# Copyright (c) 2011, Ning Li, Yunping Zhu, Fuchu He, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China.
# Released under the terms of the GNU General Public License(version 2.1 or later).
# Contact Email: pkuningonly@gmail.com, zhuyunping@gmail.com, hefc@nic.bmi.ac.cn

Introduction ===================================================================
PepDistiller is a software designed to validate the peptide identifications obtained from MASCOT search results.
The software binary are freely available at http://www.bprc.ac.cn/PepDistiller.
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 <dats file> <DecoyTag> <PeakDepth> <Thread>
<dats file>: a file with the full path to the targe and decoy MASCOT dat files in each row, or with the full path to 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
For example: PepDistiller.exe ..\data\D1\dat\semitryp\HLFT_FixDTA_semitryp20ppm_RNDSS.dats ###RND### 20 4

Change logo ===================================================================
- PepDistiller_1_26.exe: add ionscoreThreshold; can process non-enzymatic search results
- please put the two files "enzymes" and "mod_file", on the same file folder of PD
--usage: <dat file> <DecoyTag> <PeakDepth> <Thread> <IonThreshold>


Please cite: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