PRatio

pRatio
300px Screenshot of pRatio displaying the advanced options.
Last release: v.5.4.8
Release date: 20th Aug 2013
Download link: File:PRatio v5.4.8.zip Source code: pRatio at GitHub
Licence: Please read Licencing
Requirements
.NET Framework 2.0 or higher OS: Windows XP, Windows Vista or Windows 7 using msf files (from Proteome Discoverer): Community.CsharpSqlite.dll Community.CsharpSqlite.SQLiteClient.dll using srf files (from old SEQUEST versions): BioUnifiedFile.dll Xcalibur 2.0 Bioworks 3.2 (any release)

pRatio is a SEQUEST protein identification validator program created to calculate the probability of random peptide matching and the FDR when a large collection of MS2 spectra is searched against a database using SEQUEST. It has been developed at the Cardiovascular Proteomics Laboratory of Prof Jesús Vázquez, at the Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain.

Installation instructions

pRatio 5.4.8 is a portable, standalone application, so you do not need to install it to execute it. However you must to follow some steps to be able to use it.

Unzip the files and conf folder (which you will find within the above-linked zip file) where you prefer in your computer. Then execute the pRatio.exe file (make sure it is the executable file and not the pRatio.exe.config file, which will look as if it were called "QuiXoT.exe" when hiding file extensions). You may want to create a shortcut on your desktop or elsewhere to have fast access to QuiXoT.

If you are going to use msf files

msf files are the result files of Proteome Discoverer. They constitute a SQLite database. To be able to read these files you will need two dll files:

• Community.CsharpSqlite.dll
• Community.CsharpSqlite.SQLiteClient.dll

To get them, you have to:

• download last release (3.7.7.1 was the last one we have tested) of csharp-sqlite from their website: here http://code.google.com/p/csharp-sqlite/downloads/list.
• extract the concerning folders:
  • Community.CsharpSqlite
  • Community.CsharpSqlite.SQLiteClient
• for both projects, execute their .csproj file and build a solution
  • note you will need to have Microsoft Visual C# installed.
• a bin/Debug folder will appear
• if everything went fine, you should find the abovementioned dll files in these folders.
• copy both files and paste them into your pRatio folder.

If you are going to use old srf SEQUEST files

srf files are Thermo's SEQUEST results files (note that if you are using Proteome Discoverer's msf files you will not need this step).

• you have to find the library BioUnifiedFile.dll (unfortunately we cannot provide it for licencing reasons, so you will have to find it by yourself).
• copy that file to the folder C:\Xcalibur\system\programs\BioWorksBrowser\
  • note that this may vary, depending on the location where you have installed your Xcalibur version
• execute the following sentence in your run command menu:

regsvr32 C:\Xcalibur\system\programs\BioWorksBrowser\BioUnifiedFile.dll