plfdr Files

plfdr:
In this paper, we present a method for validating protein inference results. Plfdr is implemented in Java and can run on any Java Virtual Machine (JVM) regardless of computer architecture.



How to try the program:

1. Install and run Netbeans into your computer.
Important prerequisite: you must first install the Java Development Kit (JDK).

2. Download the source codes from this website into your computer.
Click on the link http://sourceforge.net/projects/plfdr/ to download Decoy_free_FDR_estimation.rar into the folder you chose as the workspace and decompress the project.


3. Execute plfdr with Netbeans.
You can use the Wizard to import the Decoy_free_FDR_estimation project into workspace. 
	From the main menu bar, select " File > Open projects". 	The wizard opens.  
	Choose "Select root directory" and click the associated "Browse" to locate the directory where you put the project. 
	Under "Projects" select the Decoy_free_FDR_estimation project to open. 
 

Select Decoy_free_FDR_estimation.java and start the Java program.

The input data is put in the folder "data". You can change the file name in the main function to run your own data.



Input and output files.

1. Input files
peptideFile			peptideFile with a list of sequences and confidence score for candidate peptide identifications.
scoreFiles                      scoreFiles with a list of proteins with their scores or probabilities assigned by protein inference algorithms

2. Output files
resultFile			output file with the FDR at each protein pvalue as threshold.


3. Formats of input and output files
3.1. Accepted formats for peptide identification file pospepfile

peptideFile:
Format (tab delimited):
pospep1	protein1	peptide_probability1
pospep2	protein2	peptide_probability2
...
Note: peptide_probability refers to the peptide spectra matching score. It can be obtained from software such as Peptideprophet. "protein" represent the candidate proteins in the database which contain at least one identified peptide.

ScoreFile:
Format (tab delimited):
protein1	protein_score1
protein2	protein_score2

3.2. Format of output resultFile(tab delimited):
protein	protein_score	protein_pvalue	fdr_at_current_protein_pvalue_as_threshold