The bioinformatics group of the Pathogen Functional Genomics Resource Center at the J. Craig Venter Institute would like to announce the release of a new free software tool for protein quantitation. The APEX Quantitative Proteomics Tool is a free and open source Java application for the simultaneous quantitation of hundreds to thousands of proteins from standard LC-MS/MS proteomic data sets. The APEX technique is a modified spectral counting technique that uses a machine learning algorithm to improve protein abundance estimate accuracy. The APEX technique is described in a paper by Lu et al., Nature Biotechnology 25(1):117-124, 2007 and was developed by the Edward Marcotte lab at the University of Texas at Austin. This software tool is an implementation of the APEX method of protein quantitation according to this paper and with consultations with the UT group.

The APEX Quantitative Proteomics Tool has an intuitive user interface with an integrated help and information system and a detailed manual. A tutorial and sample data set are included to acquaint first time users with the mechanics of using the tool.

AVAILABILITY

Please visit the APEX Tool web site for more information and download:
http://pfgrc.jcvi.org/index.php/bioinformatics/apex.html

The tool is in use by our proteomics group at JCVI and we hope the community at large can benefit from this work. We are very eager to have feedback from the community in terms of future enhancements to the tool.