Measuring cancer biomarker candidates by targeted ms and ab enrichment

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Project Title: Measuring cancer biomarker candidates by targeted ms and ab enrichment
Principal Investigators (PI): CARR STEVEN A
Project Number: 5U24CA126476-03
Organization: MASSACHUSETTS INSTITUTE OF TECHNOLOGY
 
Project Description:
[unreadable] (provided by applicant): We propose to assess the robustness of a high-throughput mass spectrometric (MS) technology platform for quantitative measurement of multiple candidate biomarker proteins in complex samples such as human plasma. Specific assays will be developed for 300 candidate biomarker proteins drawn from published literature, pathway analysis, microarray, and proteomics discovery efforts. These assays will be used to measure biomarker levels in 200 selected cancer and 200 control plasma samples at three different laboratory sites using two variant MS platforms. The results will characterize the quantitative reproducibility of the assay methodology within- and between-laboratories and over time. A series of standardized reagents will be developed allowing the assays to be implemented in other laboratories using similar standardized instrumentation. Our measurement platform makes use of well-established quantitative MS techniques used in the routine measurement of small molecules: so-called "multiple reaction monitoring" (or MRM) assays and stable isotope labeled internal standards for quantitation, here in the form of synthetic, labeled peptides. By measuring both the labeled and unlabeled (sample-derived) peptides by MS, the method provides a quantitative measure of the relative amounts of the signature peptide and therefore the protein that it is derived from. In order to access lower abundance biomarkers (those in the lower 5 orders of magnitude of the overall 10 orders of magnitude plasma abundance scale) we will employ specific enrichment techniques using immobilized anti-peptide antibodies. After extensive optimization and characterization, our assays will be deployed on clinical plasma samples from breast cancer cases and controls. Key outcomes of this project will be to demonstrate 1) that we can make sensitive and specific assays quickly and inexpensively; 2) that the assays can be highly multiplexed, greatly reducing the cost-per-analyte; and 3) that the protocols and technology can be standardized and distributed. Several members of our CPTAC team are currently involved in proteomic consortia aimed at MS-based discovery of candidate breast cancer biomarkers in human samples and mouse models. These efforts are generating robust datasets that will also be leveraged by this CPTAC team to inform selection of candidates for assay development and ultimate validation. [unreadable] [unreadable] [unreadable]
 
Project Terms:
Assay Bioassay Biologic Assays Biologic Marker Biological Assay Biological Markers Blood Plasma Cancer of Breast Cancers Clinical Complex Data Set Dataset Human Human, General Instrumentation, Other Label Laboratories Literature Malignant Neoplasms Malignant Tumor Malignant Tumor of the Breast Malignant neoplasm of breast Man (Taxonomy) Man, Modern Measurement Measures Method LOINC Axis 6 Methodology Methods Methods and Techniques Methods, Other Molecular Marker Monitor Network Analysis Outcome Pathway Analysis Peptide antibodies Peptides Plasma Proteins Proteomics Protocol Protocols documentation Publishing Reaction Reagent Relative Relative (related person) Reproducibility Reticuloendothelial System, Serum, Plasma Sampling Series Serum, Plasma Signature Molecule Site Stable Isotope Labeling Standards Standards of Weights and Measures Techniques Technology Time Validation Variant Variation assay development base biomarker case control cost gene product instrumentation malignancy malignant breast neoplasm member mouse model neoplasm/cancer small molecule
Project Title: Measuring cancer biomarker candidates by targeted ms and ab enrichment
Principal Investigators (PI): CARR STEVEN A
Project Number: 5U24CA126476-03
Organization: MASSACHUSETTS INSTITUTE OF TECHNOLOGY
 
Project Categories:
• Natural Sciences > Experimental techniques > in vitro methods > Genomic analys > DNA microarray > SNP microarray
 
Other Information:
Fiscal Year: 2006
Project Start Date: 28 September 2006
Project End Date: 30 June 2009
Administering Institute Or Center: CA
 
Project Funding Information:
Total Funding: $1,758,222
Year Funding Organization Total Funding, $
2008 NATIONAL CANCER INSTITUTE $1,758,222
Project Title: Measuring cancer biomarker candidates by targeted ms and ab enrichment
Principal Investigators (PI): CARR STEVEN A
Project Number: 5U24CA126476-03
Organization: MASSACHUSETTS INSTITUTE OF TECHNOLOGY
 
Project_number Title Year FY Total Cost
There are no results for this project in database.
Project Title: Measuring cancer biomarker candidates by targeted ms and ab enrichment
Principal Investigators (PI): CARR STEVEN A
Project Number: 5U24CA126476-03
Organization: MASSACHUSETTS INSTITUTE OF TECHNOLOGY
 
Project number Project title Organization FY Funding Organization FY Total Cost
3U24CA126476-01S1Measuring Cancer Biomarker Candidates by Targeted MS and Ab EnrichmentMASSACHUSETTS INSTITUTE OF TECHNOLOGY2007NATIONAL CANCER INSTITUTE
$15,000
5U24CA126476-02Measuring Cancer Biomarker Candidates by Targeted MS and Ab EnrichmentMASSACHUSETTS INSTITUTE OF TECHNOLOGY2007NATIONAL CANCER INSTITUTE
$2,764,919
3U24CA126476-02S1Measuring Cancer Biomarker Candidates by Targeted MS and Ab EnrichmentMASSACHUSETTS INSTITUTE OF TECHNOLOGY2008NATIONAL CANCER INSTITUTE
$56,574
5U24CA126476-03Measuring Cancer Biomarker Candidates by Targeted MS and Ab EnrichmentMASSACHUSETTS INSTITUTE OF TECHNOLOGY2008NATIONAL CANCER INSTITUTE
$1,758,222
Project Title: Measuring cancer biomarker candidates by targeted ms and ab enrichment
Principal Investigators (PI): CARR STEVEN A
Project Number: 5U24CA126476-03
Organization: MASSACHUSETTS INSTITUTE OF TECHNOLOGY
 
Project number Project title Principal investigator
There are no any related projects.
Project Title: Measuring cancer biomarker candidates by targeted ms and ab enrichment
Principal Investigators (PI): CARR STEVEN A
Project Number: 5U24CA126476-03
Organization: MASSACHUSETTS INSTITUTE OF TECHNOLOGY
 
Title Abstract Authors Year Rel