public List <MSFull> GetNext(int noSpectra)
{
List <MSFull> myScans = new List <MSFull>(noSpectra);
string thisLine = "";
MSFull thisScan;
if (cycleCounter == 0)
{
thisScan = new MSParser.MSFull();
}
else
{
thisScan = bufferScan;
}
while (true)
{
thisLine = sr.ReadLine();
if (thisLine == null)
{
break;
}
if (thisLine.Length == 0)
{
continue;
}
if (isNumber.Match(thisLine, 0, 1).Success)
{
//We are dealing with MS ion data
string[] ionData = mzSeparator.Split(thisLine);
Ion ion = new Ion(double.Parse(ionData[0]), double.Parse(ionData[1]), thisScan.CromatographyRetentionTime, thisScan.ScanNumber);
//Save our data
thisScan.MSData.Add(ion);
}
else if (thisLine.StartsWith("Z"))
{
string[] theStrings3 = tabSeparator.Split(thisLine);
if (thisScan.Charges == null)
{
thisScan.Charges = new List <int> {
int.Parse(theStrings3[1])
};
thisScan.Precursors = new List <double> {
double.Parse(theStrings3[2])
};
}
else
{
thisScan.Charges.Add(int.Parse(theStrings3[1]));
if (thisScan.Precursors == null)
{
thisScan.Precursors = new List <double>();
}
thisScan.Precursors.Add(double.Parse(theStrings3[2]));
}
}
else if (thisLine.Contains("ActivationType"))
{
string[] theStrings2 = tabSeparator.Split(thisLine);
thisScan.ActivationType = theStrings2[2];
}
else if (thisLine.Contains("InstrumentType"))
{
string[] theStrings2 = tabSeparator.Split(thisLine);
thisScan.InstrumentType = theStrings2[2];
}
else if (thisLine.Contains("RetTime"))
{
string[] theStrings2 = tabSeparator.Split(thisLine);
if (theStrings2.Length == 2)
{
//The retention time is separated with a space so we need to further break it up
string[] s = Regex.Split(theStrings2[1], @" ");
thisScan.CromatographyRetentionTime = double.Parse(s[1]);
}
else if (theStrings2.Length == 3)
{
thisScan.CromatographyRetentionTime = double.Parse(theStrings2[2]);
}
else
{
throw new Exception("Problems parsing Retention time Line.\n" + thisLine);
}
}
else if (thisLine.StartsWith("S"))
{
//Step 1:Save the Old One
if (thisScan.MSData.Count > 0) //Make sure we dont have an empty scan!
{
myScans.Add(thisScan);
}
//Step 2:Get the new one ready
thisScan = new MSParser.MSFull();
string[] theStrings = tabSeparator.Split(thisLine);
thisScan.ScanNumber = int.Parse(theStrings[1]);
thisScan.MSData = new List <Ion>();
if (theStrings.Length != 3)
{
//we are dealing with MS1 - the precursor shall be 0
//We are dealing with MS and should save precursor information
thisScan.ChargedPrecursor = double.Parse(theStrings[3]);
}
if (myScans.Count == noSpectra)
{
bufferScan = thisScan;
break;
}
}
}
if (thisLine == null)
{
sr.Close();
}
cycleCounter++;
return(myScans);
}
public void ParseFile(FileInfo file, double minimumIonIntensity) {
//Get the file to RAM
myScans.Clear();
headerLines.Clear();
ParsedFileInfo = file;
StreamReader sr = new StreamReader(file.OpenRead());
string thisLine;
MSFile thisFile = new MSFile();
thisFile.FileName = file.Name;
int lineCounter = 0; //Helps to debug.
