Proteomics and Metabolomics Facility

Overview of Services

The Wistar Proteomics and Metabolomics Shared Resource provides high sensitivity proteomics and metabolomics analyses using state-of-the-art mass spectrometry (MS) instruments and methods. Consultation with facility staff concerning experimental design and sample preparation is recommended prior to sample preparation to ensure optimal experimental design.

Proteomics services include identifications of either purified proteins or complex protein mixtures, such as sub-proteomes, complete proteomes, secretomes, or formaldehyde fixed-paraffin embedded tissues, using liquid chromatography tandem mass spectrometry (LC-MS/MS).  Typically, either individual bands are excised from 1-D SDS gels, or the entire gel lane is analyzed by slicing it into uniform fractions followed by trypsin digestion and LC-MS/MS analysis.  While colloidal Coomassie stained gels are preferred, simple protein identifications can be obtained from barely detectable silver stained bands.  Protein samples can also be digested in-solution for LC-MS/MS analysis.  Data are searched against appropriate sequence databases to identify peptides and the corresponding proteins, and results are filtered to produce low false-positive rates.  Quantitative proteomics can be performed with label-free quantitation (LFQ), SILAC metabolic labeling, TMT stable isotope tagging, and multiple reaction monitoring (MRM) either in a label-free mode or with isotopically coded internal standards.  Complementary services include reverse-phase microbore HPLC peptide mapping, MALDI MS analysis of intact proteins and purified peptides, and ESI MS analysis of intact proteins.  Posttranslational modification (PTM) analyses including identifications of specific modified residues in purified proteins or global phosphoproteome or ubiquitome analyses.  Investigators should recognize that in most cases these studies are quite complex and require substantially larger amounts of sample than simple protein identifications.

Metabolomics services include analysis of polar metabolites or lipids extracted from cells, biological fluids, conditioned media, or tissues. Specific services include: 1) targeted relative quantitation of approximately 200 polar metabolites spanning 32 different classes; 2) 13C stable isotope tracer analysis; 3) untargeted polar metabolite quantitative comparisons, 4) untargeted lipidomics for quantitative profiling of global lipids or acylceramides (after mild saponification), and 5) targeted relative quantitation of free fatty acids, total fatty acids (after saponification), and eicosanoids, including prostaglandins and HETEs. Samples for all these applications are analyzed using the Thermo Q Exactive HF-X mass spectrometer. Metabolites are separated using HILIC chromatography, global lipids and acylceramides are separated on a C30 reversed-phase column, and fatty acids and eicosanoids are separated on a C18 column.

Leadership

David W. Speicher, Ph.D.

Scientific Director

Hsin-Yao Tang, Ph.D.

Managing Director

Staff

Aaron R. Goldman, Ph.D.

Associate Managing Director

215-898-0661

agoldman@wistar.org

Thomas Beer

Research Assistant

215-898-3830

beer@wistar.org

Nicole Gorman

Research Assistant

215-898-3830

ngorman@wistar.org

Hours of Operation and Location

Links and Resources

1. Wistar: Proteomics and Metabolomics Facility
   

Contacts