PatternLab for proteomics: a tool for differential shotgun proteomics

Background: A goal of proteomics is to distinguish between states of a biological system by identifying protein expression differences. Liu et al. demonstrated a method to perform semirelative protein quantitation in shotgun proteomics data by correlating the number of tandem mass spectra obtained for each protein, or "spectral count", with its abundance in a mixture; however, two issues have remained open: how to normalize spectral counting data and how to efficiently pinpoint differences between profiles. Moreover, Chen et al. recently showed how to increase the number of identified proteins in shotgun proteomics by analyzing samples with different MScompatible detergents while performing proteolytic digestion. The latter introduced new challenges as seen from the data analysis perspective, since replicate readings are not acquired. Results: To address the open issues above, we present a program termed PatternLab for proteomics. This program implements existing strategies ...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Paulo C. Carvalho, Juliana S. G. Fischer, Emily I. Chen, John R. Yates III, Valmir C. Barbosa
• Keywords: BMCBI 2008, Chen Et, Proteins, Proteomics