Census for Proteome Quantification
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- Abstract
- Table of Contents
- Figures
- Literature Cited
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., 15 N, 18 O, 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.
Keywords: Census; mass spectrometry data; proteomics data; stable isotope label; label?free analysis
Table of Contents
- Introduction
- Basic Protocol 1: Using Census to Quantitatively Analyze Proteomic Data
- Support Protocol 1: Downloading and Installing Census
- Guidelines for Understanding Results
- Commentary
- Literature Cited
- Figures
- Tables
Materials
Figures
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Figure 13.12.1 Label‐free configuration file. The sample tag defines a group of experiments, and the each_sample tag inside it defines an individual experiment. The path in the file tag can have specific spectral file name or wildcard (asterisk) for all spectral files in the same directory. View Image -
Figure 13.12.2 Quantified protein list after loading the census_chro.xml file. To display quantified peptide information, double‐click on one of the proteins. View Image -
Figure 13.12.3 Quantified peptide list with chromatogram graph and quantitative scores. View Image -
Figure 13.12.4 A panel to generate Census report file. Various filtering options can be defined to control the quality of the output. View Image -
Figure 13.12.5 An example of a Census report file named census‐out.txt. The upper part shows the filtering options applied, and the lower part shows a protein/peptide list with scores. The report file is a tab‐delimited text file, so it is recommended to align columns properly by loading it into Microsoft Excel or OpenOffice Calc. View Image
Videos
Literature Cited
| Literature Cited | |
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