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National Resource for Translational and Developmental Proteomics

Neil Kelleher (kelleher-ofc@northwestern.edu)
P41 GM108569
Active

Center Overview

The science drivers for the National Resouce for Translational and Developmental Proteomics (NRTDP) are outlined in eight Driving Biomedical Projects that motivate the specific aims for four Technology Research and Development Projects. The impact of these combined activities, devoted to improving mass spectrometry-based proteomics using whole proteins as the primary unit of measurement, will be substantial. Integrated over all aspects of the resource (including biomedical application, technology development, dissemination and training), the projected impacts are aligned with both the spirit and the letter of a P41 Biomedical Technology Research Resource and the strategic goals of the NIH as a whole. Applying innovation to timely challenges in diverse areas of clinical and translational research will secure a leadership position for our nation in ‘next-generation’ proteomics technology. These technologies will serve driving projects and investigators to improve scientific understanding and diagnostics, ultimately improving the lives of cancer patients, recipients of kidney transplants, those afflicted with coronary heart disease, and to preserve fertility in women survivors of cancer (oncofertility). More specifically, we will focus ultra-high performance proteomics on sample sets deriving from research on various cancers, including chronic lymphocytic leukemia, multiple myeloma, and acute myeloid leukemia. In technology, we will accelerate the development of the leading platform for top-down proteomics, including two new Fourier-Transform instruments, new protein fractionation technologies, and the AUTOPILOT software suite to allow strategic objectives of biomedical projects to govern the most detailed aspects of data collection on a daily basis. A tailored workflow to enable pervasive and exhaustive analysis of core histones further augments the technology portfolio available in this deeply collaborative and deferential national resource housing a demonstrably high performing technical and administrative team. 

Tags

Proteomics Profiling, Top Down Proteomics

Resources

ResourceDescriptionSupported PlatformsSupported FormatsData TypeData Size (compressed)
ProSightLite
National Resource for Translational and Developmental Proteomics
NIGMS

ProSight Lite is a free Windows application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations.

Windows N/A N/A
TDPortal
National Resource for Translational and Developmental Proteomics
NIGMS

The NRTDP TDPortal is a high-throughput search tool for top-down proteomics data running the Galaxy framework on Northwestern University's Quest HPC Cluster.  Results are generated as .tdReport files which are viewable with the TDViewer application.  Tutorials and protocols to use the new system are available.

Web-Based Thermo Raw N/A N/A
TDViewer
National Resource for Translational and Developmental Proteomics
NIGMS

TDViewer is software for viewing top-down proteomics data acquired on TDPortal.  TDViewer displays the results from a .tdReport file by protein or proteoform and allows the user to filter by false discovery rate (FDR), compare multiple searches and produce reports.

Windows N/A N/A