Proteomics Shared Resource

The Proteomics Shared Resource (PSR) provides services for discovery and targeted proteomics using tissues, cells, and biological fluids (e.g. plasma/serum, cerebrospinal fluid and urine). The PSR performs small (≤ 20 samples) and large-scale studies with ~100 clinical samples.  Validated proteomics workflow for label (tandem-mass-tag) and label-free quantification are offered. The PSR provides quantitative proteomics data analysis with “hands-on” assistance and customized software (Proteo-Q).

Whole tissue, cell, and sub-proteomes (e.g. kinome, exosome, and protein complex) analysis is performed using current technology and validated proteomic workflows.

Deep scale proteomics (10,000 to 13,000 genes), phosphorylation (>37,000 phosphosites), acetylation (~2000 sites), and ubiquitination  (~2000 sites) is achieved using validated methods (1,2).

Both label-free and isobaric peptide labeling methods are available for high-precision quantification of proteins and post-translational modifications.

Absolute quantification (copies/cell) is performed using synthetic signature peptides with stable isotope dilution mass spectrometry.

A Kinome (381 kinases) and a metabolic enzyme (67 enzymes) libraries are available with standard assays developed under CPTAC guidelines (https://proteomics.cancer.gov/assay-portal).

Experimental design (Statistics-based), data processing, analysis and interpretation are offered by the Director and Co-directors.

References

1 Mertins, P., Qiao, J.W., Patel, J., Udeshi, N.D., Clauser, K.R., Mani, D.R., Burgess, M.W., Gillette, M.A., Jaffe, J.D., and Carr, S.A. (2013). Integrated proteomic analysis of post-translational modifications by serial enrichment. Nat Methods 10, 634-637. 10.1038/nmeth.2518

2 Mertins, P., Tang, L.C., Krug, K., Clark, D.J., Gritsenko, M.A., Chen, L., Clauser, K.R., Clauss, T.R., Shah, P., Gillette, M.A., et al. (2018). Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography-mass spectrometry. Nat Protoc 13, 1632-1661. 10.1038/s41596-018-0006-9.

Dr. R. Reid Townsend (rtownnsend@wustl.edu, 314-283-2452),

Dr. Qiang (Tim) Zhang, (zhang.qiang@wustl.edu, 314-362-9134),

Dr. Robert Sprung, (robert.sprung@wustl.edu, 314-362-9134).

Service available to All entities, including for-profit organizations.

Priority service for No distinctions.

Additional information:

Contact the Core Lab Manager, Jim Malone at jmalone@wustl.edu to schedule an initial meeting or obtain additional information.

• Deep-scale and “single-shot” (~ 6000 proteins) quantitative proteomics
• Quantitative global post-translational modification analysis of phosphorylation, acetylation and ubiquination
• Protein-complex characterization using proximity-labeling and immuno-enrichment mass spectrometry
• High-throughput Multi-affinity chromatography (selective removal of high abundance proteins from biological fluids)
• Exosome enrichment using a reproducible affinity method for large-scale studies
• Quantitative, label-free and tandem mass tag-labeled proteomics
• Customized preparation for a wide range of sample types and protein compartments
• Data quality assessment, processing, analysis and assistance with interpretation
• Development of customized assays for high-precision absolute biomarker quantification using CPTC guidelines
• (contact lab manager for a complete list of services)

• Q-Exactive™ Orbitrap™ PLUS interfaced to an EASY-Spray™ nLC 1000 – (Thermo Scientific)
• Orbitrap™ Exploris 480 Quadrupole mass spectrometer interfaced to a Dionex Ultimate RSLnano LC – (Thermo Scientific)
• timsTOF Pro ion mobility mass spectrometer interfaced to a nanoElute LC system - (Bruker Daltronics)
• UltrafleXtreme™ MALDI-TOF/TOF System – (Bruker Daltronics)
• Biomek NXp Automated liquid handling robot - (Beckman Coulter)
• 1260 Infinity II Bio-Inert LC System – (Agilent Technologies)

Pricing is subject to core verification

Pricing Examples

Please contact Jim Malone for pricing of additional services, or quotation of costs associated with an experiment.

Research awards for up to $5,000 are available through the ICTS Just-in-time (JIT) core usage funding program (https://icts.wustl.edu/funding/just-in-time-jit/)

The staff of the PSR  are available to assist with the preparation of JIT proposals