Proteomics Core

The Indiana University School of Medicine Proteomics Core is a mass spectrometry (MS)-centric protein analysis center with extensive expertise in affinity-purification mass spectrometry methods and quantitative proteomics. IUSM has recently purchased two state-of-the-art mass spectrometers, two ultra high-pressure liquid chromatography systems and a variety of ionization sources to facilitate innovative application of proteomics methods to basic and clinical research questions for all researchers at IUSM, particularly IU Simon Cancer Center members. Our central goal is to apply and develop state-of-the-art proteomics methods to measure system-wide changes in protein biology, as it relates to cancer biological questions. The Proteomics Core and cancer center leadership have developed the following specific aims to meet the critical needs of IUSCC members for proteomics services:

Specific Aim 1: To provide IU Simon Cancer Center users with state-of-the art proteomics services with a focus on global proteome and phosphoproteome profiling. The proteomics core has optimized methods to develop a standard global quantitative proteomics approach for cancer center core users which has been used by 10 IU Simon Cancer Center laboratories. Our standard method uses isobaric mass tagging to multiplex global proteome quantitation. When used for biological replicate analysis, this method has reproducibly quantified 5,000-8,000 proteins for core users. We have also applied these approaches to the phosphoproteome resulting in quantitation of many thousand phosphosites across up to 11 biological samples per experiment. These approaches can be applied to analysis of proteins in cancer cells, isolated tumors and other biosamples to measure changes in kinase pathways in response to various treatments or to establish baseline signaling profiles.

Specific Aim 2: To develop leading-edge proteomics services in chemoproteomics to facilitate drug discovery and drug characterization in IUSCC. With quantitative proteomics methods inching closer and closer to full proteome coverage, novel applications of global proteomics can facilitate biological assays with significant promise for analysis of small molecule or drug characterization including global target screening and activity analysis. The proteomics core, in cooperation with the Mosley lab, has developed a systematic service pipeline (from sample preparation to data analysis) for cellular thermal shift assays (CETSA) that is now available to all cancer center users. The CETSA approach has recently been performed as a service for Xiongbin Lu’s research group. CETSA coupled with global proteome analysis has been used to perform target engagement studies, off-target interactions, and changes in cellular signaling states.

Specific Aim 3: To expand affinity-purification MS analysis for identification of high-confidence interacting proteins. More than 60 percent of the recent proteomics core projects by cancer center members involve analysis of affinity-purification samples for either protein identification or post-translational modification analysis (Androphy, Balakrishnan, Clapp, Corson, Hollenhorst, Johnson, Xiongbin Lu, Mayo, Mosley, Nalepa, Pili, Xie, and Zhang). We have also performed amino acid site mapping of covalent small molecule modifications (Turchi and Meroueh). To increase the rigor of this type of experiment, the proteomics core provides educational training and one-on-one consultation with cancer center users to discuss quantitative approaches to identify significant interaction partners with isolated proteins of interest. The application of statistical methods to affinity-purification MS data is an area of expertise in the Mosley lab that have had recent publications in using these approaches to study dynamic protein-protein interactions as well as post-translational modifications.

Specific Aim 4: To develop, provide, and/or organize educational opportunities related to proteomics technologies, experimental design and data analysis. Since August 2016, the proteomics core has updated its instrumentation and many of the available approaches for core users. To facilitate IUSCC member research, we have and will continue to conduct workshop-style information sessions run by core staff and/or technical representatives from various companies to educate on the advances in current quantitative proteomics methods. Within this framework, we will highlight our core's existing strengths in: chromatographic separations, post-translational modification analysis, and quantitative protein-protein interaction analysis.

To learn more, visit the Proteomics Core.