private string GetMGFOutputString(Run run, int scanNum, DeconMSnResult deconMSnResult, IEnumerable <Peak> ms2Peaks)
{
var sb = new StringBuilder();
sb.Append("BEGIN IONS");
sb.Append(Environment.NewLine);
sb.Append("TITLE=" + run.DatasetName + "." + scanNum + "." + scanNum + ".1.dta");
sb.Append(Environment.NewLine);
sb.Append("PEPMASS=" + deconMSnResult.ParentMZ);
sb.Append(Environment.NewLine);
sb.Append("CHARGE=" + deconMSnResult.ParentChargeState + "+");
sb.Append(Environment.NewLine);
foreach (var peak in ms2Peaks)
{
sb.Append(Math.Round(peak.XValue, 5));
sb.Append(" ");
sb.Append(peak.Height);
sb.Append(Environment.NewLine);
}
sb.Append("END IONS");
sb.Append(Environment.NewLine);
sb.Append(Environment.NewLine);
return(sb.ToString());
}
private string GetSummaryString(DeconMSnResult result, bool includeHeader = false)
{
var headers = new List <string>
{
"MSn_Scan",
"MSn_Level",
"Parent_Scan",
"Parent_Scan_Level",
"Parent_Mz",
"Mono_Mz",
"Charge_State",
"Monoisotopic_Mass",
"Isotopic_Fit",
"Parent_Intensity",
"Mono_Intensity",
"Parent_TIC",
"Ion_Injection_Time",
"OriginalMZ",
"ExtraInfo"
};
var data = new List <string>
{
result.ScanNum.ToString(),
"2",
result.ParentScan.ToString(),
"1",
result.ParentMZ.ToString("0.00000"),
result.ParentMZ.ToString("0.00000"),
result.ParentChargeState.ToString(),
result.IsotopicProfile?.MonoIsotopicMass.ToString("0.00000") ?? "-1",
result.IsotopicProfile?.Score.ToString("0.0000") ?? "-1",
result.ParentIntensity.ToString("0"),
result.IntensityAggregate.ToString("0"),
result.ParentScanTICIntensity.ToString("0"),
result.IonInjectionTime.ToString("0.0000"),
result.OriginalMZTarget.ToString("0.0000"),
result.ExtraInfo
};
if (includeHeader)
{
return(string.Join(_delimiter, headers) + Environment.NewLine + string.Join(_delimiter, data));
}
return(string.Join(_delimiter, data));
}
private string GetSummaryString(DeconMSnResult result, bool includeHeader = false)
{
var sb = new StringBuilder();
if (includeHeader)
{
sb.Append("MSn_Scan\tMSn_Level\tParent_Scan\tParent_Scan_Level\tParent_Mz\tMono_Mz\tCharge_State\tMonoisotopic_Mass\tIsotopic_Fit\tParent_Intensity\tMono_Intensity\tParent_TIC\tIon_Injection_Time\tOriginalMZ\tExtraInfo");
sb.Append(Environment.NewLine);
}
var delimiter = "\t";
sb.Append(result.ScanNum);
sb.Append(delimiter);
sb.Append(2);
sb.Append(delimiter);
sb.Append(result.ParentScan);
sb.Append(delimiter);
sb.Append(1);
sb.Append(delimiter);
sb.Append(result.ParentMZ.ToString("0.00000"));
sb.Append(delimiter);
sb.Append(result.ParentMZ.ToString("0.00000"));
sb.Append(delimiter);
sb.Append(result.ParentChargeState);
sb.Append(delimiter);
sb.Append(result.IsotopicProfile != null ? result.IsotopicProfile.MonoIsotopicMass.ToString("0.00000") : "-1");
sb.Append(delimiter);
sb.Append(result.IsotopicProfile != null ? result.IsotopicProfile.Score.ToString("0.0000") : "-1");
sb.Append(delimiter);
sb.Append(result.ParentIntensity.ToString("0"));
sb.Append(delimiter);
sb.Append(result.IntensityAggregate.ToString("0"));
sb.Append(delimiter);
sb.Append(result.ParentScanTICIntensity.ToString("0"));
sb.Append(delimiter);
sb.Append(result.IonInjectionTime.ToString("0.0000"));
sb.Append(delimiter);
sb.Append(result.OriginalMZTarget);
sb.Append(delimiter);
sb.Append(result.ExtraInfo);
return(sb.ToString());
}
private string GetParentProfileString(DeconMSnResult result, bool includeHeader)
{
var sb = new StringBuilder();
if (includeHeader)
{
sb.Append("MSn_Scan\tParent_Scan\tAGC_accumulation_time\tTIC");
sb.Append(Environment.NewLine);
}
