public static void Launch(bool restrain = false)
{
//@"G:\Thibault\Olivier\MnR\Databases\BD_RefGenome_WithReverse_2012-06-20.fasta";
//Trypsin
string outputDir = @"C:\_IRIC\DATA\Test\testPK\";
string fastaFile = @"C:\_IRIC\DATA\Yeast\Yeast_SwissProt.fasta";//Yeast
//@"G:\Thibault\Olivier\MQ_vs_Morpheus\Yeast_SwissProt.fasta";//Yeast
//@"G:\Thibault\Olivier\Databases\SProHNoIso_20130430\current\sequences_2013-05-30.fa";
//G:\Thibault\Olivier\MnR\Databases\mini_human_reference_2013-26-03.fasta";//Yeast
string projectFile = @"C:\_IRIC\DATA\PK\NotCalibrated\project_fr1.csv";//Yeast
//@"G:\Thibault\Olivier\MQ_vs_Morpheus\project.csv";//Yeast
//@"G:\Thibault\-=Proteomics_Raw_Data=-\ELITE\JAN22_2013\_Project_FL_Single.csv";
//G:\Thibault\-=Proteomics_Raw_Data=-\ELITE\JUN27_2012\MR 4Rep DS\MassSense\_Test_ProjectFile_MF3.csv";
//G:\Thibault\-=Proteomics_Raw_Data=-\ELITE\MAR18_2013\ProjectFile_TestForProPheus.csv";
DBOptions dbOptions = new DBOptions(fastaFile);
Samples Project = new Samples(projectFile, 0, dbOptions);
dbOptions.precursorMassTolerance = new MassTolerance(80, MassToleranceUnits.ppm);
dbOptions.productMassTolerance = new MassTolerance(80, MassToleranceUnits.ppm);//0.034 is a 60 000 resolution over 2000 range in mz
dbOptions.MaximumPeptideMass = 200000;
dbOptions.OutputFolder = outputDir;
ProteaseDictionary proteases = ProteaseDictionary.Instance;
dbOptions.DigestionEnzyme = proteases["trypsin (no proline rule)"]; //"no enzyme"];
dbOptions.NoEnzymeSearch = false; // true;
dbOptions.DecoyFusion = false;
//dbOptions.protease = proteases["trypsin (no proline rule)"];
dbOptions.ToleratedMissedCleavages = 2;
dbOptions.MinimumPeptideLength = 5;
dbOptions.MaximumPeptideLength = 300;
GraphML_List <Modification> fixMods = new GraphML_List <Modification>();
fixMods.Add(ModificationDictionary.Instance["carbamidomethylation of C"]);
dbOptions.fixedModifications = fixMods;
GraphML_List <Modification> varMods = new GraphML_List <Modification>();
//Oxidation (M);Acetyl (Protein N-term);Phospho (STY)
//Mods for Yeast
if (!restrain)
{
//varMods.Add(ModificationDictionary.Instance["oxidation of M"]);
//varMods.Add(ModificationDictionary.Instance["acetylation of protein N-terminus"]);
//varMods.Add(ModificationDictionary.Instance["phosphorylation of S"]);
//varMods.Add(ModificationDictionary.Instance["phosphorylation of T"]);
//varMods.Add(ModificationDictionary.Instance["phosphorylation of Y"]);//*/
varMods.Add(ModificationDictionary.Instance["Pionylation of peptide N-terminus"]);
dbOptions.maximumVariableModificationIsoforms = 1024;// 2 * (varMods.Count + fixMods.Count);//TODO Evaluate the viability of this parameter
}
else
{
dbOptions.maximumVariableModificationIsoforms = 2;
}
dbOptions.variableModifications = varMods;
dbOptions.addFragmentLoss = false;
dbOptions.addFragmentMods = false;
dbOptions.fragments = new Fragments();
//dbOptions.fragments.Add(new FragmentA());
dbOptions.fragments.Add(new FragmentB());
//dbOptions.fragments.Add(new FragmentC());
//dbOptions.fragments.Add(new FragmentX());
dbOptions.fragments.Add(new FragmentY());
//dbOptions.fragments.Add(new FragmentZ());
//ClusterOptions clusterOptions = new ClusterOptions(Project, outputDir, 5, true, 90, true);//TODO validate its in seconds for all file types
