Software download

Peptide and Protein Identification

In a typical binary classification of the correct and incorrect PSMs, target PSMs are labelled as correct or +1, and decoy PSMs are labelled as incorrect or -1. The classifier learns from the training dataset to assign either +1 or -1 class labels to PSMs. However, in peptide identification, the target PSMs are not trustworthy.

De-Noise is a post-database search algorithm based on the resolution and mass accuracy of the mass spectrometer employed in the LC/MS/MS experiment. We have demonstrate that De-Noise validates more correct target PSMs under a series of fixed FDRs compared to PeptideProphet and Percolator. For the details, please refer to paper "A Novel Algorithm for Validating Peptide Identification from a Shotgun Proteomics Search Engine" in J Proteome Res. Mar 1, 2013; 12(3): 1108–1119.

De-Noise is a joint work with Link's Lab at Vanderbilt University and Dalian University of Technology. The software can be download by clicking on the following link:

De-Noise Package

C-Ranker

Although a number of algorithms have been proposed for identifying high quality PSMs, parameter selection remains a big challenge. C-ranker aims to overcome this problem automatically.

You can read Manual for installation and instructions. Executable versions of C-Ranker can be download from the following links

C-Ranker for Windows 32

C-Ranker for Windows 64

1. C-Ranker for Linux 2.Instructions for installing C-Ranker on Linux 3.Installer

NCI for gene regulatory network inference

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