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Tissue Imaging and Proteomics Laboratory Instruments

Thermo Orbitrap Fusion Tribrid Mass Spectrometer

Thermo Fusion_8

Our Thermo Orbitrap Fusion is the mainstay proteomics instrument in TIPL. With mass resolving power of up to 450,000 FWHM (full width at half maximum), it has the resolution to unambiguously identify peptides and their post-translational modifications (PTMs) with high mass accuracy (typically well below 0.3 ppm mass error), thereby supporting deep proteomic analyses.

This instrument routinely quantifies hundreds of proteins in less complex samples, such as animal liver, muscle or heart tissues, and thousands (between 2000 and 4000) of proteins per sample in more complex samples such as animal brain or plant tissues (yes, plant tissues are much more complex at the protein level than most animal tissues!).

When combined with an approach such as GeLC-MS/MS or mudPIT, complete, deep and broad coverage of the proteome of an organism is possible in just a few runs using the Orbitrap Fusion in TIPL.

And, yes, it is quite capable of routine protein identification experiments (such as “what is this band in my gel?”).

Because it is a very fast scanning instrument, it is suitable for high resolution label-free quantitative proteomics experiments. It is also quite capable of performing quantitative proteomic experiments that utilize stable isotopically labeled tags, such as ICAT, TMT, iTRAQ, MeCAT, SILAC and TAILS (see Wikipedia site on Quantitative Proteomics for discussions of those techniques). All of those techniques actually determine relative quantitative values across samples.

The Orbitrap Fusion is also quite suitable for use in absolute quantification of proteins (AQUA), which utilizes specially designed heavy isotope-labeled peptides and an MRM (multiple reaction monitoring) or SRM (selected reaction monitoring) MS method.

Because of (well known) issues associated with switching between proteomics and metabolomics experiments (requiring a bit of downtime between experiments to condition the instrument for the next experiment type), we typically do not switch often from proteomics to the other analysis types with the Orbitrap Fusion, although we occasionally do.

For most routine targeted or non-targeted metabolomics and lipidomics experiments we recommend use of our companion lab at WSU, the LCME Analytics Lab, part of the Murdock Metabolomics Laboratory. Dr. Gang oversees that lab as well and he can discuss with you the features and benefits of the instruments in either lab.

Talk to us if you are interested in learning more about any of these approaches and how they might be useful in your research.

Features of the Thermo Orbitrap Fusion that make it ideal for proteomics, lipidomics and metabolomics

  • Parallelization of MS and MSn acquisition to maximize the amount of high-quality data acquired.
    • This instrument has not only an orbitrap ICR cell, but also a linear ion trap and a quadrupole pre-filter. The C cell in the instrument enables swapping of ions back and forth between the orbitrap and the linear ion trap, thus enabling novel characterization methods, and generation of high mass accuracy and broad coverage data for all types of analyses, from proteomic to lipidomic to untargeted metabolomic.
  • Multiple fragmentation techniques – CID, HCD, and ETD – are available.
    • This means that we can readily apply¬†the right fragmentation approach for the target molecule.
  • Next generation ion sources and ion optics increase system ease of operation and robustness.
    • This instrument is a breeze to keep clean.
    • Routine maintenance is required less frequently than many other instruments.
    • That all means that we get better data, cleaner data, with higher sensitivity and less down time.
  • For proteomics experiments, we typically use the Easy nLC system, a nano-LC system that works well for standard proteomics runs.
  • For complex proteomics experiments, we have an Acquity 2D-nano-UPLC. That LC system is also useful for complex lipidomic analyses.