Engineering topics

Rivers, Robert

Publications and source records attributed to Rivers, Robert.

6 records

DOE OSTI2016

Using the CPTAC Assay Portal to identify and implement highly characterized targeted proteomics assays

The Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the National Cancer Institute (NCI) has launched an Assay Portal (http://assays.cancer.gov) to serve as an open-source repository of well-characterized targeted proteomic assays. The portal is designed to curate and disseminate highly characterized, targeted mass spectrometry (MS)-based assays by providing detailed assay performance characterization data, standard operating procedures, and access to reagents. Assay content is accessed via the portal through queries to find assays targeting proteins associated with specific cellular pathways, protein complexes, or specific chromosomal regions. The position of the peptide analytes for which there are available assays are mapped relative to other features of interest in the protein, such as sequence domains, isoforms, single nucleotide polymorphisms, and post-translational modifications. The overarching goals are to enable robust quantification of all human proteins and to standardize the quantification of targeted MS-based assays to ultimately enable harmonization of results over time and across laboratories.

Environmental Molecular Sciences Laboratory↗

DOE OSTI2015

Comprehensive Quantitative Analysis of Ovarian and Breast Cancer Tumor Peptidomes

Aberrant degradation of proteins is associated with many pathological states, including cancers. Mass spectrometric analysis of tumor peptidomes, the intracellular and intercellular products of protein degradation, has the potential to provide biological insights on proteolytic processing in cancer. However, attempts to use the information on these smaller protein degradation products from tumors for biomarker discovery and cancer biology studies have been fairly limited to date, largely due to the lack of effective approaches for robust peptidomics identification and quantification, and the prevalence of confounding factors and biases associated with sample handling and processing. Herein, we have developed an effective and robust analytical platform for comprehensive analyses of tissue peptidomes, which is suitable for high throughput quantitative studies. The reproducibility and coverage of the platform, as well as the suitability of clinical ovarian tumor and patient-derived breast tumor xenograft samples with post-excision delay of up to 60 min before freezing for peptidomics analysis, have been demonstrated. Moreover, our data also show that the peptidomics profiles can effectively separate breast cancer subtypes, reflecting tumor-associated protease activities. Peptidomics complements results obtainable from conventional bottom-up proteomics, and provides insights not readily obtainable from such approaches.

Environmental Molecular Sciences Laboratory↗

DOE OSTI2014

Proteogenomic characterization of human colon and rectal cancer

We analyzed proteomes of colon and rectal tumors previously characterized by the Cancer Genome Atlas (TCGA) and performed integrated proteogenomic analyses. Protein sequence variants encoded by somatic genomic variations displayed reduced expression compared to protein variants encoded by germline variations. mRNA transcript abundance did not reliably predict protein expression differences between tumors. Proteomics identified five protein expression subtypes, two of which were associated with the TCGA "MSI/CIMP" transcriptional subtype, but had distinct mutation and methylation patterns and associated with different clinical outcomes. Although CNAs showed strong cis- and trans-effects on mRNA expression, relatively few of these extend to the protein level. Thus, proteomics data enabled prioritization of candidate driver genes. Our analyses identified HNF4A, a novel candidate driver gene in tumors with chromosome 20q amplifications. Integrated proteogenomic analysis provides functional context to interpret genomic abnormalities and affords novel insights into cancer biology.

: colorectal cancer, shotgun proteomics, proteogen↗

DOE OSTI2014

CPTAC Assay Portal: a repository of targeted proteomic assays

To address these issues, the Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the National Cancer Institute (NCI) has launched an Assay Portal (http://assays.cancer.gov) to serve as a public repository of well-characterized quantitative, MS-based, targeted proteomic assays. The purpose of the CPTAC Assay Portal is to facilitate widespread adoption of targeted MS assays by disseminating SOPs, reagents, and assay characterization data for highly characterized assays. A primary aim of the NCI-supported portal is to bring together clinicians or biologists and analytical chemists to answer hypothesis-driven questions using targeted, MS-based assays. Assay content is easily accessed through queries and filters, enabling investigators to find assays to proteins relevant to their areas of interest. Detailed characterization data are available for each assay, enabling researchers to evaluate assay performance prior to launching the assay in their own laboratory.

Environmental Molecular Sciences Laboratory↗

NASA NTRS1998

Characterizing the Hazard of a Wake Vortex Encounter

The National Aeronautics and Space Administration (NASA) is conducting research with the goal of enabling safe improvements in the capacity of the nation's air transportation system. The wake vortex upset hazard is an important factor in establishing the minimum safe spacing between aircraft during landing and take-off operations, thus impacting airport capacity. Static and free-flight wind tunnel tests and flight tests have provided an extensive data set for improved understanding of vortex encounter dynamics and simulation. Piloted and batch simulation studies are also ongoing to establish a first-order hazard metric and determine the limits of an operationally acceptable wake induced upset. This paper outlines NASA's research in these areas.

Vicroy, Dan D.↗

NASA NTRS1997

Wake Vortex Encounter Model Validation Experiments

The goal of this current research is to establish a database that validate/calibrate wake encounter analysis methods for fleet-wide application; and measure/document atmospheric effects on wake decay. Two kinds of experiments, wind tunnel experiments and flight experiments, are performed. This paper discusses the different types of tests and compares their wake velocity measurement.

Vicroy, Dan↗