experiment = new MsExperiment(cliInputBean.getiExperimentID());
sample = new Sample(cliInputBean.getiSampleID());
replicateNumber = cliInputBean.getReplicate();
// Create the analysis set of this PeptideShaker process
SampleAnalysisSet analysisSet = new SampleAnalysisSet(sample, new ProteomicAnalysis(replicateNumber));
experiment.addAnalysisSet(sample, analysisSet);
// Set the project details
projectDetails = new ProjectDetails();
projectDetails.setCreationDate(new Date());