Proteomics

Instrumentation

The Molecular Medicine: Proteomics Core Facility is equipped with a Thermo Scientific Q Exactive HF-X Hybrid Quadrupole-Orbitrap Mass Spectrometer with a Nanospray Flex Series ion source that is coupled to a Thermo Easy-nLC 1200 (LC-MS/MS). Proteomic data analysis is performed by SEQUEST and MS Amanda search engines from the Proteome Discoverer software.

Q Exactive HF-X Hybrid Quadrupole-Orbitrap Mass Spectrometer

Q Exactive HF-X Hybrid Quadrupole-Orbitrap Mass Spectrometer

Features of HF-X

  • Combines HRAM (high-resolution, accurate-mass) ultra-high-field Orbitrap mass analyzer, a high capacity transfer tube with electrodynamic ion funnel and a high-performance quadrupole precursor ion selection to help deliver unsurpassed speed and sensitivity.
  • Resolution up to 240,000 (FWHM) at m/z 200
  • Mass Range from 50 to 6,000 m/z
  • Scan Rates up to 40 Hz at resolution setting of 7,500 at m/z 200
  • Better than 1 ppm mass accuracy
  • Scan Modes available:
    • Full MS scan, Selected Ion Monitoring (SIM),
    • Parallel Reaction Monitoring (PRM),
    • Data-Independent Acquisition (DIA),
    • All Ion Fragmentation (AIF),
    • in-source fragmentation,
    • rapid polarity switching
  • Improved Efficiency using the Advanced Peak Determination (APD) Algorithm
  • Femtogram-level sensitivity

Benefits of HF-X

  • New innovative instrument control features empower unrivaled data-dependent performance. The new Advanced Peak Determination (APD)­ algorithm is used to generate high quality MS/MS spectra from low signal-to-noise signals. APD helps provide extreme sensitivity and resolution by identifying the charge states and monoisotopic m/z values of isotopic envelopes at significantly improved peak depth.
  • Optimized aHCD (Accelerated Higher-Energy Collisional Dissociation) maximizes ion accumulation time within a shorter transient time to produce the highest MS2 spectral quality.
  • The enhanced HCTT and EDIF front-end design architecture as well as the new aHCD, scan rates, making proteomics discovery faster with deeper sequencing.
  • The Q Exactive HF-X MS can identify the same amount of proteins as older Q Exactive Mass Spec in half the time. Using the same gradient, the HF-X is able to identify ~40% more peptides than the Q Exactive HF MS and ~95% more than the Q Exactive MS.