private static ThermoMzPeak GetPeak(PSM psm, double oxoniumIon, ThermoRawFile rawFile)
{
DoubleRange rangeOxonium = DoubleRange.FromPPM(oxoniumIon, 20);
List <ThermoMzPeak> peaks;
ThermoSpectrum spec = rawFile.GetSpectrum(psm.scanNumber);
if (spec.TryGetPeaks(rangeOxonium, out peaks))
{
peaks = peaks.OrderBy(x => x.SignalToNoise).ToList();
}
double diff = double.MaxValue;
ThermoMzPeak returnPeak = null;
foreach (ThermoMzPeak peak in peaks)
{
var currDiff = Math.Abs(peak.MZ - oxoniumIon);
if (currDiff < diff)
{
diff = currDiff;
returnPeak = peak;
}
}
return(returnPeak);
}
private static void ChemicalFormulaGeneratorExample()
{
//// Create a generator with formula bounds. In this case, every formula needs to have at least H2 but no more than C4H2
//ChemicalFormulaGenerator generator = new ChemicalFormulaGenerator(new ChemicalFormula("H2"), new ChemicalFormula("C4H2"));
//var formulas = generator.FromMass(0, 100).ToList();
//foreach (var formula in formulas)
//{
// WriteFormulaToConsole(formula);
//}
//Console.WriteLine("Unique Formulas: " + formulas.Count);
// Create a generator with formula bounds. In this case, every formula needs to have at least H2 but no more than C4H2
ChemicalFormulaGenerator generator = new ChemicalFormulaGenerator(new ChemicalFormula("C10000N1000H1000O1000"));
DoubleRange range = DoubleRange.FromPPM(new ChemicalFormula("C62H54N42O24").MonoisotopicMass, 0.1);
double mass = range.Mean;
int count = 0;
foreach (var formula in generator.FromMass(range).Validate())
{
Console.WriteLine("{0,-15} {1:F10} {2,-5:G5} ppm", formula, formula.MonoisotopicMass,
Tolerance.GetTolerance(formula.MonoisotopicMass, mass, ToleranceUnit.PPM));
count++;
}
Console.WriteLine("Unique Formulas: " + count);
}
public static int GetSpectraCountOxonium(List <int> spectrumList, double oxoniumIon1, double oxoniumIon2, ThermoRawFile rawFile)
{
int count = 0;
foreach (int scan in spectrumList)
{
ThermoSpectrum spectrum = rawFile.GetSpectrum(scan);
bool oxoniumIsPresent = false;
DoubleRange rangeOxonium1 = DoubleRange.FromPPM(oxoniumIon1, 20);
List <ThermoMzPeak> peaks;
if (spectrum.TryGetPeaks(rangeOxonium1, out peaks))
{
peaks = peaks.OrderBy(x => x.SignalToNoise).ToList();
}
if (peaks.Count > 0)
{
if (peaks[0].SignalToNoise > 3)
{
oxoniumIsPresent = true;
}
}
if (oxoniumIon2 > 0)
{
DoubleRange rangeOxonium2 = DoubleRange.FromPPM(oxoniumIon2, 20);
List <ThermoMzPeak> peaks2;
if (spectrum.TryGetPeaks(rangeOxonium2, out peaks2))
{
peaks2 = peaks2.OrderBy(x => x.SignalToNoise).ToList();
}
if (peaks2.Count > 0)
{
if (peaks2[0].SignalToNoise > 3)
{
oxoniumIsPresent = true;
}
}
}
if (oxoniumIsPresent)
{
count++;
}
}
return(count);
}
public LFQProcessor(string rawFilePath, string peptidePath)
{
var rawFile = new ThermoRawFile(rawFilePath);
rawFile.Open();
List <int> msOneScanNumbers = new List <int>();
foreach (var scane in rawFile)
{
if (scane.MsnOrder == 1)
{
msOneScanNumbers.Add(scane.SpectrumNumber);
}
}
ReadInTargets(peptidePath, rawFile);
if (rawFile.GetMzAnalyzer(msOneScanNumbers[0]).Equals(MZAnalyzerType.Orbitrap))
{
var firstSpectrumRT = rawFile.GetRetentionTime(rawFile.FirstSpectrumNumber);
var lastSpectrumRT = rawFile.GetRetentionTime(rawFile.LastSpectrumNumber);
foreach (var pep in targetPeptides)
{
// Initial peak boundaries
var startTime = Math.Max(pep.parentMS1Time - 2, firstSpectrumRT);
var stopTime = Math.Min(pep.parentMS1Time + 2, lastSpectrumRT);
pep.startLookupTime = startTime;
pep.stopLookupTime = stopTime;
pep.FirstScan = rawFile.GetSpectrumNumber(pep.startLookupTime);
pep.LastScan = rawFile.GetSpectrumNumber(pep.stopLookupTime);
//10 ppm maass error for peak picking
pep.lookupRange = DoubleRange.FromPPM(pep.UserMZ, 10);
}
foreach (var ms1 in msOneScanNumbers)
{
var spectrum = rawFile.GetSpectrum(ms1);
GetXICs(spectrum, ms1, rawFile.GetRetentionTime(ms1));
}
}
}
public List <PSM> crunch(List <PSM> psms)
{
var rawFile = new ThermoRawFile(rawpath);
rawFile.Open();
List <int> msOneScanNumbers = new List <int>();
foreach (var scan in rawFile)
{
if (scan.MsnOrder == 1)
{
msOneScanNumbers.Add(scan.SpectrumNumber);
