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)