/// <summary>
/// Finds the XIC based on the m/z and scan parameters.
/// </summary>
/// <param name="mz"></param>
/// <param name="scan"></param>
/// <returns></returns>
public List <XYData> FindXic(double mz, int scan, bool shouldSmooth)
{
LcmsFeatureTarget target = new LcmsFeatureTarget();
target.ID = 0;
target.MZ = mz;
target.ScanLCTarget = scan;
target.ElutionTimeUnit = Globals.ElutionTimeUnit.ScanNum;
m_run.CurrentMassTag = target;
var result = m_run.ResultCollection.GetTargetedResult(m_run.CurrentMassTag);
double chromPeakGeneratorTolInPPM = MzPpmWindow;
Globals.ChromatogramGeneratorMode chromGeneratorMode = Globals.ChromatogramGeneratorMode.MZ_BASED;
var chromGen = new PeakChromatogramGenerator(chromPeakGeneratorTolInPPM,
chromGeneratorMode);
chromGen.NETWindowWidthForNonAlignedData = Convert.ToSingle(NetWindow);
int pointsToSmooth = 5;
var chromSmoother = new SavitzkyGolaySmoother(pointsToSmooth, 2);
double chromPeakDetectorPeakBR = 1;
double chromPeakDetectorSigNoise = 1;
var chromPeakDetector = new ChromPeakDetector(chromPeakDetectorPeakBR,
chromPeakDetectorSigNoise);
ChromPeakSelectorParameters chromPeakSelectorParameters = new ChromPeakSelectorParameters();
var chromPeakSelector = new BasicChromPeakSelector(chromPeakSelectorParameters);
//this generates an extracted ion chromatogram
// Since we are not using the built in generator,
chromGen.Execute(m_run.ResultCollection);
//this smooths the data - very important step!
if (shouldSmooth)
{
chromSmoother.Execute(m_run.ResultCollection);
}
//this detects peaks within an extracted ion chromatogram
chromPeakDetector.Execute(m_run.ResultCollection);
//this selects the peak
chromPeakSelector.Parameters.PeakSelectorMode = Globals.PeakSelectorMode.ClosestToTarget;
chromPeakSelector.Execute(m_run.ResultCollection);
//Here's the chromatogram data...
List <XYData> data = new List <XYData>();
for (int i = 0; i < m_run.XYData.Xvalues.Length; i++)
{
XYData datum = new XYData(m_run.XYData.Xvalues[i], m_run.XYData.Yvalues[i]);
data.Add(datum);
}
return(data);
}
private TargetBase ConvertTextToDataObject(List <string> processedData)
{
var target = new LcmsFeatureTarget();
target.DatabaseName = LookupData(processedData, datasetHeaders);
target.ID = ParseIntField(LookupData(processedData, targetIDHeaders));
target.ChargeState = (short)ParseIntField(LookupData(processedData, chargeStateHeaders));
target.ChargeStateTargets = new List <int>();
var lowerChargeState = ParseIntField(LookupData(processedData, chargeStateLowerHeaders));
var upperChargeState = ParseIntField(LookupData(processedData, chargeStateUpperHeaders));
if (lowerChargeState == -1 || upperChargeState == -1)
{
target.ChargeStateTargets.Add(target.ChargeState);
}
else
{
for (var i = lowerChargeState; i <= upperChargeState; i++)
{
target.ChargeStateTargets.Add(i);
}
}
target.ScanLCTarget = ParseIntField(LookupData(processedData, scanHeaders));
target.ElutionTimeUnit = Globals.ElutionTimeUnit.ScanNum;
target.MonoIsotopicMass = ParseDoubleField(LookupData(processedData, monomassHeaders));
target.MZ = target.MonoIsotopicMass / target.ChargeState + Globals.PROTON_MASS;
target.FeatureToMassTagID = ParseIntField(LookupData(processedData, featureToMassTagIDHeaders));
target.EmpiricalFormula = LookupData(processedData, empiricalFormulaHeaders, String.Empty);
target.Code = LookupData(processedData, peptideSequenceHeaders, String.Empty);
//UMCIndex ScanStart ScanEnd ScanClassRep
//NETClassRep UMCMonoMW UMCMWStDev UMCMWMin
//UMCMWMax UMCAbundance ClassStatsChargeBasis