Propheus propheus = new Propheus(dbOptions, Project);
dbOptions.SaveMS1Peaks = false;
dbOptions.SaveMSMSPeaks = true;
dbOptions.LoadSpectraIfFound = true;
dbOptions.NbPSMToKeep = 10;
propheus.Preload(false, false);
propheus.PrepareQueries();
//First pass (used to optimize parameters and score weights)
Result tmp = propheus.SearchLatestVersion(propheus.AllQueries, false);
//Compute number of Moded (Pionylated peptides) at given Ms tolerance
long nbPsmDecoy = 0;
long nbPsmTarget = 0;
double avgShift = 0;
foreach (Query query in tmp.queries)
{
foreach (PeptideSpectrumMatch psm in query.psms)
{
if (string.IsNullOrEmpty(psm.Peptide.VariableModificationsInString))
{
nbPsmTarget++;
avgShift += psm.PrecursorMzError;
}
else
{
nbPsmDecoy++;
}
}
}
avgShift /= (double)nbPsmTarget;
dbOptions.ConSole.WriteLine("Average shift : " + avgShift);
//tmp.WriteInfoToCsv(true);
//tmp.Export(0.02, "FirstPass_02_");
}
public static void Launch()//Trinity.UnitTest.SettePeptideSample.Launch()
{
string outputDir = @"C:\_IRIC\DATA\Test\testRTMHC\";
string fastaFile = @"C:\_IRIC\DATA\MHC Sette\MHC_Sette_Peptides_20091001.fasta";
string projectFile = //@"G:\Thibault\-=Proteomics_Raw_Data=-\ELITE\AUG06_2013\RT_MHC\Project_TEST_600mM.csv";
@"G:\Thibault\-=Proteomics_Raw_Data=-\ELITE\MAR26_2013\Project_NonFAIMS.csv";
// @"G:\Thibault\-=Proteomics_Raw_Data=-\ELITE\SEP10_2013\Project_TEST_75_100_300mM.csv";
DBOptions dbOptions = new DBOptions(fastaFile);
try
{
Samples Project = new Samples(projectFile, 0, dbOptions);
dbOptions.precursorMassTolerance = new MassTolerance(5, MassToleranceUnits.ppm);
dbOptions.productMassTolerance = new MassTolerance(0.068, MassToleranceUnits.Da);//0.034 is a 60 000 resolution over 2000 range in mz
dbOptions.MaximumPeptideMass = 200000;
dbOptions.OutputFolder = outputDir;
ProteaseDictionary proteases = ProteaseDictionary.Instance;
dbOptions.DigestionEnzyme = proteases["no enzyme"];
dbOptions.NoEnzymeSearch = false;
dbOptions.ToleratedMissedCleavages = 20;// 2;
GraphML_List <Modification> fixMods = new GraphML_List <Modification>();
//fixMods.Add(ModificationDictionary.Instance["carbamidomethylation of C"]);
dbOptions.fixedModifications = fixMods;
GraphML_List <Modification> varMods = new GraphML_List <Modification>();
varMods.Add(ModificationDictionary.Instance["oxidation of M"]); //+ Deamidation M Q
varMods.Add(ModificationDictionary.Instance["phosphorylation of S"]);
varMods.Add(ModificationDictionary.Instance["phosphorylation of T"]);
varMods.Add(ModificationDictionary.Instance["phosphorylation of Y"]); //*/
varMods.Add(ModificationDictionary.Instance["deamidation of N"]);
varMods.Add(ModificationDictionary.Instance["deamidation of Q"]);
varMods.Add(ModificationDictionary.Instance["cysteinylation of C"]);
dbOptions.variableModifications = varMods;
dbOptions.maximumVariableModificationIsoforms = 1024;// 2 * (varMods.Count + fixMods.Count);//TODO Evaluate the viability of this parameter
dbOptions.PSMFalseDiscoveryRate = 0.05;
dbOptions.addFragmentMods = false;
dbOptions.addFragmentLoss = false;
dbOptions.fragments = new Fragments();
dbOptions.fragments.Add(new FragmentB());
dbOptions.fragments.Add(new FragmentY());
