public void TestSinglePeptide2()
{
string uimfFileLocation = Cheetah;
LcImsPeptideSearchParameters parameters = new LcImsPeptideSearchParameters
{
ChargeStateMax = 5,
NetTolerance = 0.2,
IsotopicFitScoreThreshold = 0.15,
MassToleranceInPpm = 30,
NumPointForSmoothing = 9
};
string peptide = "ATVLNYLPK";
double net = 0.3612;
PeptideTarget target = new PeptideTarget(1, peptide, net);
DriftTimeTarget driftTimeTarget = new DriftTimeTarget("Test Target", 19.62, target, 2);
target.DriftTimeTargetList.Add(driftTimeTarget);
LcImsPeptideSearchWorkfow lcImsPeptideSearchWorkfow = new LcImsPeptideSearchWorkfow(uimfFileLocation, parameters);
ChargeStateCorrelationResult correlationResult = lcImsPeptideSearchWorkfow.RunInformedWorkflow(target);
using (ImsTargetResultExporter resultsExporter = new ImsTargetResultExporter("outputSingle.csv"))
{
if (correlationResult != null) resultsExporter.AppendCorrelationResultToCsv(correlationResult);
}
}
public void TestRunAllTargets()
{
string uimfFileLocation = Cheetah;
string netAlignmentFileLocation = @"";
IInterpolation interpolation = AlignmentImporter.ReadFile(netAlignmentFileLocation);
LcImsPeptideSearchParameters parameters = new LcImsPeptideSearchParameters
{
ChargeStateMax = 5,
NetTolerance = 0.03,
IsotopicFitScoreThreshold = 0.2,
MassToleranceInPpm = 30,
NumPointForSmoothing = 9
};
List<PeptideTarget> targetList = MassTagImporter.ImportMassTags("elmer", "MT_Human_Sarcopenia_P789");
Console.WriteLine(DateTime.Now + ": Using " + targetList.Count + " targets.");
using (ImsTargetResultExporter allResultsExporter = new ImsTargetResultExporter("outputTestAll.csv"))
{
using (ImsTargetResultExporter resultsExporter = new ImsTargetResultExporter("outputTest.csv"))
{
LcImsPeptideSearchWorkfow lcImsPeptideSearchWorkfow = new LcImsPeptideSearchWorkfow(uimfFileLocation, parameters, interpolation);
foreach (var imsTarget in targetList)
{
ChargeStateCorrelationResult correlationResult = lcImsPeptideSearchWorkfow.RunInformedWorkflow(imsTarget);
allResultsExporter.AppendResultsOfTargetToCsv(imsTarget);
if (correlationResult == null) continue;
resultsExporter.AppendCorrelationResultToCsv(correlationResult);
}
}
}
}