// ChargeStateMin ChargeStateMax UMCMZForChargeBasis
//UMCMemberCount UMCMemberCountUsedForAbu UMCAverageFit
//MassShiftPPMClassRep PairIndex PairMemberType ExpressionRatio //
//ExpressionRatioStDev ExpressionRatioChargeStateBasisCount
//ExpressionRatioMemberBasisCount MultiMassTagHitCount
//MassTagID MassTagMonoMW MassTagNET MassTagNETStDev SLiC Score
//DelSLiC MemberCountMatchingMassTag IsInternalStdMatch PeptideProphetProbability Peptide
return(target);
}
protected virtual TargetCollection GetLcmsFeatureTargets(string targetsFilePath)
{
if (targetsFilePath.ToLower().Contains("_msgf"))
{
var iqTargetImporter = new BasicIqTargetImporter(targetsFilePath);
var iqTargets = iqTargetImporter.Import();
var targetUtilities = new IqTargetUtilities();
var targetCollection = new TargetCollection();
targetCollection.TargetList = new List <TargetBase>();
foreach (var iqTarget in iqTargets)
{
if (iqTarget.QualityScore > MsgfFdrScoreCutoff)
{
continue;
}
targetUtilities.UpdateTargetMissingInfo(iqTarget);
TargetBase oldStyleTarget = new LcmsFeatureTarget();
oldStyleTarget.ChargeState = (short)iqTarget.ChargeState;
oldStyleTarget.Code = iqTarget.Code;
oldStyleTarget.EmpiricalFormula = iqTarget.EmpiricalFormula;
oldStyleTarget.ID = iqTarget.ID;
oldStyleTarget.MZ = iqTarget.MZTheor;
oldStyleTarget.MonoIsotopicMass = iqTarget.MonoMassTheor;
oldStyleTarget.ScanLCTarget = iqTarget.ScanLC;
oldStyleTarget.NormalizedElutionTime = (float)iqTarget.ElutionTimeTheor;
oldStyleTarget.ElutionTimeUnit = DeconTools.Backend.Globals.ElutionTimeUnit.ScanNum;
targetCollection.TargetList.Add(oldStyleTarget);
}
return(targetCollection);
}
var importer =
new LcmsTargetFromFeaturesFileImporter(targetsFilePath);
var lcmsTargetCollection = importer.Import();
return(lcmsTargetCollection);
}
private void SetCurrentWorkflowTarget(TargetedResultDTO result)
{
TargetBase target = new LcmsFeatureTarget();
target.ChargeState = (short)result.ChargeState;
target.ChargeStateTargets.Add(target.ChargeState);
target.ElutionTimeUnit = DeconTools.Backend.Globals.ElutionTimeUnit.ScanNum;
target.EmpiricalFormula = result.EmpiricalFormula;
target.ID = (int)result.TargetID;
target.IsotopicProfile = null; //workflow will determine this
target.MZ = result.MonoMZ;
target.MonoIsotopicMass = result.MonoMass;
target.ScanLCTarget = result.ScanLC;
Run.CurrentMassTag = target;
}
private void ReadResultsFromDB(TargetCollection targetCollection, DbDataReader reader)
{
while (reader.Read())
{
var result = new LcmsFeatureTarget();
result.ID = readInt(reader, "UMC_Ind");
result.FeatureToMassTagID = readInt(reader, "Mass_Tag_ID");
result.ChargeState = (short)readInt(reader, "Class_Stats_Charge_Basis");
result.MonoIsotopicMass = readDouble(reader, "Class_Mass");
result.MZ = result.MonoIsotopicMass / result.ChargeState + 1.00727649;
result.NormalizedElutionTime = readFloat(reader, "ElutionTime");
result.ScanLCTarget = readInt(reader, "Scan_Max_Abundance");
result.ElutionTimeUnit = DeconTools.Backend.Globals.ElutionTimeUnit.ScanNum;
targetCollection.TargetList.Add(result);
}
}
private void SetCurrentWorkflowTarget(SipperLcmsFeatureTargetedResultDTO result)
{
TargetBase target = new LcmsFeatureTarget();
target.ChargeState = (short)result.ChargeState;
target.ChargeStateTargets.Add(target.ChargeState);
target.ElutionTimeUnit = Globals.ElutionTimeUnit.ScanNum;
target.EmpiricalFormula = result.EmpiricalFormula;
target.ID = (int)result.TargetID;
target.IsotopicProfile = null; //workflow will determine this
target.MZ = result.MonoMZ;
target.MonoIsotopicMass = result.MonoMass;