dbOptions.MinimumPrecursorIntensityRatioInIsolationWindow = 0.05;
Propheus propheus = new Propheus(dbOptions, Project);
dbOptions.SaveMS1Peaks = true;
dbOptions.SaveMSMSPeaks = true;
dbOptions.LoadSpectraIfFound = true;
propheus.Preload(true);
propheus.PrepareQueries();
}
catch (Exception ex)
{
dbOptions.ConSole.WriteLine("Error in SettePeptideSample : " + ex.Message);
dbOptions.ConSole.WriteLine(ex.StackTrace);
}
}
public static void Launch(IConSol console)
{
//@"G:\Thibault\Olivier\MnR\Databases\BD_RefGenome_WithReverse_2012-06-20.fasta";
//Trypsin
string outputDir = @"C:\_IRIC\DATA\Yeast\Results\";
string fastaFile = @"C:\_IRIC\DATA\Yeast\Yeast_SwissProt.fasta";//Yeast
//@"G:\Thibault\Olivier\MQ_vs_Morpheus\Yeast_SwissProt.fasta";//Yeast
//@"G:\Thibault\Olivier\Databases\SProHNoIso_20130430\current\sequences_2013-05-30.fa";
//G:\Thibault\Olivier\MnR\Databases\mini_human_reference_2013-26-03.fasta";//Yeast
string projectFile = @"C:\_IRIC\DATA\Yeast\project.csv";//Yeast
//@"G:\Thibault\Olivier\MQ_vs_Morpheus\project.csv";//Yeast
//@"G:\Thibault\-=Proteomics_Raw_Data=-\ELITE\JAN22_2013\_Project_FL_Single.csv";
//G:\Thibault\-=Proteomics_Raw_Data=-\ELITE\JUN27_2012\MR 4Rep DS\MassSense\_Test_ProjectFile_MF3.csv";
//G:\Thibault\-=Proteomics_Raw_Data=-\ELITE\MAR18_2013\ProjectFile_TestForProPheus.csv";
DBOptions dbOptions = new DBOptions(fastaFile, console);
Samples Project = new Samples(projectFile, 0, dbOptions);
dbOptions.precursorMassTolerance = new MassTolerance(8 /*8*//*8withoutisotopes*/, MassToleranceUnits.ppm);
dbOptions.productMassTolerance = new MassTolerance(0.034 /*0.034*//*without isotopes*/, MassToleranceUnits.Da);//0.034 is a 60 000 resolution over 2000 range in mz
//dbOptions.productMassTolerance = new MassTolerance(20, MassToleranceUnits.ppm);
dbOptions.MaximumPeptideMass = 200000;
dbOptions.OutputFolder = outputDir;
ProteaseDictionary proteases = ProteaseDictionary.Instance;
dbOptions.DigestionEnzyme = proteases["trypsin (no proline rule)"]; //"no enzyme"];
dbOptions.NoEnzymeSearch = false; // true;
dbOptions.DecoyFusion = false;
//dbOptions.protease = proteases["trypsin (no proline rule)"];
dbOptions.ToleratedMissedCleavages = 2;
dbOptions.MinimumPeptideLength = 5;
dbOptions.MaximumPeptideLength = 300;
GraphML_List <Modification> fixMods = new GraphML_List <Modification>();
fixMods.Add(ModificationDictionary.Instance["carbamidomethylation of C"]);
dbOptions.fixedModifications = fixMods;
GraphML_List <Modification> varMods = new GraphML_List <Modification>();
//Oxidation (M);Acetyl (Protein N-term);Phospho (STY)
//Mods for Yeast
varMods.Add(ModificationDictionary.Instance["oxidation of M"]);
varMods.Add(ModificationDictionary.Instance["acetylation of protein N-terminus"]);
varMods.Add(ModificationDictionary.Instance["phosphorylation of S"]);
varMods.Add(ModificationDictionary.Instance["phosphorylation of T"]);
varMods.Add(ModificationDictionary.Instance["phosphorylation of Y"]); //*/
dbOptions.maximumVariableModificationIsoforms = 2 * (varMods.Count + fixMods.Count); //TODO Evaluate the viability of this parameter
dbOptions.variableModifications = varMods;
dbOptions.NbPSMToKeep = 16;
dbOptions.addFragmentLoss = false;
dbOptions.addFragmentMods = false;
