Proteomics & Metabolomics

Proteomics & Metabolomics

The Proteomics & Metabolomics Facility implements ultra-high performance liquid chromatography (UPLC) coupled to high resolution mass spectrometry (MS) to unambiguously identify proteins, peptides and small molecules in complex mixtures.

Contacts

Staff

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Jeremy Balsbaugh, Ph.D.

Facility Director
Office: Pharmacy/Biology Building Room 531
Lab: Pharmacy/Biology Building Rooms 511/513
jeremy.balsbaugh@uconn.edu
860.486.3319
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Jen Liddle, Ph.D.

Facility Scientist
Office: Pharmacy/Biology Building Room 513
Lab: Pharmacy/Biology Building Rooms 511/513
jennifer.liddle@uconn.edu
860.486.1591
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Sonam Tamrakar, Ph.D.

Research Assistant III
Office: Pharmacy/Biology Building Room 511
Lab: Pharmacy/Biology Building Rooms 511/513
sonam.tamrakar@uconn.edu

Faculty Scientific Advisers

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Spencer Nyholm, Ph.D.

Associate Professor
Biology Physics Building 405
spencer.nyholm@uconn.edu
860.486.4886
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Daniel Schwartz, Ph.D.

Associate Professor
Pharmacy Biology Rm 217/219
daniel.schwartz@uconn.edu
860.486.0596
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Xudong Yao, Ph.D.

Associate Professor
Chemistry A-419
x.yao@uconn.edu
860.486.6644
I-Ping Chen DDS, Ph.D. is an associate professor at the UConn School of Dental Medicine and an endodontist at UConn Health. September 25, 2019 (Tina Encarnacion/UConn Health photo)

I-Ping Chen, D.D.S., Ph.D.

Professor
Oral Health and Diagnostic Science
UConn Health
860.679.1030

Location

Campus Address

Pharmacy/Biology Building, Rooms 511/513

Mailing Address

75 North Eagleville Road, Unit 3149
TLS Room 175
Storrs, CT 06269

Instrumentation

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Sample Preparation

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Thermo Scientific Q Exactive HF Mass Spectrometer

  • Provides high resolution, accurate mass determinations for MS and MS/MS analysis of proteins and peptides in complex mixtures using High-Field (HF) Orbitrap technology
  • Capable of multiple mass spectral acquisition options including data-dependent acquisition (DDA), data-independent acquisition (DIA), and parallel-reaction monitoring (PRM) modes
  • Directly coupled to a Thermo Scientific Dionex Ultimate 3000 RSLCnano UPLC for high resolution reversed-phase liquid peptide/protein separations at variable flow regimes, including nanoflow rates for maximum sensitivity
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Waters Synapt G2-Si Mass Spectrometer

  • Provides high resolution, accurate mass measurements for MS and MS/MS analysis of small molecules in complex mixtures using q-TOF technology
  • Capable of multiple mass spectral acquisition options including DDA and DIA modes (MSe)
  • Ion mobility technology provides another dimension of separation based on collisional-cross section (analyte size and shape) when mass and retention time aren’t sufficient to separate chemically ambiguous analytes and/or isomers
  • Directly coupled to a Waters Acquity UPLC equipped with a PDA detector for high resolution liquid-phase separations at micro-flow rates (μL/min)
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Thermo Scientific Orbitrap Eclipse Tribrid Mass Spectrometer

  • Provides multiple mass analysis and detection modes for MS and MS/MS using an Orbitrap or dual-pressure linear ion trap
  • Features multiple types of gas-phase fragmentation including collision-induced dissociation (CID), higher energy C-trap dissociation (HCD), electron transfer dissociation (ETD) plus hybrid versions of these techniques: EThcD and ETciD
  • Equipped to perform Real-Time Search (RTS) and Synchronous Precursor Selection (SPS) MS3-based acquisition methods for multiplexed proteomics analyses that incorporate Thermo Scientific Tandem Mass Tags (TMT) reagents for peptide quantitation
  • Capable of multiple mass spectral acquisition options including data-dependent acquisition (DDA), data-independent acquisition (DIA), and parallel-reaction monitoring (PRM) modes
  • Directly coupled to a Thermo Scientific Dionex Ultimate 3000 RSLCnano UPLC for high resolution reversed-phase liquid peptide/protein separations at variable flow regimes, including nanoflow rates for maximum sensitivity
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Waters Xevo G2-XS q-TOF Mass Spectrometer - with SONAR

Provides high resolution, accurate mass measurements for MS and MS/MS analysis of small molecules in complex mixtures using q-TOF technology. Capable of multiple mass spectral acquisition options including DDA and DIA modes (MSe and SONAR)

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Available Software

  • Proteomics: MaxQuant (Ref), MaxQuant, Spectronaut v17, Proteome Discoverer v2.5 with XlinkX node (Thermo Scientific), Byonic (Protein Metrics, Inc.), Scaffold v5.0 (Proteome Software, Inc.)
  • Metabolomics: Metaboscape (Bruker), Progenesis QI (Nonlinear Dynamics)