Projects
Tranche Project
The Tranche Project is a free and open source file sharing tool that enables collections of computers to easily share and cite scientific data sets. Designed and built with scientists and researchers in mind, Tranche essentially solves the data sharing problem in a secure and scalable fashion.
Collaborating groups:
PRIDE, HPRD, Peptide Atlas, CPTAC,
Peptide Atlas
MSExpedite
The NRPP-MS-Viewer is an open source tool that was originally conceived during the development of the Proteome Research Information Management Environment (PRIME). It handles non-centroided and centroided data of common file formats. It has peak detection and deisotoping capabilities, and supports de novo sequencing in three different modes; manual, semi-automated, and automated. The de novo sequenced spectrum, once annotated, can be exported to a file. This annotated file can then be read back into the viewer. It can also be used as a development platform for spectrum analysis. It accomplishes this by allowing third party algorithms to be plugged in and providing a debugger that allows stepping of each node in the pipeline while projecting each output on the viewer.
Collaborators:
Visualizing results of Dr. Yergey (NIH) output of De Novo tool that uses exhaustive enumeration of peptide composition.
PRIME
The long-term success of high throughput proteomics depends in part on the ability of researchers to compile, manage, and analyze data sets generated from state-of-the-art protein separation and protein identification technologies. Systems are needed that can reduce the human effort required for a thorough analysis of these large data sets. We have developed a system, the Proteome Research Information Management Environment (PRIME), to gather, manage, and process data generated by laboratories: sample tracking of gels, relative and differential expressions of gels, data from spot pickers and digestion robots, mass spectrometers, the results from mass spectrometry database search engines, and iTRAQ quantitation information. Curation tools are continuously being developed that assist with the refinement of the evidence for protein identification.
Collaborators:
Dr. Chris Beecher MMOC (Michigan Metabolomics and Obesity Center) and the MCTP (Mich Cent for Translational Pathology): Extending PRIME to handle Metabolomics data.
Dr. Paul Tempst (MSKCC): Replaced Mascot Daemon with Hermes to allow higher throughput of wiff to mgf conversion. Also designing Web-forms in PRIME for their sample submission process and for Client reporting.
Dr. Lewis Brown (Columbia): Integrating PRIME with DIGE data.
Dr. A.L. Burlingame (UCSF): Adopting PRIME to work with custom ESI workflow.
Bonanza
Unidentified tandem mass spectra typically represent 50% to 90% of the spectra acquired in proteomics studies. Bonanza uses a novel algorithm for clustering spectra without knowledge of peptide or protein identifications. Further analysis leverages existing peptide identifications to infer related, likely valid identifications. Significantly more spectra can be identified with this approach, including spectra with unexpected potential modifications or amino-acid substitutions.
Collaborators:
Dr. Anastasia Yocum, Dr. Kathy O'Shea, Proteome Software
Isotope Calculator
Collaborators:
Dr. Alfred Yergey (NIH) for simulation of labeled compounds
with different levels of labeling and composition.
Hermes
Collaborators:
Dr. Paul Tempst (MSKCC)
T2Extractor
Collaborators:
CPAS - Has been integrated so that it can export 4700 and 4800 data into CPAS.