}
}
//ReadInTargets(peptidesPath, rawFile);
foreach (PSM psm in psms)
{
LFPeptide pep = psmToLFPeptide(psm, rawFile);
targetPeptides.Add(pep);
}
// Question: how do we sync the list of PSMs with the intensity of the LFPeptide
// They will be in same order
List <LFPeptide> pepsWithSmooth = new List <LFPeptide>();
if (rawFile.GetMzAnalyzer(msOneScanNumbers[0]).Equals(MZAnalyzerType.Orbitrap))
{
var firstSpectrumRT = rawFile.GetRetentionTime(rawFile.FirstSpectrumNumber);
var lastSpectrumRT = rawFile.GetRetentionTime(rawFile.LastSpectrumNumber);
foreach (var pep in targetPeptides)
{
var startTime = Math.Max(pep.parentMS1Time - 2, firstSpectrumRT);
var stopTime = Math.Min(pep.parentMS1Time + 2, lastSpectrumRT);
pep.startLookupTime = startTime;
pep.stopLookupTime = stopTime;
pep.FirstScan = rawFile.GetSpectrumNumber(pep.startLookupTime);
pep.LastScan = rawFile.GetSpectrumNumber(pep.stopLookupTime);
pep.lookupRange = DoubleRange.FromPPM(pep.UserMZ, 10);
}
foreach (var ms1 in msOneScanNumbers)
{
var spectrum = rawFile.GetSpectrum(ms1);
GetXICs(spectrum, ms1, rawFile.GetRetentionTime(ms1));
rawFile.ClearCachedScans();
List <LFPeptide> peptidesForExtract = targetPeptides.Where(x => x.doneBuildingXIC && !x.extractedXIC).ToList();
foreach (var pep in peptidesForExtract)
{
try
{
pep.SmoothLibrary = Smoothing.GetRollingAveragePeaks(pep, 11, true);
if (pep.SmoothLibrary.Count != 0)
{
ExtractFeatures.GetApexPeak(pep, true);
ExtractFeatures.GetFWHMWindow(pep);
LFPeptide pepSmooth = (LFPeptide)pep.Clone();
pepsWithSmooth.Add(pepSmooth);
pep.XICLibrary.Clear();
}
}catch (Exception e)
{/**
* System.Windows.Forms.MessageBox.Show("XICLibraryCount: " + pep.XICLibrary.Count
+ "Peptide: " + pep.sequence
+ "\n" + e.ToString());
**/
}
}
}
List <LFPeptide> peptidesToWrite = targetPeptides.Where(x => x.doneBuildingXIC && !x.extractedXIC).ToList();
//Changed from psms.Count to pepswithsmooth.Count
//for(int i = 0; i < psms.Count; i++)
for (int i = 0; i < pepsWithSmooth.Count; i++)
{
/**
* if(psms[i].scanTime == 20.45)
* {
* double[] xs = new double[pepsWithSmooth[i].SmoothLibrary.Count];
* double[] ys = new double[pepsWithSmooth[i].SmoothLibrary.Count];
*
* StreamWriter writer = new StreamWriter(@"C:\Users\gwilson\Desktop\GlycoQuant - Injs\TLN[NGlycan_1216.42286271]CSGAHVK_0.5_2_PolynomialFit.csv");
* for (int k = 0; k < pepsWithSmooth[i].SmoothLibrary.Count; k++)
* {
* xs[k] = pepsWithSmooth[i].SmoothLibrary[k].RT;
* ys[k] = pepsWithSmooth[i].SmoothLibrary[k].Intensity;
*
* //writer.WriteLine(pepsWithSmooth[i].SmoothLibrary[k].RT + "," + pepsWithSmooth[i].SmoothLibrary[k].Intensity);
*
*
* if (pepsWithSmooth[i].SmoothLibrary[k].RT > targetPeptides[i].LeftFWHM.RT && pepsWithSmooth[i].SmoothLibrary[k].RT < targetPeptides[i].RightFWHM.RT)
* {
* writer.WriteLine(pepsWithSmooth[i].SmoothLibrary[k].RT + "," + pepsWithSmooth[i].SmoothLibrary[k].Intensity);
* }
*
* }
*
* double[] p = Fit.Polynomial(xs, ys, 3)
*
* for(int j = 0; j < p.Length; j++)
* {
* //writer.WriteLine()
* }
*
* writer.Close();
* }
**/
double intensity = 0;
try
{
for (int j = 0; j < pepsWithSmooth[i].SmoothLibrary.Count - 1; j++)
{
// Intensity is the sum of peak intensities from Left FWHM to Right FWHM
/**
* if (pepsWithSmooth[i].SmoothLibrary[j].RT > targetPeptides[i].LeftFWHM.RT && pepsWithSmooth[i].SmoothLibrary[j].RT < targetPeptides[i].RightFWHM.RT)
* {
* intensity += pepsWithSmooth[i].SmoothLibrary[j].Intensity;
* }
**/
// Retention times
double RT1 = pepsWithSmooth[i].SmoothLibrary[j].RT;
double RT2 = pepsWithSmooth[i].SmoothLibrary[j + 1].RT;
// Intensities
double int1 = pepsWithSmooth[i].SmoothLibrary[j].Intensity;
double int2 = pepsWithSmooth[i].SmoothLibrary[j + 1].Intensity;
//Rectangle area
double rectArea = (RT2 - RT1) * Math.Min(int1, int2);
//Triangle Area
double triArea = ((RT2 - RT1) * Math.Abs(int1 - int2)) / 2;
intensity += rectArea + triArea;
}
}
catch (Exception e)
{
Console.ReadKey();
}
psms[i].intensity = intensity;
//psms[i].intensity = targetPeptides[i].apexPeakLibrary.Intensity;
}
rawFile.Dispose();
return(psms);
}
rawFile.Dispose();
return(psms);
}