private static void LoadModifications()
{
_AllModsKnown = new List <Modification>();
_AllModTypesKnown = new HashSet <string>();
ErrorsReadingMods = new List <string>();
AllModsKnownDictionary = new Dictionary <string, Modification>();
UnimodDeserialized = Loaders.LoadUnimod(Path.Combine(DataDir, @"Data", @"unimod.xml")).ToList();
PsiModDeserialized = Loaders.LoadPsiMod(Path.Combine(DataDir, @"Data", @"PSI-MOD.obo.xml"));
var formalChargesDictionary = Loaders.GetFormalChargesDictionary(PsiModDeserialized);
UniprotDeseralized = Loaders.LoadUniprot(Path.Combine(DataDir, @"Data", @"ptmlist.txt"), formalChargesDictionary).ToList();
foreach (var modFile in Directory.GetFiles(Path.Combine(DataDir, @"Mods")))
{
AddMods(PtmListLoader.ReadModsFromFile(modFile, out var errorMods), false);
}
AddMods(UniprotDeseralized.OfType <Modification>(), false);
AddMods(UnimodDeserialized.OfType <Modification>(), false);
foreach (Modification mod in AllModsKnown)
{
if (!AllModsKnownDictionary.ContainsKey(mod.IdWithMotif))
{
AllModsKnownDictionary.Add(mod.IdWithMotif, mod);
}
// no error thrown if multiple mods with this ID are present - just pick one
}
ProteaseMods = UsefulProteomicsDatabases.PtmListLoader.ReadModsFromFile(Path.Combine(DataDir, @"Mods", @"ProteaseMods.txt"), out var errors).ToList();
ProteaseDictionary.Dictionary = ProteaseDictionary.LoadProteaseDictionary(Path.Combine(DataDir, @"ProteolyticDigestion", @"proteases.tsv"), ProteaseMods);
}
public static DBOptions GetDBOptions(bool loadFromRaw, bool onlyYions, IConSol console)
{
string outputDir = @"C:\_IRIC\DATA\Test\testNB\Iso3\";
string fastaFile = @"C:\_IRIC\Data\NB\peptide.fasta";
DBOptions dbOptions = new DBOptions(fastaFile, console);
dbOptions.precursorMassTolerance = new MassTolerance(8 /*8*//*8withoutisotopes*/, MassToleranceUnits.ppm);
dbOptions.productMassTolerance = new MassTolerance(20 /*8*//*8withoutisotopes*/, MassToleranceUnits.ppm);
//dbOptions.productMassTolerance = new MassTolerance(0.05/*0.034*//*without isotopes*/, 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"]; //trypsin (no proline rule)"];
dbOptions.NoEnzymeSearch = false; // true;
dbOptions.DecoyFusion = false;
dbOptions.MaximumNumberOfFragmentsPerSpectrum = 400;
//dbOptions.protease = proteases["trypsin (no proline rule)"];
dbOptions.ToleratedMissedCleavages = 200;// 2;
dbOptions.MinimumPeptideLength = 5;
dbOptions.MaximumPeptideLength = 300;
GraphML_List <Modification> fixMods = new GraphML_List <Modification>();
//fixMods.Add(ModificationDictionary.Instance["propionylation of K"]);
dbOptions.fixedModifications = fixMods;
GraphML_List <Modification> varMods = new GraphML_List <Modification>();
varMods.Add(ModificationDictionary.Instance["acetylation of K"]);
varMods.Add(ModificationDictionary.Instance["propionylation of K"]);
dbOptions.maximumVariableModificationIsoforms = 1024;
dbOptions.variableModifications = varMods;
dbOptions.addFragmentLoss = false; // true;
dbOptions.addFragmentMods = false; // true;
dbOptions.fragments = new Fragments();
if (!onlyYions)
{
dbOptions.fragments.Add(new FragmentA());
dbOptions.fragments.Add(new FragmentB());
dbOptions.fragments.Add(new FragmentC());
