instrumentation

The Mass Spectrometry laboratory is equipped with four mass spectrometers:

Bruker Esquire 3000 Plus

This combination of a capillary HPLC with an electrospray ionization ion trap mass spectrometer is mainly used to identify proteins after enzymatic digestion. The mass spectrometer measures the intact molecule mass of peptides eluting from the capillary HPLC column and also generates fragmentation spectra for these peptides. The combined dataset is searched against a database to determine the protein identity. This instrument combination can be used to identify numerous proteins in a mixture.

Thermo LTQ-Orbitrap XL

The latest addition to the mass spectrometry core facility consists of a linear ion trap and an electrostatic Fourier transform analyzer. The instrument affords high sensitivity, in the low femtomole range for peptides, and mass accuracies in the single ppm range. Protein samples from SDS gels are separated by nano reversed-phase HPLC after enzyme digestion and introduced by electrospray ionization. Alternatively, multi-dimensional nano-LC, i.e. ion-exchange followed by reversed-phase separation, is performed in bi-phasic nano columns. Samples are again introduced by electrospray ionization and analyzed by tandem or higher order MS.

AB Perseptive DE-STR MALDI-TOF-MS

This instrument is capable of analyzing both peptides and proteins. For peptides, the intact mass can be determined in the sub-picomole range. Proteins can either be analyzed directly (mass range up to 100 kDa) or after enzymatic digestion to obtain a mass "fingerprint". Searching these data against a database allows identification of proteins.

Bruker Ultraflex TOF/TOF

This instrument is capable of determining the intact molecule mass of peptides as well as to generate fragmentation spectra. Besides its ability to perform mass "fingerprinting" this mass spectrometer has several advantages in the detection and localization of post-translational modifications.