Proteomics and Metabolomics Shared Resource

Overview of Facility and Services

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 the webpage.

Hours of Operation and Location

Services

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 and 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

Links and Resources

Wistar: Proteomics and Metabolomics Facility

Contacts