Difference between revisions of "PRatio"
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=== If you are going to use old srf SEQUEST files === | === 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). | + | 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). Note that the use of SRF files in pRatio is no longer supported. However, if you use them, you are welcome to check the program with them, or modify the source code accordingly (within the '''[[PROTEOMICA:Copyrights|terms]]'''). |
* 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). | * 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). | ||
Revision as of 09:50, 26 April 2017
| pRatio |
|---|
 Screenshot of pRatio displaying the advanced options. |
| Last release: v.5.5.06 |
| Release date: 16th Dec 2015 |
| Download link: File:PRatio v5.5.06.zip Source code: pRatio at GitHub |
| Licence: Please read Licencing |
| Requirements |
|
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.
Contents
Installation instructions
pRatio 5.5.06 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.
Follow the instructions below depending on which type of files you are going to use (either msf or srf files). 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). Note that the use of SRF files in pRatio is no longer supported. However, if you use them, you are welcome to check the program with them, or modify the source code accordingly (within the terms).
- 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
Additional information
pRatio has been developed in Visual C#, hence users must install the .NET Framework 2.0 or higher (not necessary for Windows 7 users), which can be downloaded from this link.
Help
If any problems arise during the installation, you can contact Marco Trevisan-Herraz for help.
