A Combinatorial Perspective of the Protein Inference Problem
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Source code:
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.
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Usage:
(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
Eclipse: http://www.eclipse.org/downloads/
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
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(2) Usage:
The basic command is:
java ProteinInfer.java --option value
Available options are as follows with "(*)" being compulsive parameters:
--iprophet String
(*) The full path of the iProphet result file.
--output_dir String
(*) The directory for saving results.
--lambda_1 Integer
The expected number of unique peptides of true proteins. When this value is not provided, an empirical value is estimated from data.
--lambda_2 Integer
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.
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(3) Example:
java ProteinInfer.java --iprophet e:\data\18mix\interact.iproph.pep.xml --output_dir e:\data\18mix