//Perdicted monoisotopic with 3 MS1
private MassSpectrum CalCorrectPrecursor(MassSpectrum currentMS2, MassSpectrum currentMS1Spec)
{
if (currentMS1Spec == null || currentMS2 == null)
{
return(currentMS2);
}
List <MassSpectrum> currentMS1 = new List <MassSpectrum>();
//Add current MS1
currentMS1.Add(currentMS1Spec);
CurrentIndexInMS1 = MS1ScanNum.IndexOf(currentMS1Spec.ScanNumber);
//Add current MS1 - 1
if (CurrentIndexInMS1 - 1 > 0)
{
MassSpectrum MS1spec = GetSpectrumByScanNum(MS1ScanNum[CurrentIndexInMS1 - 1]);
currentMS1.Add(MS1spec);
}
//Add current MS1 + 1
if (CurrentIndexInMS1 + 1 < MS1ScanNum.Count)
{
MassSpectrum MS1spec = GetSpectrumByScanNum(MS1ScanNum[CurrentIndexInMS1 + 1]);
currentMS1.Add(MS1spec);
}
////Add current MS1 - 2
//if (CurrentIndexInMS1 - 2 > 0)
//{
// MassSpectrum MS1spec = GetSpectrumByScanNum(MS1ScanNum[CurrentIndexInMS1 - 2]);
// currentMS1.Add(MS1spec);
//}
////Add current MS1 + 2
//if (CurrentIndexInMS1 + 2 < MS1ScanNum.Count)
//{
// MassSpectrum MS1spec = GetSpectrumByScanNum(MS1ScanNum[CurrentIndexInMS1 + 2]);
// currentMS1.Add(MS1spec);
//}
PrecursorCorrector pc = new PrecursorCorrector();
// set the precursor scan number for current spectrum;
currentMS2.PrecursorScanNumber = currentMS1Spec.ScanNumber;
// get the precursor m/z from the scan filter;
double precMz = currentMS2.Precursors.Count == 0 ? 0 : currentMS2.Precursors[0].Item1;
int precZ = currentMS2.Precursors.Count == 0 ? 0 : currentMS2.Precursors[0].Item2;
pc.CorrectPrecursor(ref currentMS2, precMz, precZ, currentMS1Spec.ScanNumber, currentMS1);
return(currentMS2);
}
private void btPredict_Click(object sender, EventArgs e)
{
lbOutput.Items.Clear();
string[] lines = tbExportedSpectrum.Lines;
// define the pattern for matching m/z lines;
string mzLinePattern = @"\d+.\d+\t[ ]+\d+.\d+";
string valuePattern = @"\d+.\d+";
List <Ion> peakList = new List <Ion>();
for (int idx = 0; idx < lines.Length; idx++)
{
MatchCollection matches = Regex.Matches(lines[idx], mzLinePattern);
if (matches.Count > 0)
{
matches = Regex.Matches(matches[0].Groups[0].Value, valuePattern);
double mz = double.Parse(matches[0].Groups[0].Value);
double h = double.Parse(matches[1].Groups[0].Value);
peakList.Add(new Ion(mz, h));
}
}
// get the instrument designated precursor m/z and charge state;
double precMz = double.Parse(lines[lines.Length - 2].Trim());
int precZ = int.Parse(lines[lines.Length - 1].Trim());
// predict the precursors;
PrecursorCorrector pc = new PrecursorCorrector();
List <Envelope> envList = pc.FindEnvelopes(peakList, precMz, precZ);
int counter = 0;
foreach (Envelope env in envList)
{
lbOutput.Items.Add("Envelope " + (++counter) + ":");
lbOutput.Items.Add("\tm/z = " + env.MonoisotPeak.MZ + ", z = " + env.Charge);
lbOutput.Items.Add("\tscore = " + env.Score);
lbOutput.Items.Add("");
}
}
public void Convert(TaskProgress progress)
{
MassSpectrum spec = null;
bool isFirstScan = true;
int currentMs1ScanNum = 0;
bool isScanMS2 = false;
List <MassSpectrum> tmpMS1 = new List <MassSpectrum>();
List <MassSpectrum> NeedToCorrectMS2 = new List <MassSpectrum>();
using (XmlReader reader = XmlReader.Create(_mzmlFile))
{
reader.ReadToFollowing("mzML");
XmlSerializer serializer = new XmlSerializer(typeof(mzMLType));
//Reading mzML file to mzMLType class
mzML = (mzMLType)serializer.Deserialize(reader);
_scanCount = mzML.run.spectrumList.spectrum.Count();
for (int i = 0; i < _scanCount; i++)
