mass spectrometry. The analysis of complex samples is also referred to as shotgun proteomics.

As mass spectrometry technologies we run:

• ESI-MS: Electrospray ionisation Mass Spectrometry is typically preceded by reversed phase liquid chromatography (LC-ESI-MS). All peptides are then analysed by tandem mass spectrometry (MS/MS). Simple protein or peptide mixtures can be directly infused.
• MALDI-MS: Matrix-assisted laser desorption/ionization mass spectrometry is utilized for mass analyses of chemical compounds, for example peptides and proteins. Analytes are desorbed and ionized by the irradiation of laser light, which is absorbed by the MALDI matrix.

Details on our mass spectrometers.

Support Modes

Protein & peptide identification is available as Protein Service and as User Lab project.

Contacts

Rene Brunisholz - Protein Service
Peter Hunziker - Protein Service
Christian Trachsel - User Lab