Apt: the analytical proteomics team

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Project Title: Apt: the analytical proteomics team
Project Number: 3U24CA126480-04S3
Project web address: Follow on NIH
Project Description:
Biomarker identification and characterization holds great promise for more precise diagnoses and for tailored therapies. The heterogeneity of human cancers and unmet medical needs in these diseases provides a compelling argument to focus biomarker development in cancer. Mass spectrometry (MS)-based proteomics approaches have provided insight into biomarkers of cancer and other diseases with femtomole sensitivity and high analytical precision, but the results have proven difficult to reproduce owing to the complexity of human biofluids and to the protocols employed in these approaches. This CPTAC proposal will develop robust protocols and standards for MS proteomics employing both electrospray ionization (ESI) and Matrix Assisted Laser Desorption Ionization (MALDI) platforms. Ion mobility MS provides several orders of magnitude increased dynamic range, and protocols for detection of cancer biomarker candidates will be further explored with this emerging technology platform. The consortium will employ high specificity immunologic reagents to develop platforms for precise detection and quantification of biomarkers of relevance for breast and prostate cancer. Immunoaffinity selection of specific biomarker proteins will be achieved as a sample fractionation step using nano-scale immunoaffinity columns prior to MS detection and quantification of specific proteins. An emerging technology incorporating specific antibodies on a microfabricated "bioCD" read by spinning disc interferometry enables label-free evaluation of hundreds of analytes from hundreds of samples in minutes. We will focus on candidate biomarkers relevant for breast and prostate cancer from the NF?B and STATS signaling pathways. Three for-profit and one not-for-profit corporate partners will join several academic groups with deep expertise and extensive resources in proteomics technologies to most efficiently evaluate and roll out robust protocols and standards for MS and affinity proteomics approaches. Prostate cancer samples will be made available from the NCI-sponsored ECOG trial;breast cancer patient and control samples will be collected specifically for this consortium by the Hoosier Oncology Group from throughout the State and region. Standardized sample collection organized from the Indiana University School of Medicine will ensure a diverse cross section of patient demographic groups. Three additional corporate partners will provide key technologies and consultation to improve team efficacy.
Project Terms:
affinity antibodies base biological markers breast cancer detection cancer patient consultations detection development diagnosis disease eastern cooperative oncology group electrospray ionization emerging technologies ensure evaluation fractionation heterogeneity human immunologics improved indiana insight interferometry ion mobility label malignant breast neoplasm malignant neoplasm of prostate malignant neoplasms mass spectrum analysis medical medical schools nanoscale oncology group patients proteins proteomics protocols documentation reading reagent resources sample collection sampling signal pathway specificity spectrometry mass matrix-assisted laser desorption-ionization technology universities kidney and urologic - prostate disease kidney and urologic diseases inc. nephritis biotechnology breast cancer prostate cancer urologic diseases aging cancer
Project Title: Apt: the analytical proteomics team
Project Number: 3U24CA126480-04S3
Project web address: Follow on NIH
Organization: Purdue University West Lafayette, United States, Indiana, WEST LAFAYETTE
Principal Investigators (PI): Regnier Fred E, US
Project Categories:
Natural Sciences
Other Information:
Fiscal Year: 2006
Project Start Date: 28 September 2006
Project End Date: 31 August 2011
Project program: Resource-Related Research Projects--Cooperative Agreements
Project Funding Information:
Funding Mechanism: Other Research Related
Year Funding Organization Total Funding, $
2009 NIH - National Cancer Institute $42,515
Project Title: Apt: the analytical proteomics team
Project Number: 3U24CA126480-04S3
Project web address: Follow on NIH
Title FY Funding
There are no results for this project in database.