{
int scanNum = System.Convert.ToInt32(mzML.run.spectrumList.spectrum[i].index.Replace("\"", ""));
InstrumentType instType = InstrumentType.ELSE;
string filter = "";
string refParGup = "";
double retentionTime = 0;
int msLevel = 0;
double lowMz = 0;
double highMz = 0;
double basePeakMz = 0;
double basePeakIntensity = 0;
double totIonCurrent = 0;
double precursorMz = 0;
int precursorCharge = 0;
byte[] uncompressedMz = null;
byte[] uncompressedIntensity = null;
int shiftByte = 8;
if (mzML.run.spectrumList.spectrum[i].referenceableParamGroupRef != null)
{
// get referenceableParamGroup
refParGup = mzML.run.spectrumList.spectrum[i].referenceableParamGroupRef[0].@ref;
// reference to referenceableParamGroup includes ms level, low MZ, High MZ, basePeak MZ and basePeak Intensity
foreach (var refPargup in mzML.referenceableParamGroupList.referenceableParamGroup)
{
if (refPargup.id == refParGup)
{
foreach (var cvParm in refPargup.cvParam)
{
switch (cvParm.name)
{
case "ms level":
msLevel = System.Convert.ToInt32(cvParm.value.Replace("\"", ""));
break;
case "lowest observed m/z":
lowMz = System.Convert.ToDouble(cvParm.value.Replace("\"", ""));
break;
case "highest observed m/z":
highMz = System.Convert.ToDouble(cvParm.value.Replace("\"", ""));
break;
case "base peak m/z":
basePeakMz = System.Convert.ToDouble(cvParm.value.Replace("\"", ""));
break;
case "base peak intensity":
basePeakIntensity = System.Convert.ToDouble(cvParm.value.Replace("\"", ""));
break;
case "total ion current":
totIonCurrent = System.Convert.ToDouble(cvParm.value.Replace("\"", ""));
break;
}
}
}
}
}
else
{
// if there is no referenceableParamGroupRef get parameters from spectrum's cvParam
foreach (var cvParm in mzML.run.spectrumList.spectrum[i].cvParam)
{
switch (cvParm.name)
{
case "ms level":
msLevel = System.Convert.ToInt32(cvParm.value.Replace("\"", ""));
break;
case "lowest observed m/z":
lowMz = System.Convert.ToDouble(cvParm.value.Replace("\"", ""));
break;
case "highest observed m/z":
highMz = System.Convert.ToDouble(cvParm.value.Replace("\"", ""));
break;
case "base peak m/z":
basePeakMz = System.Convert.ToDouble(cvParm.value.Replace("\"", ""));
break;
case "base peak intensity":
basePeakIntensity = System.Convert.ToDouble(cvParm.value.Replace("\"", ""));
break;
case "total ion current":
totIonCurrent = System.Convert.ToDouble(cvParm.value.Replace("\"", ""));
break;
}
}
}
foreach (var cvParm in mzML.run.spectrumList.spectrum[i].scanList.scan[0].cvParam)
{
switch (cvParm.name)
{
case "scan start time":
//get retention Time
retentionTime = System.Convert.ToDouble(cvParm.value.Replace("\"", ""));
break;
case "filter string":
//get filter
filter = cvParm.value.Replace("\"", "");
break;
}
}
//set current MS1
if (msLevel == 1)
{
currentMs1ScanNum = scanNum;
}
//create a spectrum;
spec = new MassSpectrum(scanNum, mzML.run.spectrumList.spectrum[i].index.Replace("\"", ""), retentionTime, new List <Ion>(), 0, instType, filter, 0, false);
spec.MsLevel = msLevel;
spec.LowMz = lowMz;
spec.HighMz = highMz;
spec.BasePeakMz = basePeakMz;
spec.BasePeakIntensity = basePeakIntensity;
spec.TotIonCurrent = totIonCurrent;
spec.PrecursorScanNumber = currentMs1ScanNum;
spec.Precursors = new List <Tuple <double, int> >();
//set MS2's precursor
if (msLevel == 2)
{
spec.PrecursorScanNumber = currentMs1ScanNum;
//get precursor
foreach (var precursorData in mzML.run.spectrumList.spectrum[i].precursorList.precursor[0].selectedIonList.selectedIon[0].cvParam)