dbOptions.fragments.Add(new FragmentX());
dbOptions.fragments.Add(new FragmentZ());
}
dbOptions.fragments.Add(new FragmentY());
dbOptions.SaveMS1Peaks = true;
dbOptions.SaveMSMSPeaks = true;
dbOptions.LoadSpectraIfFound = !loadFromRaw;
dbOptions.NbPSMToKeep = 100;
return(dbOptions);
}
private DBOptions CreateOptions(string fastaFile, string outputFolder, IConSol consol)
{
DBOptions dbOptions = new DBOptions(fastaFile, consol);
dbOptions.precursorMassTolerance = new MassTolerance(precTolPpm, MassToleranceUnits.ppm);
dbOptions.productMassTolerance = new MassTolerance(prodTolPpm, MassToleranceUnits.ppm);
dbOptions.MaximumPeptideMass = 200000;
dbOptions.OutputFolder = outputFolder;
ProteaseDictionary proteases = ProteaseDictionary.Instance;
dbOptions.DigestionEnzyme = proteases["no enzyme"];
//dbOptions.DigestionEnzyme = proteases["top-down"];
dbOptions.NoEnzymeSearch = false;
dbOptions.DecoyFusion = false;
dbOptions.MaximumNumberOfFragmentsPerSpectrum = 400;
dbOptions.ToleratedMissedCleavages = 200;
dbOptions.MinimumPeptideLength = 5;
dbOptions.MaximumPeptideLength = 300;
GraphML_List <Modification> fixMods = new GraphML_List <Modification>();
dbOptions.fixedModifications = fixMods;
GraphML_List <Modification> varMods = new GraphML_List <Modification>();
foreach (string strMod in ModificationDictionary.Instance.Keys)
{
varMods.Add(ModificationDictionary.Instance[strMod]);
}
dbOptions.maximumVariableModificationIsoforms = 1024;
dbOptions.variableModifications = varMods;
dbOptions.addFragmentLoss = false;
dbOptions.addFragmentMods = false;//Gives very bad results... might by off
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.SaveMS1Peaks = true;
dbOptions.SaveMSMSPeaks = true;
dbOptions.LoadSpectraIfFound = true;
dbOptions.NbPSMToKeep = 100;
return(dbOptions);
}
public static void ProteaseLoader()
{
string path1 = Path.Combine(TestContext.CurrentContext.TestDirectory, "ProteaseFilesForLoadingTests", "TestProteases_badMod.tsv");
string path2 = Path.Combine(TestContext.CurrentContext.TestDirectory, "ProteaseFilesForLoadingTests", "TestProteases_badMod_dupName.tsv");
string path3 = Path.Combine(TestContext.CurrentContext.TestDirectory, "ProteaseFilesForLoadingTests", "TestProteases_dupName.tsv");
string path4 = Path.Combine(TestContext.CurrentContext.TestDirectory, "ProteaseFilesForLoadingTests", "TestProteases_Mod_dupName.tsv");
var proteaseMods = PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "ModificationTests", "ProteaseMods.txt"), out var errors).ToList();
Assert.Throws <MzLibUtil.MzLibException>(() => ProteaseDictionary.LoadProteaseDictionary(path1, proteaseMods));
Assert.Throws <MzLibUtil.MzLibException>(() => ProteaseDictionary.LoadProteaseDictionary(path2, proteaseMods));
Assert.Throws <MzLibUtil.MzLibException>(() => ProteaseDictionary.LoadProteaseDictionary(path3, proteaseMods));
Assert.Throws <MzLibUtil.MzLibException>(() => ProteaseDictionary.LoadProteaseDictionary(path4, proteaseMods));
}
public static DBOptions CreateOptions(string outputDir)
{
//@"G:\Thibault\Olivier\MnR\Databases\BD_RefGenome_WithReverse_2012-06-20.fasta";
string fastaFile = @"C:\_IRIC\DATA\MHC\human_reference_2013-26-03.fasta";// Ref genome
//@"C:\_IRIC\DATA\Test\testMHC\MHC_Sette_Peptides_20091001.fasta";//Sette Peptides
//C:\_IRIC\DATA\MHC\4468.fasta";//MnR\Mixed_M_2013-21-01.fasta";//MHC M One sample
DBOptions dbOptions = new DBOptions(fastaFile);
dbOptions.precursorMassTolerance = new MassTolerance(8 /*8withoutisotopes*/, MassToleranceUnits.ppm);
dbOptions.productMassTolerance = new MassTolerance(0.05 /*without isotopes*/, 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 = true;
dbOptions.ToleratedMissedCleavages = 20;// 2;
GraphML_List <Modification> fixMods = new GraphML_List <Modification>();
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 = 0.01;
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());
return(dbOptions);
}
public static void ReadCustomFile()
{
Protein ParentProtein = new Protein("OKAREDY", "accession1");
string path = Path.Combine(TestContext.CurrentContext.TestDirectory, "DoubleProtease.tsv");
Assert.That(File.Exists(path));
var proteaseDict = ProteaseDictionary.LoadProteaseDictionary(path);
Assert.That(proteaseDict.ContainsKey("Test1"));
Assert.That(proteaseDict.ContainsKey("Test2"));
Assert.That(proteaseDict.ContainsKey("Test3"));
ProteaseDictionary.Dictionary.Add("Test1", proteaseDict["Test1"]);
DigestionParams multiProtease1 = new DigestionParams(protease: "Test1", maxMissedCleavages: 0, minPeptideLength: 1, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain);
var digestedList1 = ParentProtein.Digest(multiProtease1, new List <Modification>(), new List <Modification>()).ToList();
ProteaseDictionary.Dictionary.Remove("Test1");
var sequences = digestedList1.Select(p => p.BaseSequence).ToList();
Assert.That(sequences.Count == 3);
Assert.That(sequences.Contains("OK"));
Assert.That(sequences.Contains("A"));
Assert.That(sequences.Contains("REDY"));
ProteaseDictionary.Dictionary.Add("Test2", proteaseDict["Test2"]);
DigestionParams multiProtease2 = new DigestionParams(protease: "Test2", maxMissedCleavages: 0, minPeptideLength: 1, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain);
var digestedList2 = ParentProtein.Digest(multiProtease2, new List <Modification>(), new List <Modification>()).ToList();
ProteaseDictionary.Dictionary.Remove("Test2");
var sequences2 = digestedList2.Select(p => p.BaseSequence).ToList();
Assert.That(sequences2.Count == 3);
Assert.That(sequences2.Contains("OK"));
Assert.That(sequences2.Contains("ARED"));
Assert.That(sequences2.Contains("Y"));
ProteaseDictionary.Dictionary.Add("Test3", proteaseDict["Test3"]);
DigestionParams multiProtease3 = new DigestionParams(protease: "Test3", maxMissedCleavages: 0, minPeptideLength: 1, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain);
var digestedList3 = ParentProtein.Digest(multiProtease3, new List <Modification>(), new List <Modification>()).ToList();
ProteaseDictionary.Dictionary.Remove("Test3");
var sequences3 = digestedList3.Select(p => p.BaseSequence).ToList();
Assert.That(sequences3.Count == 2);
Assert.That(sequences3.Contains("OK"));
Assert.That(sequences3.Contains("AREDY"));
}
public static void ProteaseModTest()
{
Loaders.LoadElements();
string subFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"DigestionTest");
Directory.CreateDirectory(subFolder);
string databasePath1 = Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", "ProteaseModTest.fasta");
var protDic = ProteaseDictionary.LoadProteaseDictionary(Path.Combine(GlobalVariables.DataDir, @"ProteolyticDigestion", @"proteases.tsv"), GlobalVariables.ProteaseMods);
DigestionParams param = new DigestionParams(protease: "CNBr", maxMissedCleavages: 0);
var proteinList = ProteinDbLoader.LoadProteinFasta(databasePath1, true, DecoyType.None, false, out List <string> errors);
var protein = proteinList[0];
var peptides = protein.Digest(param, new List <Modification>(), new List <Modification>()).ToList();
Assert.AreEqual(2, peptides.Count());
Assert.AreNotEqual(peptides[0].FullSequence, peptides[1].FullSequence);
Assert.AreEqual(882.39707781799996, peptides[0].MonoisotopicMass);
Assert.AreEqual(930.400449121, peptides[1].MonoisotopicMass);
}
// Status log stuff
public SettingsForAnalysis(string name)
{
this.Name = name;
this.fixedModifications = new List <Modification>();
this.variableModifications = new List <Modification>();
this.Adducts = new List <Adduct>();
this.Polymers = new List <Polymer>();
ProteaseDictionary proteases = null;
try
{
proteases = ProteaseDictionary.Instance;
_proteases = proteases.Values.ToArray();
}
catch
{
//MessageBox.Show("Your proteases file (" + Path.Combine(Path.GetDirectoryName(Environment.GetCommandLineArgs()[0]), "Morpheus\\proteases.tsv") + ") is likely corrupt. Please correct it. Program will now exit.");
//Application.Exit();
}
}
public static DBOptions CreateOptions()
{
DBOptions dbOptions = new DBOptions("");
dbOptions.precursorMassTolerance = new MassTolerance(8 /*8withoutisotopes*/, MassToleranceUnits.ppm);
dbOptions.productMassTolerance = new MassTolerance(0.034 /*without isotopes*/, MassToleranceUnits.Da);//0.034 is a 60 000 resolution over 2000 range in mz
dbOptions.MaximumPeptideMass = 20000;
dbOptions.OutputFolder = "";
ProteaseDictionary proteases = ProteaseDictionary.Instance;
dbOptions.DigestionEnzyme = proteases["no enzyme"];
dbOptions.ToleratedMissedCleavages = 20000;
GraphML_List <Modification> fixMods = new GraphML_List <Modification>();
dbOptions.fixedModifications = fixMods;
GraphML_List <Modification> varMods = new GraphML_List <Modification>();
dbOptions.variableModifications = varMods;
dbOptions.maximumVariableModificationIsoforms = 2 * (varMods.Count + fixMods.Count);//TODO Evaluate the viability of this parameter
dbOptions.MinimumPeptideLength = 4;
return(dbOptions);
}
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);
}
}
static GlobalVariables()
{
ProteaseGuruVersion = typeof(GlobalVariables).Assembly.GetName().Version.ToString();
if (ProteaseGuruVersion.Equals("1.0.0.0"))
{
#if DEBUG
ProteaseGuruVersion = "Not a release version. DEBUG.";
#else
ProteaseGuruVersion = "0.0.23";
#endif
}
else
{
// AppVeyor appends the build number
// this is intentional; it's to avoid conflicting AppVeyor build numbers
// trim the build number off the version number for displaying/checking versions, etc
var foundIndexes = new List <int>();
for (int i = 0; i < ProteaseGuruVersion.Length; i++)
{
if (ProteaseGuruVersion[i] == '.')
{
foundIndexes.Add(i);
}
}
ProteaseGuruVersion = ProteaseGuruVersion.Substring(0, foundIndexes.Last());
}
{
var pathToProgramFiles = Environment.GetFolderPath(Environment.SpecialFolder.ProgramFiles);
if (!String.IsNullOrWhiteSpace(pathToProgramFiles) && AppDomain.CurrentDomain.BaseDirectory.Contains(pathToProgramFiles) && !AppDomain.CurrentDomain.BaseDirectory.Contains("Jenkins"))
{
DataDir = Path.Combine(Environment.GetFolderPath(Environment.SpecialFolder.LocalApplicationData), "ProteaseGuru");
}
else
{
DataDir = AppDomain.CurrentDomain.BaseDirectory;
}
}
ElementsLocation = Path.Combine(DataDir, @"Data", @"elements.dat");
UsefulProteomicsDatabases.Loaders.LoadElements();
UnimodDeserialized = UsefulProteomicsDatabases.Loaders.LoadUnimod(Path.Combine(DataDir, @"Data", @"unimod.xml")).ToList();
PsiModDeserialized = UsefulProteomicsDatabases.Loaders.LoadPsiMod(Path.Combine(DataDir, @"Data", @"PSI-MOD.obo.xml"));
var formalChargesDictionary = UsefulProteomicsDatabases.Loaders.GetFormalChargesDictionary(PsiModDeserialized);
UniprotDeseralized = UsefulProteomicsDatabases.Loaders.LoadUniprot(Path.Combine(DataDir, @"Data", @"ptmlist.txt"), formalChargesDictionary).ToList();
foreach (var modFile in Directory.GetFiles(Path.Combine(DataDir, @"Mods")))
{
AddMods(UsefulProteomicsDatabases.PtmListLoader.ReadModsFromFile(modFile, out var errorMods), false);
}
AddMods(UniprotDeseralized.OfType <Modification>(), false);
AddMods(UnimodDeserialized.OfType <Modification>(), false);
// populate dictionaries of known mods/proteins for deserialization
AllModsKnownDictionary = new Dictionary <string, Modification>();
foreach (Modification mod in AllModsKnown)
{
if (!AllModsKnownDictionary.ContainsKey(mod.IdWithMotif))
{
AllModsKnownDictionary.Add(mod.IdWithMotif, mod);
}
// no error thrown if multiple mods with this ID are present - just pick one
}
ProteaseMods = UsefulProteomicsDatabases.PtmListLoader.ReadModsFromFile(Path.Combine(DataDir, @"Mods", @"ProteaseMods.txt"), out var errors).ToList();
ProteaseDictionary.Dictionary = ProteaseDictionary.LoadProteaseDictionary(Path.Combine(DataDir, @"ProteolyticDigestion", @"proteases.tsv"), ProteaseMods);
RefreshAminoAcidDictionary();
}
/// <summary>
/// Creates the options used through the system for peptide identification
/// </summary>
/// <param name="fastaFile"></param>
/// <param name="outputFolder"></param>
/// <param name="consol"></param>
/// <returns></returns>
public static DBOptions CreateOptions(string fastaFile, string outputFolder, double precTolPpm, double prodTolDa, IConSol consol)
{
DBOptions dbOptions = new DBOptions(fastaFile, consol);
dbOptions.precursorMassTolerance = new MassTolerance(precTolPpm, MassToleranceUnits.ppm);
dbOptions.productMassTolerance = new MassTolerance(prodTolDa, MassToleranceUnits.Da);
dbOptions.MaximumPeptideMass = 200000;
dbOptions.OutputFolder = outputFolder;
ProteaseDictionary proteases = ProteaseDictionary.Instance;
dbOptions.DigestionEnzyme = proteases["no enzyme"];
//dbOptions.DigestionEnzyme = proteases["top-down"];
dbOptions.NoEnzymeSearch = false;
dbOptions.DecoyFusion = false;
dbOptions.MaximumNumberOfFragmentsPerSpectrum = 400;
dbOptions.ToleratedMissedCleavages = 200;
dbOptions.MinimumPeptideLength = 5;
dbOptions.MaximumPeptideLength = 300;
List <Modification> fixMods = new List <Modification>();
dbOptions.fixedModifications = fixMods;
List <Modification> varMods = new List <Modification>();
foreach (string strMod in ModificationDictionary.Instance.Keys)
{
varMods.Add(ModificationDictionary.Instance[strMod]);
}
dbOptions.maximumVariableModificationIsoforms = 4096;// 2048;// 1024;
dbOptions.variableModifications = varMods;
dbOptions.addFragmentLoss = false;
dbOptions.addFragmentMods = false;
dbOptions.SaveMS1Peaks = true;
dbOptions.SaveMSMSPeaks = true;
dbOptions.LoadSpectraIfFound = true;
dbOptions.NbPSMToKeep = 16;
dbOptions.fullFragment = new FullFragments(false);//true by default
//18 Mars 2014 Uptimized scores
dbOptions.dProduct = 0.0917981081138356;
dbOptions.dPrecursor = 0.345789190542786;
dbOptions.dMatchingProductFraction = 0.427418045898628;
dbOptions.dMatchingProduct = 0;
dbOptions.dIntensityFraction = 0.429418127252449;
dbOptions.dIntensity = 0;
dbOptions.dProtein = 0.692270441303156;
dbOptions.dPeptideScore = 0.636739763262095;
dbOptions.dFragmentScore = 0.0229058195943506;
/*
* dbOptions.dProduct = 0.0886869235377232;
* dbOptions.dPrecursor = 0.714634842572098;
* dbOptions.dMatchingProductFraction = 0.432872176371921;
* dbOptions.dMatchingProduct = 0.00492531899592156;
* dbOptions.dIntensityFraction = 0.73908941342453;
* dbOptions.dIntensity = 0;// 0.687398171372431;
* dbOptions.dProtein = 0.574124578188231;
* dbOptions.dPeptideScore = 0.315866923572434;
* dbOptions.dFragmentScore = 0.0322849750669137;//*/
/*
* dbOptions.dProduct = 0.0;
* dbOptions.dPrecursor = 0.12;
* dbOptions.dMatchingProductFraction = 0.45;
* dbOptions.dMatchingProduct = 0;// 0;
* dbOptions.dIntensityFraction = 0.13;
* dbOptions.dIntensity = 0;
* dbOptions.dProtein = 0;
* dbOptions.dPeptideScore = 0.3;
* dbOptions.dFragmentScore = 0.0;//*/
/*
* //Morpheus original score
* dbOptions.dProduct = 1.0;
* dbOptions.dPrecursor = 0;
* dbOptions.dMatchingProductFraction = 0;
* dbOptions.dMatchingProduct = 0;
* dbOptions.dIntensityFraction = 1;
* dbOptions.dIntensity = 0;
* dbOptions.dProtein = 0;
* dbOptions.dPeptideScore = 0;
* dbOptions.dFragmentScore = 0.0;//*/
return(dbOptions);
}
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(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 UIsettings()//SettingsForAnalysis analysisSettings)
{
//this.analysisSettings = analysisSettings;
this.informationKey = new BindingList <InformationKey>();
this.rawFiles = new BindingList <RawFileName>();
this.codeNames = new BindingList <CodeName>();
this.UserList = new BindingList <FileNameCategoryRow>();
this.SamplesList = new BindingList <FileNameCategoryRow>();
this.LcList = new BindingList <FileNameCategoryRow>();
this.MsList = new BindingList <FileNameCategoryRow>();
this.statusLogItems = new BindingList <StatusLogItem>();
this.ExternalResults = new BindingList <ExternalResultParseSetting>();
//this.emails = new BindingList<string>();
//this.proteaseList = new BindingList<Protease>();
//this.proteaseList.Clear();
this.initiatorMethionine = (InitiatorMethionineBehavior[])Enum.GetValues(typeof(InitiatorMethionineBehavior));
this.massToleranceUnitsPrecursor = (MassToleranceUnits[])Enum.GetValues(typeof(MassToleranceUnits));
this.massToleranceUnitsProduct = (MassToleranceUnits[])Enum.GetValues(typeof(MassToleranceUnits));
this.massTypePrecursor = (MassType[])Enum.GetValues(typeof(MassType));
this.massTypeProduct = (MassType[])Enum.GetValues(typeof(MassType));
ProteaseDictionary proteases = null;
try
{
proteases = ProteaseDictionary.Instance;
//foreach (Protease protease in proteases.Values)
//{
// proteaseList.Add(protease);
//}
proteaseList = proteases.Values.ToArray();
}
catch
{
//MessageBox.Show("Your proteases file (" + Path.Combine(Path.GetDirectoryName(Environment.GetCommandLineArgs()[0]), "Morpheus\\proteases.tsv") + ") is likely corrupt. Please correct it. Program will now exit.");
//Application.Exit();
}
ModificationDictionary modifications = null;
try
{
modifications = ModificationDictionary.Instance;
this.modificationList1 = new Modification[modifications.Count];
this.modificationList2 = new Modification[modifications.Count];
int i = 0;
foreach (Modification modification in modifications.Values)
{
modificationList1[i] = modification;
modificationList2[i] = modification;
i++;
}
}
catch
{
//MessageBox.Show("Your modifications file (" + Path.Combine(Path.GetDirectoryName(Environment.GetCommandLineArgs()[0]), "modifications.tsv") + ") is likely corrupt. Please correct it.");
}
}
public static void CNBrProteinDigestion()
{
var proteaseMods = PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "ModificationTests", "ProteaseMods.txt"), out var errors).ToList();
var prot = new Protein("PEPTIDEMPEPTIDEM", null);
var prot2 = new Protein("MPEPTIDEMPEPTIDE", null);
string path = Path.Combine(TestContext.CurrentContext.TestDirectory, "DoubleProtease.tsv");
Assert.That(File.Exists(path));
var proteaseDict = ProteaseDictionary.LoadProteaseDictionary(path, proteaseMods);
ProteaseDictionary.Dictionary = ProteaseDictionary.LoadProteaseDictionary(Path.Combine(AppDomain.CurrentDomain.BaseDirectory, "ProteolyticDigestion", "proteases.tsv"), proteaseMods);
var protease1 = proteaseDict["CNBr"];
DigestionParams digestionParams1 = new DigestionParams(
protease: protease1.Name,
maxMissedCleavages: 0,
minPeptideLength: 1,
initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain);
List <Modification> variableModifications1 = new List <Modification>();
var protease2 = proteaseDict["CNBr_old"];
DigestionParams digestionParams2 = new DigestionParams(
protease: protease2.Name,
maxMissedCleavages: 0,
minPeptideLength: 1,
initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain);
List <Modification> variableModifications2 = new List <Modification>();
var protease3 = proteaseDict["CNBr_N"];
DigestionParams digestionParams3 = new DigestionParams(
protease: protease3.Name,
maxMissedCleavages: 0,
minPeptideLength: 1,
initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain);
List <Modification> variableModifications3 = new List <Modification>();
var peps1 = prot.Digest(digestionParams1, new List <Modification>(), variableModifications1).ToList();
var peps2 = prot.Digest(digestionParams2, new List <Modification>(), variableModifications2).ToList();
var peps3 = prot2.Digest(digestionParams3, new List <Modification>(), variableModifications1).ToList();
Assert.AreNotEqual(null, protease3.CleavageMod);
Assert.AreEqual("M", protease3.CleavageMod.Target.ToString());
Assert.AreNotEqual(peps3[0].MonoisotopicMass, peps3[1].MonoisotopicMass);
Assert.AreEqual(882.39707781799996, peps3[1].MonoisotopicMass);
Assert.AreEqual(930.400449121, peps3[0].MonoisotopicMass);
Assert.AreEqual(null, protease2.CleavageMod);
Assert.AreNotEqual(null, protease1.CleavageMod);
Assert.AreEqual("M", protease1.CleavageMod.Target.ToString());
