Proteomics Shared Resource


R. Reid Townsend, MD, PhD

The Siteman Cancer Center (SCC) Proteomics Shared Resource (PSR) provides access to advanced proteomic technologies and expertise to support SCC’s basic and translational research, as highlighted under “Contributions to Science.” PSR provides SCC members with access to “state-of-the-art” instrumentation and standardized protocols that have been optimized under the guidelines of the National Institutes of Health, National Cancer Institute (NCI) Clinical Proteomics Tumor Analysis Consortium (CPTAC). A full-time staff of technicians, doctoral level proteomic experts, and PSR leadership provide guidance on proteomic experimental design and feasibility to generate reproducible and repeatable data from small (> 20 samples) or large (> 100) scale studies. The PSR collaborates with The McDonnell Genome Institute (MGI) to integrate genomic and proteomic data for the discovery of new cancer biology. Over the last funding period, the PSR has expanded its capabilities as detailed in the “Response to the Prior Critique.” PSR has added new technologies and workflows in response to SCC research program goals and the proteomic needs of SCC members, as detailed under “Major services, technologies, equipment and expertise.” PSR’s overarching goals for the next project period are to continue providing the most advanced, highest quality proteomic data at depths that will reveal new cancer biology and to introduce new technology and validated protocols that will ultimately provide actionable proteogenomic information in clinical trials and practice.

The following Specific Aims will direct accomplishment of these overarching goals:

Aim 1: Continue to provide advanced proteomic platforms that support basic and translational research, as described in “Contributions to Science.” PSR will leverage the expertise acquired through CPTAC membership and the refined protocols for tumor procurement and processing for proteogenomic analysis to perform the first large-scale proteogenomic study of pre- and post-treatment tumors using the CPTAC inter-laboratory harmonized protocol for deep-scale proteomics and phosphoproteomics. The SCC Acute Myeloid Leukemia (AML) repository of ~300 cases of clinically-annotated and genomically-characterized specimens will be used for the first large scale proteogenomic study of AML. These data will be integrated with the genomic and outcome data in collaboration with the MGI.

Aim 2: Expand and improve our CPTAC assays for the absolute quantification (copies/cell) of kinases, metabolic enzymes and other cancer-related proteins and phosphorylation sites. These assays will be developed and validated using CPTAC guidelines, designed for progression to FDA approval and clinical utility. The PSR has developed assays for 361 kinases and hosts a library of high-purity stable isotope labeled and natural abundance proteotypic peptides (n = 760 labeled and unlabeled peptide pairs) for development of cancer-type specific, high multiplex assay panels. By 2023, we will have developed assays for all kinases in the human kinome. We will exploit new MS technology to increase sensitivity and assay multiplexing in a single LC-MS analysis as described under “New Shared Resource Services under Development.”

Aim 3: Develop and optimize methods for new services as driven by new technology and SCC member research requirements, as detailed under “New Shared Resource Services under Development.” We will work closely with PSR Faculty Advisor Ben Major, Director of the recently-established Washington University School of Medicine (WUSM) Mass Spectrometry Center, to access next generation instrumentation. We will focus on the following areas: i) development and optimization and scaling of protein-protein-protein interactions and proximity networks for the cancer proteome in collaboration with Major’s laboratory; ii) single cell proteomics using MS; iii) development of data acquisition and analysis algorithms for improved protein sequencing and proteomic depth; and iv) migration of automated analysis pipelines to a computer cluster for accelerated processing of large-scale datasets. Dennis Goldfarb will assist the PSR with analysis of large-scale data sets from our studies with computer clusters at the WUSM Mass Spectrometry Center. In parallel, we will expand and customize our computational tools for user-interactive proteogenomic analysis (Proteo-Q) with seamless integration into bioinformatics software (e.g. CompBio developed by the GTAC shared resource).

LOCATION: Southwest Tower, Room 721.

PRICING: Please contact the shared resource for current pricing of services offered.

TO ACCESS: Call 314-286-2452.

NIH PUBLIC ACCESS POLICY: As of April 7, 2008, the NIH requires investigators with a publication using Siteman (or other NIH-funded) shared resources to submit (or have submitted for them) their final, peer reviewed manuscripts to PubMed Central(PMC) upon acceptance of publication, to be made publicly available within 12 months of publication. Many journals automatically submit these for authors, but Washington University also has assistance available through the Becker Medical Library. Please see,upon%20acceptance%20of%20the%20publication for more information.

PUBLICATION ACKNOWLEDGEMENT: If research supported by the Proteomics Shared Resource results in publication, please acknowledge this support by including the following in your publication(s):

We thank the Alvin J. Siteman Cancer Center at Washington University School of Medicine and Barnes-Jewish Hospital in St. Louis, MO. and the Institute of Clinical and Translational Sciences (ICTS) at Washington University in St. Louis, for the use of the Proteomics Shared Resource, which provided __________ service. The Siteman Cancer Center is supported in part by an NCI Cancer Center Support Grant #P30 CA091842 and the ICTS is funded by the National Institutes of Health’s NCATS Clinical and Translational Science Award (CTSA) program grant #UL1 TR002345.