dbOptions.fragments = new Fragments();
dbOptions.fragments.Add(new FragmentA());
dbOptions.fragments.Add(new FragmentB());
dbOptions.fragments.Add(new FragmentC());
dbOptions.fragments.Add(new FragmentX());
dbOptions.fragments.Add(new FragmentY());
dbOptions.fragments.Add(new FragmentZ());
dbOptions.dProduct = 0.0;
dbOptions.dPrecursor = 0.1; // 0.12;
dbOptions.dMatchingProductFraction = 0.8; // 0.45;
dbOptions.dMatchingProduct = 0.0; // 0.5;
dbOptions.dIntensityFraction = 0.1; // 45;// 0.0;//0.13;
dbOptions.dIntensity = 0;
dbOptions.dProtein = 0;
dbOptions.dPeptideScore = 0.0; // 0.3;
dbOptions.dFragmentScore = 0.0; // 0.5;
//ClusterOptions clusterOptions = new ClusterOptions(Project, outputDir, 5, true, 90, true);//TODO validate its in seconds for all file types
dbOptions.SaveMS1Peaks = true;
dbOptions.SaveMSMSPeaks = true;
dbOptions.LoadSpectraIfFound = true;
Propheus propheus = new Propheus(dbOptions, Project);
propheus.Preload(false, false);
propheus.PrepareQueries();
//To beat : 4653 (MaxQuant) Psm at 2%FDR
//First pass (used to optimize parameters and score weights)
Result tmp = propheus.SearchLatestVersion(propheus.AllQueries, true, false);//, 1.0, false, false, null);
tmp.WriteInfoToCsv(true);
tmp.Export(0.02, "FirstPass_02_");
//Second search
propheus.Preload(true);
propheus.PrepareQueries();
Result finalRez = propheus.SearchLatestVersion(propheus.AllQueries, false);//, 1.0, false, false, null);
//tmp.Export(0.05, "05_");
tmp.Export(0.02, "02_");
//tmp.Export(0.05, "05_AllFragments");
// tmp.Export(0.01, "01_");
//tmp.Export(double.MaxValue, "All_");
//tmp.WriteInfoToConsole();
/*
* Optimizer op = new Optimizer(propheus);
* op.LaunchBestPSMOptimization(tmp);//.proteins, propheus.AllQueries);
* //*/
//Optimizer op = new Optimizer(propheus);
//MSSearcher.Export(dbOptions.outputFolder + "5PercentOptimized_precursors.csv", Optimizer.PrecursorOptimizer(tmp.precursors, 0.05));
//op.LaunchBestPSMOptimization(tmp);//.proteins, propheus.AllQueries);
//op.LaunchPrecursorScoreOptimization(tmp);//.proteins, propheus.AllQueries);
//op.Launch(tmp.proteins, propheus.AllQueries);
/*
* propheus.Align(tmp);
*
* Result tmp2 = propheus.Search(1.0, false, null, propheus.CreateQueries(propheus.AllSpectras));
* tmp2.Export(0.05, "Aligned_05_");
* tmp2.Export(double.MaxValue, "Aligned_All_");
* MSSearcher.Export(dbOptions.outputFolder + "Aligned_5PercentOptimized_precursors.csv", Optimizer.PrecursorOptimizer(tmp2.precursors, 0.05));
* tmp.WriteInfoToConsole();//*/
}
public static void Launch()//Trinity.UnitTest.SettePeptideSample.Launch()
{
string outputDir = @"C:\_IRIC\DATA\Test\testMHCSette\";
string fastaFile = @"C:\_IRIC\DATA\MHC Sette\MHC_Sette_Peptides_20091001.fasta";
string projectFile = @"G:\Thibault\-=Proteomics_Raw_Data=-\ELITE\JUL03_2013\ProjectFile_SETTEpep_OneRAW.csv";
DBOptions dbOptions = new DBOptions(fastaFile);
try
{
Samples Project = new Samples(projectFile, 0, dbOptions);
dbOptions.precursorMassTolerance = new MassTolerance(5, MassToleranceUnits.ppm);
dbOptions.productMassTolerance = new MassTolerance(0.068, MassToleranceUnits.Da);//0.034 is a 60 000 resolution over 2000 range in mz
dbOptions.MaximumPeptideMass = 200000;
dbOptions.OutputFolder = outputDir;