var delimiter = "\t";
sb.Append(result.ScanNum);
sb.Append(delimiter);
sb.Append(result.ParentScan);
sb.Append(delimiter);
sb.Append(result.IonInjectionTime.ToString("0.0000"));
sb.Append(delimiter);
sb.Append(result.ParentScanTICIntensity.ToString("0"));
return(sb.ToString());
}
private string GetParentProfileString(DeconMSnResult result, bool includeHeader)
{
var headers = new List <string> {
"MSn_Scan",
"Parent_Scan",
"AGC_accumulation_time",
"TIC"
};
var data = new List <string>
{
result.ScanNum.ToString(),
result.ParentScan.ToString(),
result.IonInjectionTime.ToString("0.0000"),
result.ParentScanTICIntensity.ToString("0")
};
if (includeHeader)
{
return(string.Join(_delimiter, headers) + Environment.NewLine + string.Join(_delimiter, data));
}
return(string.Join(_delimiter, data));
}
protected override void IterateOverScans()
{
DeconMSnResults.Clear();
_scanCounter = 0;
var resultCounter = 0;
foreach (var scanSet in Run.ScanSetCollection.ScanSetList)
{
_scanCounter++;
if (BackgroundWorker != null)
{
if (BackgroundWorker.CancellationPending)
{
return;
}
}
//check ms level
var currentMSLevel = Run.GetMSLevel(scanSet.PrimaryScanNumber);
if (currentMSLevel == 1)
{
Run.ResultCollection.IsosResultBin.Clear();
Run.CurrentScanSet = scanSet;
MSGenerator.Execute(Run.ResultCollection);
_currentMS1XYValues = new XYData
{
Xvalues = Run.XYData.Xvalues,
Yvalues = Run.XYData.Yvalues
};
_currentMS1TICIntensity = Run.GetTICFromInstrumentInfo(scanSet.PrimaryScanNumber);
PeakDetector.Execute(Run.ResultCollection);
_currentMS1Peaks = new List <Peak>(Run.PeakList);
}
else if (currentMSLevel == 2)
{
if (_currentMS1Peaks == null || _currentMS1Peaks.Count == 0)
{
continue;
}
var precursorInfo = Run.GetPrecursorInfo(scanSet.PrimaryScanNumber);
Run.CurrentScanSet = scanSet;
var inaccurateParentMZ = precursorInfo.PrecursorMZ;
resultCounter++;
var deconMSnResult = new DeconMSnResult {
ParentScan = Run.GetParentScan(scanSet.PrimaryScanNumber)
};
deconMSnResult.IonInjectionTime = Run.GetIonInjectionTimeInMilliseconds(deconMSnResult.ParentScan);
deconMSnResult.ScanNum = scanSet.PrimaryScanNumber;
deconMSnResult.OriginalMZTarget = inaccurateParentMZ;
deconMSnResult.ParentScanTICIntensity = _currentMS1TICIntensity;
MSGenerator.Execute(Run.ResultCollection);
var lowerMZ = inaccurateParentMZ - 1.1;
var upperMZ = inaccurateParentMZ + 1.1;
var dataIsCentroided = Run.IsDataCentroided(scanSet.PrimaryScanNumber);
if (dataIsCentroided)
{
_ms2PeakDetectorForCentroidData.Execute(Run.ResultCollection);
}
else
{
_ms2PeakDetectorForProfileData.Execute(Run.ResultCollection);
}
var ms2Peaks = new List <Peak>(Run.PeakList);
var filteredMS1Peaks = _currentMS1Peaks.Where(p => p.XValue > lowerMZ && p.XValue < upperMZ).ToList();
IsotopicProfile selectedMS1Feature = null;
for (var attemptNum = 0; attemptNum < NumMaxAttemptsAtLowIntensitySpecies; attemptNum++)
{
var candidateMS1Features = GetCandidateMS1Features(inaccurateParentMZ, filteredMS1Peaks);
//if none were found, will regenerate MS1 spectrum and find peaks again
if (candidateMS1Features.Count == 0)
{
var numSummed = attemptNum * 2 + 3;
var ms1Scan = precursorInfo.PrecursorScan;
var ms1ScanSet = new ScanSetFactory().CreateScanSet(Run, ms1Scan, numSummed);
//get MS1 mass spectrum again. This time sum spectra
Run.CurrentScanSet = ms1ScanSet;
MSGenerator.Execute(Run.ResultCollection);
//run MS1 peak detector, with greater sensitivity
var isLastAttempt = attemptNum >= NumMaxAttemptsAtLowIntensitySpecies - 2; //need to do -2 because of the way the loop advances the counter.
