Proteomics Services at ISB

ISB’s Proteomics program houses mass spectrometers for self-service use and collaborative research.

The mission of our facility is to make our mass spectrometry instruments, expertise, and methods for proteome analysis available to faculty and staff of ISB and collaborating researchers both in Seattle and beyond. We offer self-service and collaborative research options.

Orbitrap Eclipse Mass Spectrometer

TheThermo Scientific™ Orbitrap Eclipse™ provides high mass accuracy resolution with fast scan rates (40Hz). Cutting-edge ion-funnel optics focus the ions through 2 separate traps, employing high pressure for better collision and low pressure for quicker ion detection. The Orbitrap Eclipse is capable of both Collision-Induced Dissociation (CID) and Higher-energy Collisional Dissociation (HCD) fragmentation modalities. HCD is often utilized to experimentally detect and analyze low mass ions such as the reporter ions used in TMT/ITRAQ experiments in high-resolution or to discover other peptide modifications.


The Orbitrap Eclipse can be operated by experienced users only. Your experience will be reviewed by ISB’s service application engineer.The self-service per day rate for using the Orbitrap Eclipse equipment is $1800.
Please contact us to set up a conversation about using the instrument.

Get a quote→

Collaborative Research

Collaborative research is also available. Depending on the complexity and scope of the project, we will determine the best strategy for moving forward.

Please contact us and we can start the discussion.

Applications supported by Orbitrap Eclipse:

  • Data-dependent acquisition (DDA), a.k.a “shotgun” proteomics
  • Data-Independent Acquisition (DIA) for unbiased quantitative proteomics
  • Parallel Reaction Monitoring (PRM) for targeted quantitative proteomics
  • Detection of post-translational modifications
  • Analysis of protein-protein complexes by cross-linking
  • Quantitative proteomics by stable isotope labeling or label-free approaches