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.

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Contacts

Staff

Faculty Scientific Advisers

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)

Location

Campus Address

Pharmacy/Biology Building, Rooms 511/513

Mailing Address

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

Instrumentation

Sample Preparation

Internal Rates

Reagant cost	Non-trypsin endoproteinases	UConn price plus 7% up-charge
$165/sample	FASP	Includes reduction, alkylation, tryptic digestion, peptide clean up
$65/sample + reagent cost	In-vitro labeling
$65/hour + reagent costs	PTM enrichment
$84/sample	Offline fractation
$24/sample	Intact protein sample clean-up
$68/hour + reagent cost	Custom sample prep
$65/band	Coomassie blue stained gel band	Includes destaining, reduction, alkylation, tryptic digestion, peptide extraction and clean up
$65/band	TrainingSilver-stained gel band	Includes destaining, reduction, alkylation, tryptic digestion, peptide extraction and clean up
$65/sample	In-solution tryptic digestion (<25 ug)	Includes reduction, alkylation, tryptic digestion and peptide clean up
$85/sample	In-solution tryptic digestion (>25 ug)	Includes reduction, alkylation, tryptic digestion and peptide clean up

External Rates

Reagant cost	Non-trypsin endoproteinases	UConn price plus 7% up-charge
$222.75/sample	FASP	External Academic includes reduction, alkylation, tryptic digestion, peptide clean-up
$330/sample	FASP	Industry includes reduction, alkylation, tryptic digestion, peptide clean-up
$87.75/sample + reagent cost	In-vitro labeling	External Academic
$130/sample + reagent cost	In-vitro labeling	Industry
$87.75/hour + reagent cost	PTM enrichment	External Academic
$130/hour + reagent cost	PTM enrichment	Industry
$113.40/sample	Offline fractionation	External Academic
$168/sample	Offline fractionation	Industry
$32.40/sample	Intact protein sample Clean up	External Academic
$48/sample	Intact protein sample clean-up	Industry
$108.80/hour + reagent cost	Custom sample prep	External Academic
$136/hour + reagent cost	Custom sample prep	Industry
$87.75/band	Coomassie blue-stained gelband	External Academic, Includes destaining, reduction, alkylation, tryptic digestion, peptide extraction and clean-up.
$130/band	Coomassie blue-stained gelband	Industry, Includes destaining, reduction, alkylation, tryptic digestion, peptide extraction and clean-up.
$87.75/band	Silver-stained gelband	External Academic, Includes destaining, reduction, alkylation, tryptic digestion, peptide extraction and clean-up.
$130/band	Silver-stained gelband	Industry, Includes destaining, reduction, alkylation, tryptic digestion, peptide extraction and clean-up.
$87.75/sample	In-solution tryptic digestion (<25 ug)	External Academic Includes reduction, alkylation, tryptic digestion, peptide clean-up
$130/sample	In-solution tryptic digestion (<25 ug)	Industry Includes reduction, alkylation, tryptic digestion, peptide clean-up.
$107.75/sample	In-solution tryptic digestion (>25 ug)	External Academic Includes reduction, alkylation, tryptic digestion, peptide clean-up.
$150/sample	In-solution tryptic digestion (>25 ug)	Industry Includes reduction, alkylation, tryptic digestion, peptide clean-up.

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

Internal Rates

External Rates

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)

Internal Rates

External Rates

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

Internal Rates

External Rates

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)

Internal Rates

External Rates

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)

$66/hour	Analysis
$34.50/sample	Intact protein mass measurement
$68/hour	Manual data analysis (e.g PTM localization, custom quantitation

$89/hour	Analysis	External Academic
$138.50/hour	Analysis	Industry
$46.58/sample	Intact protein mass measurement	External Academic
$69/sample	Intact protein mass measurement	Industry
$108.80/hour	Manual data analysis(e.g. PTM localization, custom quantitation)	External Academic
$136/hour	Manual data analysis(e.g. PTM localization, custom quantitation)	Industry

$68/hour	Training Fee
$64/hour	Assisted Analysis	Unassisted run time following training by facility faculty
$44/hour	User-operation

$108.80/hour	Training Fee	External Academic
$136/hour	Training Fee	Industry
$86.50/hour	Assisted Analysis	External Academic
$141/hour	Assisted Analysis	Industry
$62/hour	User-operation	External Academic
$92.50/hour	User-operation	Industry

$116.50/hour	Analysis	External Academic
$172/hour	Analysis	Industry

Proteomics & Metabolomics

Proteomics & Metabolomics

Contacts

Staff

Jeremy Balsbaugh, Ph.D.

Facility Director

Jen Liddle, Ph.D.

Facility Scientist

Sonam Tamrakar, Ph.D.

Research Assistant III

Faculty Scientific Advisers

Spencer Nyholm, Ph.D.

Associate Professor

Daniel Schwartz, Ph.D.

Associate Professor

Xudong Yao, Ph.D.

Associate Professor

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

Professor

Location

Campus Address

Mailing Address

Instrumentation

Sample Preparation

Thermo Scientific Q Exactive HF Mass Spectrometer

Waters Synapt G2-Si Mass Spectrometer

Thermo Scientific Orbitrap Eclipse Tribrid Mass Spectrometer

Waters Xevo G2-XS q-TOF Mass Spectrometer - with SONAR

Available Software

$68/hour	Training Fees
$51/hour	Assisted Analysis
$35/hour	User-operation