Resources and Tools

Census - Software Tool for Quantitative Analysis 
High-throughput mass spectrometry data from shotgun proteomics experiments necessitate an efficient and automated way to analyze large amounts of quantitative data.

Software tool for researching annotations of proteins: open-source protein annotation software with data visualization
Dr. Catherine E. Costello and Dr. Mark E. McComb, Boston University Cardiovascular Proteomics Center.

The Cardiac Organellar Protein atlas Knowledgebase (COPaKB): released in summer 2011
Dr. Peipei Ping, UCLA Proteomics Center, Global Proteomics Initiative of Cardiovascular Medicine.

SILAC - Stable isotope labeling with amino acids in cell culture 
Dr. Pandey, Johns Hopkins Proteomics Center.

PPC: Peak Probability Contrasts Class Prediction Software for Protein Mass Spectometry Data
Dr. Robert Tibshirani, Stanford University.

Development of Semantic Web Technologies for Protemics Research: Resource Description Framework (RDF), DLG2, and ontologies for 2D Gel data (BOSS, CCBase, CCGel)
Charleston Proteomics Center.

DeNovoID is a program that has been specifically designed to use degenerate amino acid sequence and mass data derived from MS experiments to search a peptide database.
Dr. Simon N. Twigger, Medical College of Wisconsin-Proteomics Center.

Proteomics Informatics Course
Dr. Jimmy Eng, Seattle Proteome Center (SPC).

The Need for Guidelines in Publication of Peptide and Protein Identification Data
Carr et al. Mol Cell Proteomics, 2004;3: 531-533.

Revised draft guidelines for proteomic data publication
Bradshaw RA. Mol Cell Proteomics, 2005;4:1223-5.