Instrumentation and Services



The Proteomics Core Facility offers a range of techniques for the identification, characterization and quantification of proteins. These include the following techniques and approaches, often used in combination – please inquire for additional applications that may fit your needs.

  1. Protein identification
    • from gels or solutions.
    • from complex mixtures or tissues.
    • of co-immunoprecipitated complexes.
    • from proximity tagging experiments. 
    • serum/plasma, saliva, urine, cerebrospinal and amniotic fluid.
    • exosomes from biological fluids.
  2. Protein quantification
    • Targeted quantitation
    • Targeted for absolute quantification (internal standards)
    • Global – Unlabeled (LFQ, iBAQ)
    • Global – Labeled (SILAC, TMT)
  3. Structural studies
    • Chemical crosslinking and identification.

The Proteomics Core Facility is equipped with the instrumentation and expertise to perform detailed proteomic analysis. Major instrumentation in the facility include the following:



LTQ Orbitrap Velos Pro

LTQ Orbitrap Velos Pro with ETD source and an Eksigent 2D Ultra UPLC system

Hybrid linear ion trap-Orbitrap high resolution mass spectrometer. This instrument is used for proteomic applications, including protein identification and detailed peptide mapping.  Identification of proteins is performed on proteolytic digests by means of nanoflow LC-ESI-MS/MS with subsequent database searches using software packages such as Mascot and Protein Prospector.  This instrument is capable of electron transfer dissociation (ETD) which is useful for analysis of many post-translational modifications.  This instrument was funded by the National Institutes of Health-National Center for Research Resources (NCRR).



Q-Exactive HF with Easy nLC 1200 UPLC system

Q-Exactive HF with Easy nLC 1200 UPLC system

The Q Exactive HF system combines a state-of-the-art segmented quadrupole for high-performance precursor ion selection with a high-resolution, accurate-mass (HR/AM) ultra-high-field Orbitrap mass analyzer to deliver a superior combination of scan speed, resolving power, mass accuracy, spectral quality and sensitivity. Identify, quantify and confirm in a single analysis with a single instrument with the Q Exactive HF mass spectrometer.



Orbitrap Fusion Lumos with Easy nLC 1200 UPLC system

Orbitrap Fusion Lumos with Easy nLC 1200 UPLC system

Tribrid linear ion trap-quadrupole-Orbitrap mass spectrometer. The tribrid architecture, with an independent ion-routing multipole which enables parallelization, significantly increases scan rates, and maximizes versatility. Any of two dissociation techniques – CID and HCD - can be performed at any fragmentation stage, followed by analysis in either the linear ion trap or Orbitrap mass analyzer.



Bruker timsTOF Pro with Evosep one

Bruker timsTOF Pro with Evosep one

The instrument offers a unique separation technique, Trapped Ion Mobility Separation (TIMS), and a unique acquisition method, Parallel Accumulation Serial Fragmentation (PASEF). PASEF acquisition method provides extremely high speed and sensitivity to reach new depths in shotgun proteomics and phosphoproteomics, using low sample amounts.