APEX Quantitative Proteomics Tool

Category Proteomics>Mass Spectrometry Analysis/Tools

Abstract The APEX (Absolute Protein Expression) Quantitative Proteomics Tool, is a free and open source Java implementation of the APEX technique for the quantitation of proteins based on standard liquid chromatography- tandem mass spectrometry (LC- MS/MS) proteomics data (Lu et al., Nature Biotech., 25(1):117-124, 2007).

It can compute protein abundance values for LC- MS/MS datasets, quantifying hundreds or thousands of proteins.

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.

Also provides 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.

Note: Please refer to the software manual for a full description of the tools capabilities.

Feature List --

1) Computes Protein Abundances Based on LC-MS/MS Proteomics Data.

2) Graphical Interface with Integrated Help and Process Information System.

3) Complete Manual, Analysis Tutorial and Sample Data Set.

4) Utilities to Support Analysis of Differential Expression.

5) Algorithm Performance Analysis - Cross Validation.

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 is recommended - 512MB is adequate.


Java Runtime Environment (JRE): Version 1.5 or greater.

Data Preprocessing -

Trans-Proteomic Pipeline (TPP) (see G6G Abstract Number 20084): 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 (see G6G Abstract Number 20087) dat files to produce protXML format files as input to the APEX Tool.


Manufacturer Web Site APEX Quantitative Proteomics Tool

Price Contact manufacturer.

G6G Abstract Number 20273

G6G Manufacturer Number 101593