Bioinformatics Collaborations

Tranche Project

Collaborating groups:
PRIDE, HPRD, Peptide Atlas, CPTAC, Peptide Atlas

MSExpedite

Collaborators:
Visualizing results of Dr. Yergey (NIH) output of De Novo tool that uses exhaustive enumeration of peptide composition.

PRIME

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

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.