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APEX Quantitative Proteomics Tool: Protein Abundance Estimates from Standard LC-MS/MS Proteomics Data

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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 (v. 1.1.0, released 3.24.2010)

Click here for application: Download Application

This application is released under the GPL v3. License: View License

Click here for source code: Download Source Code

Click here for release notes: Download Release Notes

Older Software Links

Older application downloads:

Older source downloads:

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.

View Manual

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.

Download Java v1.6.0

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 Quantitative Proteomics Tool Software Paper:

The following article describes the APEX tool. Please cite this article when referencing the APEX tool in your work.

John C Braisted, Srilatha Kuntumalla, Christine Vogel, Edward M Marcotte, Alan R Rodrigues, Rong Wang, Shih-Ting Huang, Erik S Ferlanti, Alexander I Saeed, Robert D Fleischmann, Scott N Peterson, Rembert Pieper. The APEX Quantitative Proteomics Tool: Generating protein quantitation estimates from LC-MS/MS proteomics results. BMC Bioinformatics 2008 Dec; 9:529. Epub 2008 Dec 09

APEX Technique Paper:

Peng Lu, Christine Vogel, Rong Wang, Xin Yao, Edward M Marcotte. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. 2007 Jan;25(1):117-24. Epub 2006 Dec 2

APEX Protocol Paper:

Christine Vogel & Edward M Marcotte. Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data. Nat. Protoc 2008 3(9):1444-1451.

APEX vs. 2D Gel Electrophoresis – A Comparison of Quantitation Methodologies

Srilatha Kuntumalla, John C Braisted, Shih-Ting Huang, Prashanth P Parmar, David J Clark, Hamid Alami, Quanshun Zhang, Arthur Donohue-Rolfe, Saul Tzipori, Robert D Fleischmann, Scott N Peterson, Rembert Pieper. Comparison of two label-free global quantitation methods, APEX and 2D gel electrophoresis, applied to the Shigella dysenteriae proteome. Proteome Science 2009, 7:22

Prediction of Proteotypic Peptides - A key principle behind the APEX technology:

Parag Mallick, Markus Schirle, Sharon S Chen, Mark R Flory, Hookeun Lee, Daniel Martin, Jeffrey Ranish, Brian Raught, Robert Schmitt, Thilo Werner, Bernhard Kuster, Ruedi Aebersold. Computational prediction of proteotypic peptides for quantitative proteomics. Nat Biotechnol. 2007 Jan;25(1):125-31. Epub 2006 Dec 31

Trans-Proteomic Pipeline Paper:

Keller A, Eng J, Zhang N, Li X, Aebersold R. A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol Syst Biol. 2005;1:2005.0017. Epub 2005 Aug 2

PFGRC - Pathogen Functional Genomics Resource Center

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