Enabling proteomics discovery through visual analysis

• Published in: IEEE engineering in medicine and biology magazine Vol. 24; no. 3; pp. 50 - 57
• Main Authors: Havre, S.L., Singhal, M., Payne, D.A., Weir Lipton, M.S., Webb-Robertson, B.-J.M.
• Format: Journal Article
• Language: English
• Published: New York IEEE 01-05-2005; The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
• Subjects: Amino acids; Bioinformatics; Genomics; Mass spectroscopy; Organisms; Peptides; Proteins; Proteomics; Sequences
• ISSN: 0739-5175; 1937-4186
• DOI: 10.1109/MEMB.2005.1436460

This article presents the motivation for developing visual analysis tools for proteomic data and demonstrates their application to proteomics research with a visualization tool named Peptide Permutation and Protein Prediction, or PQuad, a functioning visual analytic tool for the study of systems biology, is in operation at the Pacific Northwest National Laboratory (PNNL). PQuad supports the exploration of proteins identified by proteomic techniques in the context of supplemental biological information. In particular, PQuad supports differential proteomics by simplifying the comparison of peptide sets from different experimental conditions as well as different proteins identification or confidence scoring techniques. Finally, PQuad supports data validation and quality control by providing a variety of resolutions for huge amounts of data to reveal errors undetected by other methods.