Project Title: Apt: the analytical proteomics team
Project Number: 3U24CA126480-04S3
Project web address: Follow on NIH
Title Journal Year Country Rel
A method for identifying discriminative isoform-specific peptides for clinical proteomics application. BMC Genomics 2016 england
Disparities between immobilized enzyme and solution based digestion of transferrin with trypsin. J Sep Sci 2013 germany
Extending the coverage of spectral libraries: a neighbor-based approach to predicting intensities of peptide fragmentation spectra. Proteomics 2013 germany
Simple, miniaturized blood plasma extraction method. Anal Chem 2013 united states
Breast cancer subtyping from plasma proteins. BMC Med Genomics 2013 england
Novel alternative splicing isoform biomarkers identification from high-throughput plasma proteomics profiling of breast cancer. BMC Syst Biol 2013 england
Native protein proteolysis in an immobilized enzyme reactor as a function of temperature. Anal Chem 2012 united states
Effect of single amino acid substitution on oxidative modifications of the Parkinson's disease-related protein, DJ-1. Mol Cell Proteomics 2012 united states
Computational approaches to protein inference in shotgun proteomics. BMC Bioinformatics 2012 england
Oxidative stress induced carbonylation in human plasma. J Proteomics 2011 netherlands
Differential carbonylation of proteins as a function of in vivo oxidative stress. J Proteome Res 2011 united states
A large, consistent plasma proteomics data set from prospectively collected breast cancer patient and healthy volunteer samples. J Transl Med 2011 england
An integrated proteomics analysis of bone tissues in response to mechanical stimulation. BMC Syst Biol 2011 england
Determining the effects of antioxidants on oxidative stress induced carbonylation of proteins. Anal Chem 2011 united states
Data mining methods in Omics-based biomarker discovery. Methods Mol Biol 2011 united states
On the accuracy and limits of peptide fragmentation spectrum prediction. Anal Chem 2011 united states
HOMER: a human organ-specific molecular electronic repository. BMC Bioinformatics 2011 england
Coupling protein complex analysis to peptide based proteomics. J Chromatogr A 2010 netherlands
PEPPI: a peptidomic database of human protein isoforms for proteomics experiments. BMC Bioinformatics 2010 england
Prediction of drift time in ion mobility-mass spectrometry based on Peptide molecular weight. Protein Pept Lett 2010 netherlands
Proteomic identification of carbonylated proteins and their oxidation sites. J Proteome Res 2010 united states
Dynamics of protein damage in yeast frataxin mutant exposed to oxidative stress. OMICS 2010 united states
Artificial neural networks for the prediction of peptide drift time in ion mobility mass spectrometry. BMC Bioinformatics 2010 england
Combinatorial libraries of synthetic peptides as a model for shotgun proteomics. Anal Chem 2010 united states
The importance of peptide detectability for protein identification, quantification, and experiment design in MS/MS proteomics. J Proteome Res 2010 united states
Screening antibody and immunosorbent selectivity by two-dimensional liquid chromatography-MS/MS (2-D LC-MS/MS). J Sep Sci 2010 germany
Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry. J Proteome Res 2010 united states
Sialylated Lewis x antigen bearing glycoproteins in human plasma. J Proteome Res 2010 united states
Targeted quantitative analysis of superoxide dismutase 1 in cisplatin-sensitive and cisplatin-resistant human ovarian cancer cells. J Chromatogr B Analyt Technol Biomed Life Sci 2010 netherlands
Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses. Mol Cell Proteomics 2010 united states
Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance. Mol Cell Proteomics 2010 united states
Unraveling human complexity and disease with systems biology and personalized medicine. Per Med 2010
Profiling carbonylated proteins in human plasma. J Proteome Res 2010 united states
Discovery of pathway biomarkers from coupled proteomics and systems biology methods. BMC Genomics 2010 england
Multi-dimensional liquid chromatography in proteomics--a review. Anal Chim Acta 2010 netherlands
Dissecting the human plasma proteome and inflammatory response biomarkers. Proteomics 2009 germany
Glycoproteomics of plasma based on narrow selectivity lectin affinity chromatography. J Proteome Res 2009 united states
A bayesian approach to protein inference problem in shotgun proteomics. J Comput Biol 2009 united states
Intrinsic subtype-associated changes in the plasma proteome in breast cancer. Proteomics Clin Appl 2009 germany
Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat Biotechnol 2009 united states
Development of a high-throughput IMS-IMS-MS approach for analyzing mixtures of biomolecules. J Proteomics 2008 netherlands
Fast and accurate identification of semi-tryptic peptides in shotgun proteomics. Bioinformatics 2008 england
A hierarchical statistical model to assess the confidence of peptides and proteins inferred from tandem mass spectrometry. Bioinformatics 2008 england
Use of glycan targeting antibodies to identify cancer-associated glycoproteins in plasma of breast cancer patients. Anal Chem 2008 united states
Project Title: Apt: the analytical proteomics team
Project Number: 3U24CA126480-04S3
Project web address: Follow on NIH
Title Year
Detection of oxidized polypeptides 2006
Project Title: Apt: the analytical proteomics team
Project Number: 3U24CA126480-04S3
Project web address: Follow on NIH
Title Phase Year