- TM4 Microarray Software
- Proteomics Tools
- APEX
- Microarray Tools
- Ginkgo
- Magnolia
Three New Bioinformatics Tools Available
The NIAID sponsored Pathogen Functional Genomics Resource Center (PFGRC) at the J. Craig Venter Institute is pleased to announce the release of three new, free open-source software tools: Magnolia, Ginkgo and APEX. Magnolia is a microarray data management and export system for researchers who use PFGRC microarrays. The software greatly simplifies the tasks of organizing experimental data and submitting it to a public data repository. Ginkgo is a Comparative Genomic Hybridization (CGH) and expression microarray data analysis package. Several normalization, data filtering and imputation, and replicate microarray functions are implemented in an intuitive graphical framework. The APEX tool is an implementation of the Absolute Protein Expression quantitation technique. It can compute protein abundance values for LC-MS/MS proteomics datasets, quantifying hundreds or thousands of proteins. Links to additional information on each of these new software tools is available from the PFGRC's bioinformatics page.
Microarray Suggestion Criteria
The National Institute of Allergy and Infectious Diseases (NIAID) supported Pathogen Functional Genomics Resource Center (PFGRC) designs, constructs, and distributes glass slide DNA microarrays for pathogens and biodefense related organisms (Select A-C agents). Currently, the PFGRC supports DNA microarrays for the 38 organisms listed here. In continuing its efforts to provide the infectious disease and biodefense communities with the microarray resources most relevant to their research efforts, the PFGRC is soliciting input for selection of its next set of reference/species microarrays. The criteria for organism selection may be found here.
APEX Quantitative Proteomics Tool: Protein Abundance Estimates from Standard LC-MS/MS Proteomics Data
The APEX Quantitative Proteomics Tool, is a free and open source Java implementation of the APEX technique for the quantitation of proteins based on standard LC- MS/MS proteomics data (Lu et al., Nature Biotech., 25(1):117-124, 2007). The underlying technique improves upon label free quantitation techniques such as MS/MS spectral counting. This technique uses machine learning algorithms to help correct for variable peptide detection related to certain peptide physicochemical properties which favor or hinder detection. The APEX tool provides a graphical user interface, an extensive integrated user help system, and a complete user’s manual. A sample data set and descriptive tutorial help to acquaint users with the operation of the tool. The APEX tool provides full support for all aspects of the APEX protein quantitation method and offers several utilities to help support downstream analysis. Please refer to the manual for a full description of the tool’s capabilities.
Feature List
- Computes Protein Abundances Based on LC-MS/MS Proteomics Data
- Graphical Interface with Integrated Help and Process Information System
- Complete Manual, Analysis Tutorial and Sample Data Set
- Utilities to Support Analysis of Differential Expression
- Algorithm Performance Analysis – Cross Validation
Download Latest Version
This application is released under the GPL v3. License: View License
Click here for source code: Download Source Code
Software Manual
The APEX tool manual contains a detailed overview of the basic theory behind the APEX method and describes the use of the tool. The manual also provides technical details regarding computational aspects of the technique. The manual, in combination with the integrated tutorial, lays a solid understanding on how to use the tool and the nature of the input files.
System Requirements
- Operating Systems: Windows XP/Vista, Linux, Mac OSX 10.4 or greater.
- Memory Requirement (RAM): 1 GB recommended, 512MB is adequate.
- Java Runtime Environment (JRE): Version 1.5 or greater.
Software Requirements
Data Preprocessing
Trans-Proteomic Pipeline (TPP): The APEX tool imports LC-MS/MS data in protXML format. Two components of the TPP, PeptideProphet™ and ProteinProphet™, should be used to process SEQUEST HTML summary files or MASCOT dat files to produce protXML format files as input to the APEX Tool.
More information about TPP as well as TPP downloads can be found on its homepage:
Trans-Proteomic Pipeline (TPP)
Contact
The developers of the APEX tool encourage questions on the use of the tool and constructive comments or ideas for future enhancements.
Contact the PFGRC's APEX Development Team by email: apex@jcvi.org
References
APEX Technique Paper:
APEX Protocol Paper:
The protocol manuscript is under review and will be posted soon.
Prediction of Proteotypic Peptides - A key principal behind the APEX technology:
Trans-Proteomic Pipeline Paper: