UNIT 13.12 Census for Proteome Quantification

Abstract

Quantitative analysis has become increasingly important in the proteomics field; however, the large amount of mass spectrometric data and the different types of quantitative strategies make data analysis ever challenging. Here we describe a quantitative software tool called Census to analyze high-throughput mass spectrometry data from shotgun proteomics experiments in an efficient way. Census is capable of analyzing various stable isotope labeling experiments (using, e.g., ¹⁵N, ¹⁸O, SILAC, iTRAQ, TMT) in addition to labeling-free experiments. With high-resolution data, Census increases the quantitative accuracy by minimizing the contributions of interfering peaks and chemical noise with a small accuracy tolerance for each isotope peak. Census provides various scoring algorithms including least-squares correlation, weight average, singleton peptide detection with discriminant analysis, and probability score for each peptide. Furthermore, Census has built-in multiple statistical filters to maintain robust quality control on quantitative results. Curr. Protoc. Bioinform. 29:13.12.1-13.12.11. © 2010 by John Wiley & Sons, Inc.