MSParser.MSFull thisScan = new MSParser.MSFull();
while ((thisLine = sr.ReadLine()) != null)
{
lineCounter++;
if (thisLine.Length == 0) { continue; }
if (isNumber.Match(thisLine, 0, 1).Success)
{
//We are dealing with MS ion data
string[] ionData = mzSeparator.Split(thisLine);
Ion ion = new Ion(double.Parse(ionData[0]), double.Parse(ionData[1]), thisScan.CromatographyRetentionTime, thisScan.ScanNumber);
//Save our data
thisScan.MSData.Add(ion);
}
else if (thisLine.StartsWith("H"))
{
headerLines.Add(thisLine);
}
else if (thisLine.StartsWith("Z"))
{
string[] theStrings3 = tabSeparator.Split(thisLine);
if (thisScan.Charges == null)
{
thisScan.Charges = new List<int> { int.Parse(theStrings3[1]) };
thisScan.Precursors = new List<double> { double.Parse(theStrings3[2]) };
}
else
{
thisScan.Charges.Add(int.Parse(theStrings3[1]));
if (thisScan.Precursors == null)
{
thisScan.Precursors = new List<double>();
}
thisScan.Precursors.Add(double.Parse(theStrings3[2]));
}
}
else if (thisLine.Contains("ActivationType"))
{
string[] theStrings2 = tabSeparator.Split(thisLine);
thisScan.ActivationType = theStrings2[2];
}
else if (thisLine.Contains("InstrumentType"))
{
string[] theStrings2 = tabSeparator.Split(thisLine);
thisScan.InstrumentType = theStrings2[2];
}
else if (thisLine.Contains("RetTime"))
{
string[] theStrings2 = tabSeparator.Split(thisLine);
if (theStrings2.Length == 2)
{
//The retention time is separated with a space so we need to further break it up
string[] s = Regex.Split(theStrings2[1], @" ");
thisScan.CromatographyRetentionTime = double.Parse(s[1]);
}
else if (theStrings2.Length == 3)
{
thisScan.CromatographyRetentionTime = double.Parse(theStrings2[2]);
}
else
{
throw new Exception("Problems parsing Retention time Line.\n" + thisLine);
}
}
else if (thisLine.StartsWith("S"))
{
//We have a new spectra // scan
//Denoise our scan
thisScan.MSData.RemoveAll(p => p.Intensity < minimumIonIntensity);
//Compute the ion intensity
foreach (var scan in thisScan.MSData)
{
thisScan.TotalIonIntensity += scan.Intensity;
}
//Step 1:Save the Old One
if (thisScan.MSData.Count > 0) //Make sure we dont have an empty scan!
{
myScans.Add(thisScan);
}
//Step 2:Get the new one ready
thisScan = new MSParser.MSFull();
thisScan.TotalIonIntensity = 0;
string[] theStrings = tabSeparator.Split(thisLine);
thisScan.ScanNumber = int.Parse(theStrings[1]);
thisScan.MSData = new List<Ion>();
if (theStrings.Length != 3)
{
//we are dealing with MS1 - the precursor shall be 0
//We are dealing with MS and should save precursor information
thisScan.ChargedPrecursor = double.Parse(theStrings[3]);
}
}
}
//Save our last scan
myScans.Add(thisScan);
sr.Close();
}
/// <summary>
/// If we dont fint any precursor, we will return 0; this method will only search for 3's and 2's
/// </summary>
/// <param name="percentileTolerance">Suggested 0.05</param>
/// <param name="ppmTolerance"></param>
/// <param name="thePeaks"></param>
/// <returns></returns>
public static Ion FindPrecursorAndCharge(double percentileTolerance, double ppmTolerance, List <Ion> thePeaks, bool considerCharge2)
{
Ion precursor = new Ion(0, 0, 0, 0);
if (thePeaks.Count <= 50)
{
return(precursor);
}
if (percentileTolerance > 1 || percentileTolerance < 0)
{
throw (new Exception("Percentile tolerance out of bounds; use the recomended 0.95"));
}
thePeaks.Sort((a, b) => b.Intensity.CompareTo(a.Intensity));
int chopper = (int)Math.Round((double)thePeaks.Count * percentileTolerance);
List <Ion> mostIntensePeaks = new List <Ion>(chopper);
for (int i = 0; i < chopper; i++)
{
mostIntensePeaks.Add(thePeaks[i]);
}
if (mostIntensePeaks.Count < 10)
{
return(precursor);
}
mostIntensePeaks.Sort((a, b) => a.MZ.CompareTo(b.MZ));
Ion chosenPeak = mostIntensePeaks[0];
//and just a tweak lets find if there is a higher peak within a 5 da range
for (int i = 0; i < mostIntensePeaks.Count; i++)
{
if (mostIntensePeaks[i].Intensity > chosenPeak.Intensity && Math.Abs(chosenPeak.MZ - mostIntensePeaks[i].MZ) < 7)
{
chosenPeak = mostIntensePeaks[i];
}
}
//Now lets verify if there is signal for a charge 2, 3, 4 for this peak; the signal must be at least 10% of the precursor
//For the 4 charge, we will search for 3 and 2, if we dont find nothing, we try the 3, then the two, since the signal is more limited.
