Instrumentation and Software
Mass spectrometers
MALDI: Ultraflex I (Bruker, Bremer)
ESI: Orbitrap Eclipse Tribrid Mass Spectrometer (Thermo Fisher Scientific, Waltham, USA) with Advion Triversa Nanomate spray system (Advion, San Diego, USA) and nano-LC system RSLC 3000 Ultimate (Thermo Fisher Scientific)
Single-Quadrupole Mass Spectrometer ZQ4000 (Waters, Milford, USA)
Fractionation
We offer HPLC methods for isolation of proteins, peptides and other biomolecules. The methods include gel permeation-, ion-exchange-, normal- and reverse-phase-chromatography.
For LC-MALDI coupling we have a nano-LC system which can be coupled with a fraction collector which allows direct spotting of complete LC-runs on a MALDI-TOF target to obtain a higher sequence coverage compared to total digest MS analysis.
Available instruments include:
IEF device
HPLCs
UHPLCs
ÄKta FPLC (GE Healthcare, Chicago, USA)
Other instruments
Edman sequencer
The amino acid sequence of proteins and peptides can be determined by Edman sequencing. If the N-terminus is not blocked, this is still the method of choice for identification of the N-terminus.
1D and 2D PAGE: Roboter systems for gel picking and in-gel digestion
Software
Mascot (Matrix Science, London, UK)
SequestHT (ThermoFisher, Waltham, USA)
Proteome Discoverer (Thermo Fisher, Waltham, USA)
MaxQuant (Max Planck Institute of Biochemistry, Martinsried, Germany)
Perseus (Max Planck Institute of Biochemistry, Martinsried, Germany)
COMET (University of Washington, Seattle, USA)
Skyline (University of Washington, Seattle, USA)
Crux (University of Washington, Seattle, USA)
SpectraST (Institute for Systems Biology, Seattle, USA)
PMI-Byonic (Protein Metrics Inc., Cupertino, USA)
PEAKS (Bioinformatics Solutions Inc., Waterloo, Canada)