PEAKS Q: Protein QuantificationAs researchers press further into the understanding of life sciences, quantification provides greater insight into proteomic mysteries. PEAKS Q is the optional module of PEAKS for protein quantification analysis based on mass spectrometry data. PEAKS Q has both labeling and label-free methods, including:
 PEAKS Q uses well-accepted methods for feature detection and calculates the peptide ratios based on either peak intensity (for labeling method) or peak areas (for label free method). The protein ratios are calculated based on the total intensities or peak areas of the top-3 unique peptides identified for the protein. The use of the unique peptides ensures that the protein ratio is not adversely affected by peptides shared by multiple proteins. Ratios and absolute intensities of the detected features and identified peptides can be easily exported to text files (.csv) for customized analyses by the users, such as ratio calculation using a different algorithm (e.g. spectrum count). PEAKS Q provides a very user-friendly graphical interface to easily visualize the quantification results and the detected features used for the ratio calculation. For the table view of peptide/protein ratios, users can choose to display absolute intensities or ratios to a reference sample or the sum of the samples. Further, the summary view clusters the proteins according to their ratios and provides a bird's eye view of all protein changes. Users can easily examine the supporting evidences of each peptide's ratio calculation. There are several ways that PEAKS Q provides to examine a peptide feature. 
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Quantification