The APEX Quantitative Proteomics Tool: A free analysis tool for deriving large scale protein expression estimates using the APEX technology.

摘要

The APEX Quantitative Proteomics Tool has been developed to provide a means to simultaneously assess the abundance of hundreds of proteins using standard LC-MS/MS proteomics datasets. The APEX Tool is designed to generate APEX values, Absolute Protein Expression Estimates, according to the technique described by Lu et al. Nature Biotech. 25(1):117-124, 2007. The APEX technique uses a modified spectral counting method that utilizes machine learning techniques to arrive at protein abundance values with improved accuracy over traditional spectral counting techniques. The APEX tool provides computational support for this technique through a set of graphical user interfaces designed to guide the user through the process of generating APEX protein abundance estimates. In addition to support for protein abundance, the tool also includes a Z-score test for differential expression, a utility to assess classifier performance via cross validation, and a utility to merge multiple results into a standardized format in preparation for further statistical analysis by other software packages.