The APEX Quantitative Proteomics Tool: Generating protein quantitation estimates from LC-MS/MS proteomics results

The APEX Quantitative Proteomics Tool, introduced here, is a free open source Java application that supports the APEX protein quantitation technique. The APEX tool uses data from standard tandem mass spectrometry proteomics experiments and provides computational support for APEX protein abundance quantitation through a set of graphical user interfaces that partition thparameter controls for the various processing tasks. The tool also provides a Z-score analysis for identification of significant differential protein expression, a utility to assess APEX classifier performance via cross validation, and a utility to merge multiple APEX results into a standardized format in preparation for further statistical analysis.The APEX Quantitative Proteomics Tool provides a simple means to quickly derive hundreds to thousands of protein abundance values from standard liquid chromatography-tandem mass spectrometry proteomics datasets. The APEX tool provides a straightforward intuitive interface design overlaying a highly customizable computational workflow to produce protein abundance values from LC-MS/MS datasets.The field of proteomics has used mass spectrometry (MS) techniques to provide qualitative results that describe the protein complement of complex protein samples [1]. Researchers also use modifications of these MS technologies for the quantitative analysis of proteins in complex samples [1-3], and often hundreds to thousands of proteins are quantified per experiment. Some quantitative techniques involve peptide isotopic labeling [4-8]. In contrast, label-free techniques have focused on analysis of MS/MS peak heights or observed peptide spectral count information [9-12]. Peptides are produced in an enzymatic digestion of the protein mixture, often using trypsin, which generally cleaves the proteins at the C-terminus of lysine or arginine amino acid residues [13].Spectral counting techniques typically infer the relative quantity of a protein by counting the number of MS d