if (isLastAttempt)
{
_superSensitiveMS1PeakDetector.MinX = lowerMZ;
_superSensitiveMS1PeakDetector.MaxX = upperMZ;
_superSensitiveMS1PeakDetector.Execute(Run.ResultCollection);
filteredMS1Peaks = new List <Peak>(Run.PeakList);
}
else
{
_moreSensitiveMS1PeakDetector.Execute(Run.ResultCollection);
var moreSensitiveMS1Peaks = new List <Peak>(Run.PeakList);
filteredMS1Peaks = moreSensitiveMS1Peaks.Where(p => p.XValue > lowerMZ && p.XValue < upperMZ).ToList();
}
}
else if (candidateMS1Features.Count == 1)
{
selectedMS1Feature = candidateMS1Features.First();
break; //we found something, so no need for any further attempts
}
else
{
var highQualityCandidates = candidateMS1Features.Where(p => p.Score < 0.15).ToList();
if (highQualityCandidates.Count == 0)
{
selectedMS1Feature = candidateMS1Features.OrderByDescending(p => p.IntensityMostAbundantTheor).First();
}
else if (highQualityCandidates.Count == 1)
{
selectedMS1Feature = highQualityCandidates.First();
}
else
{
selectedMS1Feature = highQualityCandidates.OrderByDescending(p => p.IntensityMostAbundantTheor).First();
}
deconMSnResult.ExtraInfo = "Warning - multiple MSFeatures found for target parent MZ";
break; //we found something, so no need for any further attempts
}
}
if (selectedMS1Feature != null)
{
deconMSnResult.ParentMZ = selectedMS1Feature.MonoPeakMZ;
deconMSnResult.ParentChargeState = selectedMS1Feature.ChargeState;
deconMSnResult.ParentIntensity = selectedMS1Feature.IntensityMostAbundantTheor;
deconMSnResult.IntensityAggregate = selectedMS1Feature.IntensityMostAbundantTheor;
deconMSnResult.IsotopicProfile = selectedMS1Feature;
}
else
{
var candidatePeaks = new List <Peak>();
foreach (var peak in filteredMS1Peaks)
{
var currentDiff = Math.Abs(peak.XValue - inaccurateParentMZ);
var toleranceInMZ = ToleranceInPPM * peak.XValue / 1e6;
if (currentDiff < toleranceInMZ)
{
candidatePeaks.Add(peak);
}
}
Peak selectedPeak = null;
if (candidatePeaks.Count == 0)
{
//cannot even find a suitable MS1 peak. So can't do anything
}
else if (candidatePeaks.Count == 1)
{
selectedPeak = candidatePeaks.First();
}
else
{
selectedPeak = candidatePeaks.OrderByDescending(p => p.Height).First();
}
if (selectedPeak != null)
{
deconMSnResult.ParentMZ = selectedPeak.XValue;
deconMSnResult.ParentChargeState = 1; //not sure what charge I should assign... Ask SangTae
deconMSnResult.ParentIntensity = selectedPeak.Height;
deconMSnResult.IsotopicProfile = null;
deconMSnResult.ExtraInfo = "Failure code 1: No MSFeature, but peak found";
}
else
{
deconMSnResult.ParentMZ = precursorInfo.PrecursorMZ; //could not find the accurate parentMZ, so just report what the instrument found.
deconMSnResult.ParentChargeState = 1; //not sure what charge I should assign... Ask SangTae
deconMSnResult.ParentIntensity = 0;
deconMSnResult.IsotopicProfile = null;
deconMSnResult.ExtraInfo = "Failure code 2: No MSFeature or peak found";
}
}
//Build export data.
var outputString = GetMGFOutputString(Run, scanSet.PrimaryScanNumber, deconMSnResult, ms2Peaks);
var includeHeader = resultCounter == 1;
var summaryString = GetSummaryString(deconMSnResult, includeHeader);
var parentProfileString = GetParentProfileString(deconMSnResult, includeHeader);
if (ExportData)
{
WriteOutMainData(outputString);
WriteOutDeconMSnSummary(summaryString);
if (IsParentProfileDataExported)
{
WriteOutParentProfileInfoString(parentProfileString);
}
}
if (deconMSnResult.ParentIntensity > 0)
{
DeconMSnResults.Add(deconMSnResult);
}
}
else
{
throw new ApplicationException(
"DeconMSn only works on MS1 and MS2 data; You are attempting MS3");
}
ReportProgress();
}
}