{
if (precursorData.name == "selected ion m/z")
{
precursorMz = System.Convert.ToDouble(precursorData.value.Replace("\"", ""));
}
if (precursorData.name == "charge state")
{
precursorCharge = System.Convert.ToInt32(precursorData.value.Replace("\"", ""));
}
}
spec.Precursors.Add(new Tuple <double, int>(precursorMz, precursorCharge));
}
// get peaks
foreach (var data in mzML.run.spectrumList.spectrum[i].binaryDataArrayList.binaryDataArray)
{
bool mzArray = false;
bool intensityArray = false;
bool zlibCompression = false;
foreach (var cvParm in data.cvParam)
{
switch (cvParm.name)
{
case "m/z array":
mzArray = true;
break;
case "intensity array":
intensityArray = true;
break;
case "zlib compression":
zlibCompression = true;
break;
case "32-bit float":
shiftByte = 4;
break;
}
}
if (mzArray)
{
if (zlibCompression)
{
//uncompression m/z
uncompressedMz = Ionic.Zlib.ZlibStream.UncompressBuffer(data.binary);
}
else
{
uncompressedMz = data.binary;
}
}
else if (intensityArray)
{
if (zlibCompression)
{
//uncompression intensity
uncompressedIntensity = Ionic.Zlib.ZlibStream.UncompressBuffer(data.binary);
}
else
{
uncompressedIntensity = data.binary;
}
}
}
for (int byteIdx = 0; byteIdx < uncompressedMz.Length; byteIdx += shiftByte)
{
byte[] mzBytes = new byte[8];
Buffer.BlockCopy(uncompressedMz, byteIdx, mzBytes, 0, shiftByte);
// retrieve the mz and intensity;
double mz = BitConverter.ToDouble(mzBytes, 0);
byte[] intBytes = new byte[8];
Buffer.BlockCopy(uncompressedIntensity, byteIdx, intBytes, 0, shiftByte);
double intensity = BitConverter.ToDouble(intBytes, 0);
spec.Peaks.Add(new Ion(mz, intensity));
}
// Precursor Correct
if (_correctPrecMz)
{
if (spec.MsLevel == 1)
{
if (isScanMS2)
{
List <MassSpectrum> currentMS1 = new List <MassSpectrum>();
currentMS1.AddRange(tmpMS1);
currentMS1.Add(spec);
for (int j = 0; j < NeedToCorrectMS2.Count; j++)
{
PrecursorCorrector pc = new PrecursorCorrector();
// get the precursor m/z from the scan filter;
double precMz = NeedToCorrectMS2[j].Precursors.Count == 0 ? 0 : NeedToCorrectMS2[j].Precursors[0].Item1;
int precZ = NeedToCorrectMS2[j].Precursors.Count == 0 ? 0 : NeedToCorrectMS2[j].Precursors[0].Item2;
MassSpectrum currentMS2 = NeedToCorrectMS2[j];
pc.CorrectPrecursor(ref currentMS2, precMz, precZ, currentMS2.PrecursorScanNumber, currentMS1);
WriteToOutFiles(currentMS2, isFirstScan);
//clear variable in program
if (j == (NeedToCorrectMS2.Count - 1))
{
WriteToOutFiles(spec, isFirstScan);
isScanMS2 = false;
currentMS1.Clear();
NeedToCorrectMS2.Clear();
if (tmpMS1.Count() >= 2)
{
tmpMS1.RemoveAt(1);
}
tmpMS1.Insert(0, spec);
}
}
}
else
{
if (tmpMS1.Count() >= 2)
{
tmpMS1.RemoveAt(1);
}
tmpMS1.Insert(0, spec);
}
}
else if (spec.MsLevel == 2)
{
NeedToCorrectMS2.Add(spec);
isScanMS2 = true;
}
}
else
{
WriteToOutFiles(spec, isFirstScan);
}
isFirstScan = false;
_spectrumProcessed++;
if (progress.Aborted)
{
break;
}
progress.CurrentProgress = (int)((double)_spectrumProcessed / _scanCount * 100);
//Console.WriteLine(_spectrumProcessed + "\t" + progress.CurrentProgress);
if (progress.CurrentProgress > _lastProgress)
{
_lastProgress = progress.CurrentProgress;
int currentLineCursor = Console.CursorTop;
Console.SetCursorPosition(0, Console.CursorTop);
Console.Write(" Reading mzML File: " + _lastProgress + "%");
Console.SetCursorPosition(0, currentLineCursor);
}
}
}
}