target.ScanLCTarget = result.ScanLC;
Run.CurrentMassTag = target;
}
public void Test1()
{
var testFile =
@"D:\Data\Orbitrap\BrianIQTesting\QC_Shew_11_02_pt5-b_6Jun11_Sphinx_11-03-27.RAW";
var peaksTestFile =
@"D:\Data\Orbitrap\BrianIQTesting\QC_Shew_11_02_pt5-b_6Jun11_Sphinx_11-03-27_peaks.txt";
var run = RunUtilities.CreateAndLoadPeaks(testFile, peaksTestFile);
var target = new LcmsFeatureTarget();
target.ID = 0;
target.MZ = 715.39214;
target.ScanLCTarget = 7343;
target.ElutionTimeUnit = Globals.ElutionTimeUnit.ScanNum;
run.CurrentMassTag = target;
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag);
double chromPeakGeneratorTolInPPM = 20;
var chromGeneratorMode = Globals.ChromatogramGeneratorMode.MZ_BASED;
var chromGen = new PeakChromatogramGenerator(chromPeakGeneratorTolInPPM, chromGeneratorMode);
// If we want to use the Execute Command
//BLL .1 and .5 NET windows work. .02 NET window does not BR and SN was set to 1 however)
chromGen.ChromWindowWidthForNonAlignedData = .02F;
var pointsToSmooth = 5;
var chromSmoother = new SavitzkyGolaySmoother(pointsToSmooth, 2);
//BLL We also tried to set the BR and SIG NOISE to 0. This did not work
var chromPeakDetectorPeakBR = 0.5;
var chromPeakDetectorSigNoise = 0.5;
var chromPeakDetector = new ChromPeakDetector(chromPeakDetectorPeakBR, chromPeakDetectorSigNoise);
var chromPeakSelectorParameters = new ChromPeakSelectorParameters();
chromPeakSelectorParameters.PeakSelectorMode = Globals.PeakSelectorMode.ClosestToTarget;
var chromPeakSelector = new BasicChromPeakSelector(chromPeakSelectorParameters);
var smartChromPeakParameters = new SmartChromPeakSelectorParameters();
var smartChromPeakSelector = new SmartChromPeakSelector(smartChromPeakParameters);
//this generates an extracted ion chromatogram
// Since we are not using the built in generator,
chromGen.Execute(run.ResultCollection);
//this smooths the data - very important step!
//BLL. This didnt work for me when we first started, instead of using the NET window above.
//chromGen.GenerateChromatogram(run,
// target.ScanLCTarget - 300,
// target.ScanLCTarget + 300,
// target.MZ,
// chromPeakGeneratorTolInPPM);
chromSmoother.Execute(run.ResultCollection);
//this detects peaks within an extracted ion chromatogram
chromPeakDetector.Execute(run.ResultCollection);
//this selects the peak
chromPeakSelector.Execute(run.ResultCollection);
//smartChromPeakSelector.Execute(run.ResultCollection);
//TestUtilities.DisplayXYValues(run.XYData);
TestUtilities.DisplayPeaks(run.PeakList);
Console.WriteLine("Number of peaks detected = " + run.PeakList.Count);
Console.WriteLine("Selected peak= " + result.ChromPeakSelected);
}
public TargetCollection Import(out Dictionary <int, PrsmData> prsmData)
{
StreamReader reader;
prsmData = new Dictionary <int, PrsmData>();
if (!File.Exists(_filename))
{
throw new FileNotFoundException("Input file not found: " + _filename);
}
try
{
reader = new StreamReader(_filename);
}
catch (Exception ex)
{
throw new IOException("There was a problem importing from the file.", ex);
}
var targets = new TargetCollection();
// Group LcmsFeatureTargets by their code
var proteinSpeciesGroups = new Dictionary <string, List <LcmsFeatureTarget> >();
using (var sr = reader)
{
if (sr.Peek() == -1)
{
sr.Close();
throw new InvalidDataException("There is no data in the file we are trying to read.");
}
var columnHeaders = sr.ReadLine().Split('\t').ToList();
var columnMapping = GetColumnMapping(columnHeaders);
var lineCounter = 0; //used for tracking which line is being processed.
//read and process each line of the file
while (sr.Peek() > -1)
{
++lineCounter;
_dataRowsProcessed = lineCounter;
var processedData = sr.ReadLine().Split('\t').ToList();
//ensure that processed line is the same size as the header line
if (processedData.Count != columnHeaders.Count)
{
throw new InvalidDataException("Data in row #" + lineCounter.ToString(CultureInfo.InvariantCulture) +
"is invalid - \nThe number of columns does not match that of the header line");
}
// Get Prsm_ID
int prsmId;
if (!int.TryParse(processedData[columnMapping[PRSM_ID_HEADER]], out prsmId))
{
throw new InvalidDataException("Could not parse Prsm ID.");
}
// Get scan
int scanLcTarget;
if (!int.TryParse(processedData[columnMapping[SCAN_HEADER]], out scanLcTarget))
{
throw new InvalidDataException("Could not parse scan number.");
}
// Get charge state
short chargeState;
if (!short.TryParse(processedData[columnMapping[CHARGE_HEADER]], out chargeState))
{
throw new InvalidDataException("Could not parse charge.");
}
// Get code
var code = processedData[columnMapping[PEPTIDE_HEADER]];
string empiricalFormula;
// Modified species, try to get empirical formula
if (code.Contains("("))
{
empiricalFormula = GetEmpiricalFormulaForSequenceWithMods(code);
// Unknown modification in sequence, skip
if (String.IsNullOrEmpty(empiricalFormula))
{
++_dataRowsSkippedUnknownMods;
continue;
}
}
else
{
empiricalFormula = _peptideUtils.GetEmpiricalFormulaForPeptideSequence(code);
}
// Get monoisotopic mass
var monoisotopicMass = EmpiricalFormulaUtilities.GetMonoisotopicMassFromEmpiricalFormula(empiricalFormula);
// Get Protein_mass
double proteinMass;
if (!double.TryParse(processedData[columnMapping[PROTEIN_MASS_HEADER]], out proteinMass))
{
throw new InvalidDataException("Could not parse protein mass.");
}
// Get protein name
var proteinName = processedData[columnMapping[PROTEIN_NAME_HEADER]];
// Get score
double eValueDbl;
if (!double.TryParse(processedData[columnMapping[E_VALUE_HEADER]], out eValueDbl))
{
if (processedData[columnMapping[E_VALUE_HEADER]].ToLower() == "Infinity")
{
eValueDbl = float.MaxValue;
}
else
{
throw new InvalidDataException("Could not parse e-value.");
}
}
float eValue;
if (eValueDbl > float.MaxValue)
{
eValue = float.MaxValue;
}
else
{
eValue = (float)eValueDbl;
}
// Make Prsm
prsmData.Add(prsmId, new PrsmData {
ProteinMass = proteinMass, ProteinName = proteinName, EValue = eValue
});
// Create target
var target = new LcmsFeatureTarget
{
FeatureToMassTagID = prsmId,
ID = -1,
ElutionTimeUnit = DeconTools.Backend.Globals.ElutionTimeUnit.ScanNum,
ScanLCTarget = scanLcTarget,
Code = code,
EmpiricalFormula = empiricalFormula,
MonoIsotopicMass = monoisotopicMass,
ChargeState = chargeState,
MZ = monoisotopicMass / chargeState + DeconTools.Backend.Globals.PROTON_MASS,
};
if (!proteinSpeciesGroups.ContainsKey(code))
{
proteinSpeciesGroups.Add(code, new List <LcmsFeatureTarget>());
}
proteinSpeciesGroups[code].Add(target);
/*
* // Create range
* const int maxOffset = 0;
*
* for (short offset = -maxOffset; offset <= maxOffset; offset++)
* {
* // Create new target
* var newCharge = (short) (chargeState + offset);
* var targetCopy = new LcmsFeatureTarget(target)
* {
* ID = ++idCounter,
* ChargeState = newCharge,
* MZ = target.MonoIsotopicMass / newCharge + DeconTools.Backend.Globals.PROTON_MASS
* };
* // Add target
* targets.TargetIDList.Add(idCounter);
* targets.TargetList.Add(targetCopy);
* }
*/
}
sr.Close();
}
// Loop through each protein species group and add in the missing charge states
var idCounter = 0;
foreach (var keyValuePair in proteinSpeciesGroups)
{
var targetGroup = AddChargeStates(keyValuePair.Value, EXTEND_CHARGE_RANGE);
var chargeStates = new List <short> {
0
};
// Add all targets in group and IDs to list
foreach (var target in targetGroup)
{
if (!chargeStates.Contains(target.ChargeState))
{
chargeStates.Add(target.ChargeState);
target.ID = ++idCounter;
targets.TargetList.Add(target);
targets.TargetIDList.Add(idCounter);
}
}
}
return(targets);
}
/// <summary>
/// Finds the XIC based on the m/z and scan parameters.
/// </summary>
/// <param name="mz"></param>
/// <param name="scan"></param>
/// <returns></returns>
public List<PNNLOmics.Data.XYData> FindXic(double mz, int scan, bool shouldSmooth)
{
LcmsFeatureTarget target = new LcmsFeatureTarget();
target.ID = 0;
target.MZ = mz;
target.ScanLCTarget = scan;
target.ElutionTimeUnit = Globals.ElutionTimeUnit.ScanNum;
m_run.CurrentMassTag = target;
var result = m_run.ResultCollection.GetTargetedResult(m_run.CurrentMassTag);
double chromPeakGeneratorTolInPPM = MzPpmWindow;
Globals.ChromatogramGeneratorMode chromGeneratorMode = Globals.ChromatogramGeneratorMode.MZ_BASED;
var chromGen = new PeakChromatogramGenerator( chromPeakGeneratorTolInPPM,
chromGeneratorMode);
chromGen.NETWindowWidthForNonAlignedData = Convert.ToSingle(NetWindow);
int pointsToSmooth = 5;
var chromSmoother = new SavitzkyGolaySmoother(pointsToSmooth, 2);
double chromPeakDetectorPeakBR = 1;
double chromPeakDetectorSigNoise = 1;
var chromPeakDetector = new ChromPeakDetector( chromPeakDetectorPeakBR,
chromPeakDetectorSigNoise);
ChromPeakSelectorParameters chromPeakSelectorParameters = new ChromPeakSelectorParameters();
var chromPeakSelector = new BasicChromPeakSelector(chromPeakSelectorParameters);
//this generates an extracted ion chromatogram
// Since we are not using the built in generator,
chromGen.Execute(m_run.ResultCollection);
//this smooths the data - very important step!
if (shouldSmooth)
{
chromSmoother.Execute(m_run.ResultCollection);
}
//this detects peaks within an extracted ion chromatogram
chromPeakDetector.Execute(m_run.ResultCollection);
//this selects the peak
chromPeakSelector.Parameters.PeakSelectorMode = Globals.PeakSelectorMode.ClosestToTarget;
chromPeakSelector.Execute(m_run.ResultCollection);
//Here's the chromatogram data...
List<PNNLOmics.Data.XYData> data = new List<PNNLOmics.Data.XYData>();
for (int i = 0; i < m_run.XYData.Xvalues.Length; i++)
{
PNNLOmics.Data.XYData datum = new PNNLOmics.Data.XYData(m_run.XYData.Xvalues[i], m_run.XYData.Yvalues[i]);
data.Add(datum);
}
return data;
}
