# 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: email@example.com, firstname.lastname@example.org, email@example.com
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).
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.
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>