CCSG Proteomics & Metabolomics Facility

Overview

The PROTEOMICS AND METABOLOMICS SHARED RESOURCE provides high-sensitivity proteomics, metabolomics, and lipidomics analyses using state-of-the-art mass spectrometry instrumentation and analytical methods.

Consultation with facility staff prior to sample preparation is strongly recommended to ensure optimal experimental design, appropriate methodology selection, and overall experimental success. Our experienced team provides end-to-end support, from experimental planning and sample preparation guidance to data analysis and interpretation. Facility contact information is available at the bottom of this page.

Proteomics services include:

Quantitative, in-depth global comparisons of proteomes from cells, secretomes, tissues, or biological fluids using label-free quantitation (LFQ) based on integrated ion current, SILAC labeling, or TMT isobaric mass tags
Global quantitative comparisons of post-translational modifications including ubiquitination, acetylation, phosphorylation, and glycosylation
Detailed characterization of individual purified proteins including identification of post-translational modifications, and protein truncation sites
Identification of components in protein complexes and interacting proteins (e.g. co-immunoprecipitations, affinity purifications of tagged proteins, proximity labeling, RIME)
Cross-linking MS using MS-cleavable crosslinkers for structural analysis of protein complexes
Characterization of intact protein and peptide masses

Sample preparation including protein extraction, SDS-PAGE with staining, BCA assay to determine protein concentration, C18 peptide desalting, high-pH peptide fractionation, and in-gel or in-solution protease digestion
Targeted quantitation of selected proteins using PRM-MS
Data analysis support and custom data interpretation for experiments performed at the Wistar Proteomics Shared Resource

Metabolomics services include:

Untargeted metabolomics for global profiling and relative quantification of polar metabolites
Untargeted lipidomics for global profiling and relative quantification of lipids
Stable isotope (13C, 15N, or 2H) tracing to interrogate metabolic pathway activity
Targeted metabolomics for measuring relative or absolute levels of analyte panels
- Bile acids
- Gut microbial metabolites
- D- and L-2-hydroxyglutaric acid
- Free and total fatty acids
- Glycolysis and TCA cycle intermediates
- Nucleotides
- Amino acids
- Short-chain fatty acids
Validation of specific analytes (e.g., chemical synthesis products) by accurate mass (<5 ppm)
Measurement of drug concentrations for PK-PD studies
Development of custom LC-MS assays for relative or absolute quantification of specific small molecules
Sample preparation including tissue homogenization, organic extraction for small molecules, saponification for total fatty acid and sphingolipid analysis, chemical derivatization for specialized applications, BCA assay to determine protein concentration for sample normalization
Data analysis support and custom data interpretation for experiments performed at the Wistar Metabolomics Shared Resource

Equipment & Features

Thermo Orbitrap Astral mass spectrometer with Vanquish Neo UHPLC system
Thermo Orbitrap Eclipse Tribrid mass spectrometer with Ultimate 3000 RSLCnano UHPLC
Thermo Q Exactive Plus mass spectrometer with Vanquish UHPLC system
Thermo Q Exactive HF-X mass spectrometer with Vanquish UHPLC system
Agilent Seahorse XFe96 Analyzer for real-time cell metabolic analysis
Multiple PC servers and comprehensive software for proteomic, metabolomic, and lipidomic data analysis
Retch CryoMill for cryogenic tissue homogenization
Organomation N-EVAP 34-position nitrogen evaporator for metabolomics sample preparation

Pricing and Submission Forms

For pricing information, visit iLab or contact the facility.

Through inter-institutional agreements, members of the Fox Chase Cancer Center at Temple University and the Sidney Kimmel Cancer Center at Thomas Jefferson University have access to the Wistar Proteomics & Metabolomics Shared Resource at the same rates as Wistar Cancer Center members.

Download the submission form for proteomics.
Download the submission form for metabolomics.

Sample Acknowledgement Statement:

“We are grateful to The Wistar Institute’s Proteomics & Metabolomics Shared Resource for providing technical support. Funding support for The Wistar Institute core facilities was provided by Cancer Center Support Grant P30 CA010815.”

Sample S10 Instrumentation Acknowledgement (for applicable projects):

“This work was supported by National Institutes of Health instrument award S10 OD023586 for the acquisition of the Thermo Q Exactive HF-X mass spectrometer.”

Wistar Proteomics & Metabolomics Facility Presentation

See recording of facility presentation.

The Wistar Institute
Proteomics and Metabolomics Facility
Rooms 252 and 264
3601 Spruce St
Philadelphia, PA 19104
proteomics@wistar.org, (215) 898-3830
metabolomics@wistar.org, (215) 898-2384

Directors and Staff

Hsin-Yao Tang, Ph.D.
Co-Scientific Director

Aaron R. Goldman, Ph.D.
Co-Scientific Director

Wujuan Zhang, Ph.D.
Managing Director of Metabolomics

Anneliese Faustino, Ph.D.
Associate Managing Director of Proteomics

Thomas Beer and Nicole Gorman
Wistar Research Assistants

Facility Hours

Monday-Friday
9:00 am – 5:00 pm