Cancer Proteomics Core

The Cancer Proteomics Core (CPC) provides all HCC members access to comprehensive interdisciplinary, translational, and clinically-oriented facilities for high-sensitivity, high-resolution, and high-throughput proteomics and metabolomics services. The core has a particular emphasis on clinical sample analysis and in-depth scientific consultation for proteomics, metabolomics, lipidomics, and data analysis. The CPC also provides access to proteomic services for basic cancer research exploring signaling pathways and other aspects of cancer biology related to the goals of HCC. The CPC is the exclusive service provider in the Boston/Longwood Medical Area for the exciting and powerful new, state-of-the-art biomarker discovery platform, SOMAscan.

The Core allows investigators to use the most cost-effective, state-of-the-art proteomics strategies for extracting the most relevant information for each project. It provides assistance in study design, experimental execution, data analysis, and systems biology, while also serving as a forum for education, scientific interactions, and cross-fertilization in proteomics and metabolomics.

Publication Acknowledgement

If research supported by this core facility results in publication, please acknowledge this support by including the following in your publication(s):

We thank Harvard Cancer Consortium in Boston, MA, for the use of the Cancer Proteomics Core Facility, which provided ______________________________ service. Harvard Cancer Consortium is supported in part by a NCI Cancer Center Support Grant # NIH 5 P30 CA06516.

Proteomics Services

• High multiplex, high sensitivity aptamer-based SOMAscan-1310 protein biomarker discovery
• Protein sample preparation and digestion
• Protein and peptide profiling of bodily fluids and tissue or cell extracts
• Profiling by µLC/MS
• Multidimensional protein and peptide fractionation by µLC
• Protein identification by µLC/MS/MS
• Coomassie and silver-stained gel bands
• Identification of protein and peptide post-translational modifications
• Phosphorylation sites
• Protein modifications, such as acetylation, methylation, and ubiqitination
• By µLC/MS/MS
• Coomassie stain only, purified proteins
• Protein-protein interaction (PPI) determination using antibody and tagged based IP-MS
• Relative quantitation of proteins and peptides, including modified peptides, by µLC/MS/MS
• SILAC: Stable isotope labeling of amino acids in cell culture (a biosynthetic approach)
• GIST: Global internal standard technology, a post-digestion peptide level labeling technique
• ICAT: Isotope coded affinity tag-based protein profiling
• ITRAQ: Isobaric peptide tagging system that enables labeling all primary amines, regardless of peptide class
• Targeted proteomics
• Metabolomic profiling of cancer cells and tissues
• Lipidomic profiling of cancer cells and tissues
• Analytic procedures to explore the data sets for further hypothesis generation

Protein and Biomarker Discovery

• SOMAscan Protein and Biomarker Discovery Platform: SOMAscan (SomaLogic) is a high multiplex, high sensitivity aptamer-based immune-like protein and biomarker discovery platform that simultaneously quantifies 1,310 human proteins in all types of protein extracts from bodily fluids such as serum, plasma, urine, saliva, CSF, cyst fluid, and tissue, cells, lavage, animal models, exosomes, etc.  The assay needs very low amounts of starting material such as 65μl human plasma or serum. SOMAscan advantages are a median lower limit of detection of 40 fM (<1pg/ml), an exceptional dynamic range of >8 logs (femtomolar to micromolar), high reproducibility (~5% median CV), and throughput. SOMAscan’s depth of coverage offers unprecedented power for biomarker discovery with more multiplex capability, and a >10,000-fold greater dynamic range than other proteomic technologies
• Quantitative proteomics: Relative and absolute protein quantitation applying isotopic, isobaric, and label-free methods, such as iTRAQ, ICAT, SILAC, TMT, GIST, TIC ratio, and spectral counting
• Targeted proteomics: With the acquisition of the 5500 QTRAP instrument, the core offers a service for targeted quantitative proteomics involving multiple reaction monitoring (MRM)
• Metabolomics: A service for targeted metabolomics using selected reaction monitoring (SRM) triple quadruple MS technology, which has become very popular for investigating more than 250 polar metabolites in cancer using cell cultures, bodily fluids, and tumor tissues. The CPC is the first to provide these analyses at Harvard
• Sources for biomarker discovery: While originally focused on serum, the core has now optimized workflows for quantitative proteomics analysis of urine, saliva, tumor tissue, proximal tumor fluids such as cyst fluid, CSF, and isolated subfractions of cells, such as mitochondria
• Data analysis: New services for bioinformatics and systems biology analysis of proteomic data, including pathway analysis tools (Ingenuity, GeneGo) and quantitative proteomics analysis tools (Protein Pilot 4.0)
• The core now offers automated Western analysis service using the ProteinSimple Peggy instrument. The core offers this new automated process (Simple WesternTM) using a novel capillary electrophoresis (CE) based immunodetection platform for protein separation and characterization. Proteins can be separated by size as in traditional PAGE Western or by their pI as in traditional CE. This high throughput system is able to multiplex and normalize to standard proteins and is highly reproducible
• ELISA analysis for high throughput validation of individual biomarkers

Bioinformatics Analyses

• Personalized consulting
• Customized data analysis and interpretation
• Web-based bioinformatics tools
• Comprehensive and innovative bioinformatics and visualization tools
• Comprehensive annotation tools
• Identification of global relationships
• Incorporation of biological knowledge
• Pathway analysis

Please contact the Core Director's for additional services.

In the last 5 years, Cancer Proteomics has collaborated with >170 researchers resulting in more than 150 co-authored manuscripts many which include HCC members​

• Projects range from proteomics, lipidomics, to metabolomics studies​
• HCC collaborators always take priority over other users​