Assert.AreEqual(peps1[1].MonoisotopicMass, peps2[1].MonoisotopicMass);
Assert.AreEqual(peps1[1].MonoisotopicMass, peps2[0].MonoisotopicMass);
Assert.AreEqual(peps2[0].MonoisotopicMass, peps2[1].MonoisotopicMass);
Assert.AreNotEqual(peps1[0].MonoisotopicMass, peps1[1].MonoisotopicMass);
Assert.AreNotEqual(peps1[0].MonoisotopicMass, peps2[0].MonoisotopicMass);
Assert.AreNotEqual(peps1[0].MonoisotopicMass, peps2[1].MonoisotopicMass);
Assert.AreEqual(882.39707781799996, peps1[0].MonoisotopicMass);
Assert.AreEqual(930.400449121, peps1[1].MonoisotopicMass);
}
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);
}
}
//Save all the user provided information in the proteases file for future use
private void SaveCustomProtease_Click(object sender, RoutedEventArgs e)
{
string proteaseDirectory = System.IO.Path.Combine(GlobalVariables.DataDir, @"ProteolyticDigestion");
string proteaseFilePath = System.IO.Path.Combine(proteaseDirectory, @"proteases.tsv");
List <string> proteaseFileText = new List <string>();
proteaseFileText = File.ReadAllLines(proteaseFilePath).ToList();
//all of the protease properties that the user provided
string name = proteaseNameTextBox.Text;
string allCleavageResidues = sequencesInducingCleavageTextBox.Text;
string allResiduesStoppingCleavage = sequencesPreventingCleavageBox.Text;
var cleavageTerminus = (string)cleavageTerminusListBox.SelectedItem;
var cleavageSpecificity = (string)cleavageSpecificityListBox.SelectedItem;
string psiAccession = psiAccessionNumber.Text;
string psiNames = psiName.Text;
//formatting these properties for writing to the protease file, so they can be read in each time ProteaseGuru is used
string proteaseInfo = name + "\t";
var singleCleavageSites = new List <string>();
var singlePreventionSites = new List <string>();
if (allCleavageResidues != "")
{
singleCleavageSites = allCleavageResidues.Split(',').ToList();
}
if (allResiduesStoppingCleavage != "")
{
singlePreventionSites = allResiduesStoppingCleavage.Split(',').ToList();
}
if (cleavageTerminus == "C")
{
string cleavageMotif = "";
var residues = singleCleavageSites.Count();
var count = 1;
foreach (var residue in singleCleavageSites)
{
cleavageMotif += residue;
if (singlePreventionSites.Count() != 0)
{
foreach (var prevent in singlePreventionSites)
{
cleavageMotif += "[" + prevent + "]";
}
}
if (count < residues)
{
cleavageMotif += "|,";
count++;
}
else if (count == residues)
{
cleavageMotif += "|";
}
}
proteaseInfo += cleavageMotif;
}
else if (cleavageTerminus == "N")
{
string cleavageMotif = "";
var residues = singleCleavageSites.Count();
var count = 1;
foreach (var residue in singleCleavageSites)
{
cleavageMotif += "|" + residue;
if (singlePreventionSites.Count() != 0)
{
foreach (var prevent in singlePreventionSites)
{
cleavageMotif += "[" + prevent + "]";
}
}
if (count < residues)
{
cleavageMotif += ",";
count++;
}
}
proteaseInfo += cleavageMotif;
}
if (modName != "")
{
proteaseInfo += "\t" + "\t" + "\t" + cleavageSpecificity + "\t" + psiAccession + "\t" + psiNames + "\t" + "\t" + modName;
}
else
{
proteaseInfo += "\t" + "\t" + "\t" + cleavageSpecificity + "\t" + psiAccession + "\t" + psiNames + "\t" + "\t";
}
proteaseFileText.Add(proteaseInfo);
File.WriteAllLines(proteaseFilePath, proteaseFileText);
ProteaseDictionary.Dictionary = ProteaseDictionary.LoadProteaseDictionary(proteaseFilePath, GlobalVariables.ProteaseMods);
proteaseAdded = true;
}
