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 (rtownsend@wustl.edu),

Dr. Qiang (Tim) Zhang, (zhang.qiang@wustl.edu),

Dr. Robert Sprung, (robert.sprung@wustl.edu).

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

Priority service for No distinctions.

Additional information:

Contact the Core Lab Manager, Petra Erdmann-Gilmore at pegilmore@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 CPTAC 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 Dr. Robert Sprung at robert.sprung@wustl.edu 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