Introduction

1. PepDistiller is a software designed to validate the peptide identifications obtained from MASCOT search results.

2. The software binary are freely available at http://www.bprc.ac.cn/PepDistiller or https://sourceforge.net/projects/pepdistiller/.

3. The package also include a script for calcualting the refined FDR (RefinedSSFDRPercolator.pl).

Installation

1. For Windows platform, download the windows executables from the above URL. Note all the files in the directory named "bin" should be placed in the same directory;
2. The current version of PepDistiller reads the two MASCOT config files named "enzymes" and "mod_file" from the path "d:/inetpub/mascot/config/", therefore users should place the two files in the above directory.Further version will discard this limitation;
3. Download the Percolator binary from http://per-colator.com/, rename the binary file as "percolator.exe", put it in the "bin" directory;
4. Enjoy and have fun.

Usage

PepDistiller.exe <dat file> <DecoyTag> <PeakDepth> <Thread> <Peptide length cutoff>

• <dat file>: the absolute path of the MASCOT auto-decoy search dat file;
• <DecoyTag>: a tag indicating the decoy hits, e.g. ###RND### for randomized decoy database. PepDistiller can auto-detect the decoy hits in an auto-decoy search result, thus it doesn't matter for the auto-decoy search results;
• <PeakDepth>: the number of most intense peaks in each 100 m/z bin, recommend 20
• <Thread>: the number of threads to use
• <Peptide length cutoff>: the peptide length cutoff, default: 7

For example: PepDistiller.exe c:\test.dat ###RND### 20 4 7

Citation

Li, N., S. Wu, et al. (2012). "PepDistiller: A quality control tool to improve the sensitivity and accuracy of peptide identifications in shotgun proteomics." Proteomics 12(11): 1720-1725

Contact

• Author and Developer: Dr. Ning Li (pkuningonly@gmail.com)
• Maintainer: Dr. Cheng Chang (1987ccpacer@163.com)