ProteaseDictionary proteases = ProteaseDictionary.Instance;
dbOptions.DigestionEnzyme = proteases["no enzyme"];
dbOptions.NoEnzymeSearch = false;
dbOptions.ToleratedMissedCleavages = 20;// 2;
GraphML_List <Modification> fixMods = new GraphML_List <Modification>();
//fixMods.Add(ModificationDictionary.Instance["carbamidomethylation of C"]);
dbOptions.fixedModifications = fixMods;
GraphML_List <Modification> varMods = new GraphML_List <Modification>();
varMods.Add(ModificationDictionary.Instance["oxidation of M"]); //+ Deamidation M Q
varMods.Add(ModificationDictionary.Instance["phosphorylation of S"]);
varMods.Add(ModificationDictionary.Instance["phosphorylation of T"]);
varMods.Add(ModificationDictionary.Instance["phosphorylation of Y"]); //*/
varMods.Add(ModificationDictionary.Instance["deamidation of N"]);
varMods.Add(ModificationDictionary.Instance["deamidation of Q"]);
varMods.Add(ModificationDictionary.Instance["cysteinylation of C"]);
dbOptions.variableModifications = varMods;
dbOptions.maximumVariableModificationIsoforms = 1024;// 2 * (varMods.Count + fixMods.Count);//TODO Evaluate the viability of this parameter
dbOptions.PSMFalseDiscoveryRate = 0.05;
dbOptions.addFragmentMods = false;
dbOptions.addFragmentLoss = false;
dbOptions.fragments = new Fragments();
// dbOptions.fragments.Add(new FragmentA());
dbOptions.fragments.Add(new FragmentB());
// dbOptions.fragments.Add(new FragmentC());
// dbOptions.fragments.Add(new FragmentX());
dbOptions.fragments.Add(new FragmentY());
// dbOptions.fragments.Add(new FragmentZ());
//ClusterOptions clusterOptions = new ClusterOptions(Project, outputDir, 5, true, 90, true);//TODO validate its in seconds for all file types
Propheus propheus = new Propheus(dbOptions, Project);
dbOptions.SaveMS1Peaks = false;
dbOptions.SaveMSMSPeaks = false;
dbOptions.LoadSpectraIfFound = true;
propheus.Preload(true);
propheus.PrepareQueries();
//First pass (used to optimize parameters and score weights)
Result tmp = propheus.SearchVersionAugust2013(propheus.AllQueries, true);//, 1.0, false, false, null);
tmp.WriteInfoToCsv(true);
tmp.Export(0.02, "FirstPass_02_");
dbOptions.SaveMS1Peaks = true;
dbOptions.SaveMSMSPeaks = true;
//Second search
propheus.Preload(true);
propheus.PrepareQueries();
Result finalRez = propheus.SearchLatestVersion(propheus.AllQueries, false);//, 1.0, false, false, null);
//tmp.Export(0.05, "05_");
tmp.Export(0.02, "02_");
//tmp.Export(1.0, "All_");
//UnitTest.Tests.MatchAllFragments(tmp);
//tmp.WriteInfoToConsole();
//tmp.Save();
/*
* Optimizer op = new Optimizer(propheus);
* op.LaunchBestPSMOptimization(tmp);
* op.LaunchPrecursorScoreOptimization(tmp);
* /*
* propheus.Align(tmp);
*
* Result tmp2 = propheus.Search(1.0, false, null, propheus.CreateQueries(propheus.AllSpectras));
* tmp2.Export(0.05, "Aligned_05_");
* tmp2.Export(0.02, "Aligned_02_");
* tmp2.Export(double.MaxValue, "Aligned_All_");
* MSSearcher.Export(dbOptions.outputFolder + "Aligned_5PercentOptimized_precursors.csv", Optimizer.PrecursorOptimizer(tmp2.precursors, 0.05));
* tmp2.WriteInfoToConsole();//*/
}
catch (Exception ex)
{
dbOptions.ConSole.WriteLine("Error in SettePeptideSample : " + ex.Message);
dbOptions.ConSole.WriteLine(ex.StackTrace);
}
}