PRatio - Revision history

Mtrevisan: /* If you are going to use old srf SEQUEST files */

2017-04-26T08:52:11Z

‎If you are going to use old srf SEQUEST files

Mtrevisan: /* If you are going to use old srf SEQUEST files */

2017-04-26T08:51:58Z

‎If you are going to use old srf SEQUEST files

Mtrevisan: /* If you are going to use old srf SEQUEST files */

2017-04-26T08:50:28Z

‎If you are going to use old srf SEQUEST files

Mtrevisan at 09:13, 4 April 2017

2017-04-04T09:13:17Z

Mtrevisan: /* Installation instructions */

2013-09-23T15:16:56Z

‎Installation instructions

Mtrevisan: other minor changes

2013-09-23T15:16:38Z

other minor changes

Mtrevisan: image

2013-09-23T15:13:30Z

image

Mtrevisan: category

2013-09-23T15:11:36Z

Mtrevisan: creation

2013-09-23T15:10:19Z

creation

New page

{{lowercase}}
{{Software
|screenshot = File:Screenshot pRatio-advanced options.PNG
|name = pRatio
|screenshot_description = Screenshot of pRatio displaying the advanced options.
|last_release = 5.4.8|date = 20th Aug 2013
|link = File:PRatio v5.4.8.zip
|requirements =
* [http://www.microsoft.com/en-us/download/details.aspx?id=1639 .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 [http://www.microsoft.com/visualstudio/eng/products/visual-studio-express-products 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

@@ Line 54: / Line 54: @@
 ) 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
+:* note that this location may vary, depending on the location where you have installed your Xcalibur version
 ) execute the following sentence in your ''run command'' menu:

@@ Line 27: / Line 27: @@
 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 ===
@@ Line 60: / Line 56: @@
 * execute the following sentence in your ''run command'' menu:
   regsvr32 C:\Xcalibur\system\programs\BioWorksBrowser\BioUnifiedFile.dll
 === Help ===

← Older revision		Revision as of 15:11, 23 September 2013
Line 54:		Line 54:
	* execute the following sentence in your ''run command'' menu:		* execute the following sentence in your ''run command'' menu:
	regsvr32 C:\Xcalibur\system\programs\BioWorksBrowser\BioUnifiedFile.dll		regsvr32 C:\Xcalibur\system\programs\BioWorksBrowser\BioUnifiedFile.dll
		+
		+	[[Category:pRatio]]

@@ Line 51: / Line 51: @@
 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).
-* 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
+) copy that file to the folder C:\Xcalibur\system\programs\BioWorksBrowser\
-* execute the following sentence in your ''run command'' menu:
+:* note that this may vary, depending on the location where you have installed your Xcalibur version
   regsvr32 C:\Xcalibur\system\programs\BioWorksBrowser\BioUnifiedFile.dll

@@ Line 4: / Line 4: @@
 |name = pRatio
 |screenshot_description = Screenshot of pRatio displaying the advanced options.
-|last_release = 5.4.8|date = 20th Aug 2013
+|last_release = 5.5.06|date = 16th Dec 2015
-|link = File:PRatio v5.4.8.zip
+|link = File:PRatio v5.5.06.zip
 |requirements =
 * [http://www.microsoft.com/en-us/download/details.aspx?id=1639 .NET Framework 2.0] or higher
@@ Line 22: / Line 22: @@
 == 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.
+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.

@@ Line 1: / Line 1: @@
 {{lowercase}}
 {{Software
-|screenshot = File:Screenshot pRatio-advanced options.PNG
+|screenshot = Screenshot pRatio-advanced options.PNG
 |name = pRatio
 |screenshot_description = Screenshot of pRatio displaying the advanced options.