//We shal not try higher charges since they are less likey to happen so we could be introducing false positives
double CRP3to2 = (chosenPeak.MZ * 3 - 1) / 2;
double CRP2to1 = (chosenPeak.MZ * 2) - 1;
double CRP3to2Acumulator = 0;
double CRP2to1Acumulator = 0;
for (int i = 0; i < mostIntensePeaks.Count; i++)
{
if (PatternTools.pTools.PPM(CRP3to2, mostIntensePeaks[i].MZ) < ppmTolerance)
{
CRP3to2Acumulator += mostIntensePeaks[i].Intensity;
}
else if (PatternTools.pTools.PPM(CRP2to1, mostIntensePeaks[i].MZ) < ppmTolerance)
{
CRP2to1Acumulator += mostIntensePeaks[i].Intensity;
}
}
if (CRP3to2Acumulator > chosenPeak.Intensity * 0.15)
{
precursor = new Ion(chosenPeak.MZ, chosenPeak.Intensity, chosenPeak.RetentionTime, 0);
precursor.Charge = 3;
}
else if (CRP2to1Acumulator > mostIntensePeaks[0].Intensity * 0.2)
{
precursor = new Ion(chosenPeak.MZ, chosenPeak.Intensity, chosenPeak.RetentionTime, 0);
precursor.Charge = 2;
}
//Make sure we get the peaks back in order by mz
thePeaks.Sort((a, b) => a.MZ.CompareTo(b.MZ));
if ((precursor.Charge == 2 && considerCharge2) || precursor.Charge > 2)
{
return(precursor);
}
else
{
return(new Ion(0, 0, 0, 0));
}
}
/// <summary>
/// Careful! Works only for ions of charge 2
/// </summary>
public static List <Ion> ETDComplementaryIons3(List <Ion> theSpectra, double ppm, Ion precursor, double minimumComplementaryIntensity)
{
List <Ion> cleanedMS = new List <Ion>();
//if the ion is a charge two, //Lets assume that both fragments have charge +1
double predictedPrecursorSumWithProtons = (precursor.MZ * 3) - 1.008;
for (int i = 0; i < theSpectra.Count; i++)
{
if (theSpectra[i].Intensity < minimumComplementaryIntensity)
{
continue;
}
for (int j = 0; j < theSpectra.Count; j++) //Lets associate j with list 2;
{
double massSum = (theSpectra[i].MZ + theSpectra[j].MZ);
if (massSum > (predictedPrecursorSumWithProtons + 2))
{
break;
}
if (PatternTools.pTools.PPM(massSum, predictedPrecursorSumWithProtons) < ppm)
{
if (!cleanedMS.Contains(theSpectra[i]))
{
cleanedMS.Add(theSpectra[i]);
}
if (!cleanedMS.Contains(theSpectra[j]))
{
cleanedMS.Add(theSpectra[j]);
}
}
}
}
return(cleanedMS);
}