A Combinatorial Perspective of the Protein Inference Problem
The souce code of ProteinInfer can be downloaded at: proteininfer.zip.
The supplementary document is available at: supplementary.pdf.
The protein probabilities obtained by our method and ProteinProphet from four datasets are available at: probs.zip.
(1) Prerequisite: Our program is implemented in Java. The source code is provided in an Eclipse project. You can access the following link for the latest versions of Java and Eclipse:
Java (JDK): http://www.oracle.com/technetwork/java/javase/downloads/index.html
TPP: We use X!Tandem, PeptideProphet, iProphet and ProteinProphet embedded in TPP to infer proteins in our experiments.The version we use is v4.5 and the homepage of TPP is: http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP
The basic command is:
java ProteinInfer.java --option value
Available options are as follows with "(*)" being compulsive parameters:
(*) The full path of the iProphet result file.
(*) The directory for saving results.
The expected number of unique peptides of true proteins. When this value is not provided, an empirical value is estimated from data.
The expected number of unique peptides of false proteins. When this value is not provided, the default value is 1.
--print_subset true | false
Output subset proteins in a separate file. The subset proteins are output by default.
java ProteinInfer.java --iprophet e:\data\18mix\interact.iproph.pep.xml --output_dir e:\data\18mix