public static void PrintSpectrumMS2(StreamWriter sr, MSLight theSpectrum, string identification = null, string fileName = null)
{
sr.WriteLine("S\t" + theSpectrum.ScanNumber + "\t" + theSpectrum.ScanNumber + "\t" + theSpectrum.ChargedPrecursor);
sr.WriteLine("I\tRetTime\t" + theSpectrum.CromatographyRetentionTime);
sr.WriteLine("I\tActivationType\t" + theSpectrum.ActivationType);
sr.WriteLine("I\tInstrumentType\t" + theSpectrum.InstrumentType);
foreach (string i in theSpectrum.ILines)
{
sr.WriteLine(i);
}
if (identification != null)
{
sr.WriteLine("I\tPeptide\t" + identification);
}
if (fileName != null)
{
sr.WriteLine("I\tFileName\t" + fileName);
}
foreach (string zLine in theSpectrum.ZLines)
{
sr.WriteLine(zLine);
}
for (int i = 0; i < theSpectrum.MZ.Count; i++)
{
sr.WriteLine(Math.Round(theSpectrum.MZ[i], 5) + " " + Math.Round(theSpectrum.Intensity[i], 5));
}
}
public MSUltraLight(MSLight m, short fileNameIndex)
{
this.CromatographyRetentionTime = (float)m.CromatographyRetentionTime;
this.ScanNumber = m.ScanNumber;
Precursors = new List <Tuple <float, short> >()
{
new Tuple <float, short>((float)m.ChargedPrecursor, (short)m.Zs[0])
};
this.FileNameIndex = fileNameIndex;
// Get list of ion MZs and intensities
this.Ions = new List <Tuple <float, float> >(m.MZ.Count);
for (int i = 0; i < m.MZ.Count; i++)
{
float mz = (float)m.MZ[i];
float intensity = (float)m.Intensity[i];
this.Ions.Add(new Tuple <float, float>(mz, intensity));
}
}
/// <summary>
/// The result is sorted by scan number
/// </summary>
/// <param name="fileName"></param>
/// <returns></returns>
public static List <MSLight> ParseLightMS2(string fileName)
{
FileInfo fi = new FileInfo(fileName);
if (!fi.Exists)
{
throw new Exception("File " + fi.FullName + " not found.");
}
List <MSLight> theSpectra = new List <MSLight>(100);
if (fi.Extension.Equals(".ms2") || fi.Extension.Equals(".ms3"))
{
//The PathCandidates
Regex tabSeparator = new Regex(@"\t");
Regex mzSeparator = new Regex(@"\s+", RegexOptions.Compiled);
Regex isNumber = new Regex(@"^[0-9]", RegexOptions.Compiled);
Regex RegExRetTime = new Regex(@"RetTime");
Regex RegexActivationType = new Regex(@"ActivationType");
Regex RegexInstrumentType = new Regex(@"InstrumentType");
StreamReader sr = new StreamReader(fileName);
string line;
MSLight ms = new MSLight();
while ((line = sr.ReadLine()) != null)
{
if (isNumber.IsMatch(line))
{
string[] cols = mzSeparator.Split(line);
ms.MZ.Add(double.Parse(cols[0]));
ms.Intensity.Add(double.Parse(cols[1]));
}
else if (RegexActivationType.IsMatch(line))
{
string[] theStrings2 = tabSeparator.Split(line);
ms.ActivationType = theStrings2[2];
}
else if (line.StartsWith("I\t"))
{
ms.ILines.Add(line);
}
else if (RegExRetTime.IsMatch(line))
{
string[] theStrings2 = tabSeparator.Split(line);
ms.CromatographyRetentionTime = double.Parse(theStrings2[2]);
}
else if (RegexInstrumentType.IsMatch(line))
{
string[] theStrings2 = tabSeparator.Split(line);
ms.InstrumentType = theStrings2[2];
}
else if (line.StartsWith("Z"))
{
ms.ZLines.Add(line);
}
else if (line.StartsWith("S"))
{
//We have a new spectra // scan
theSpectra.Add(ms);
//Step 2:Get the new one ready
ms = new MSLight();
string[] cols = tabSeparator.Split(line);
ms.ScanNumber = int.Parse(cols[1]);
if (cols.Length == 4)
{
//This is an MS2 spectra
ms.ChargedPrecursor = double.Parse(cols[3]);
}
ms.FileInformation = fi;
}
}
theSpectra.Add(ms);
sr.Close();
//Just in case
theSpectra.Sort((a, b) => a.ScanNumber.CompareTo(b.ScanNumber));
theSpectra.RemoveAt(0);
return(theSpectra);
}
else if (fi.Extension.Equals(".xxmzML"))
{
Console.WriteLine("CSMSL mzML parser activated");
//Mzml mm = new Mzml(fileName);
//mm.Open();
//foreach (MSDataScan<MZSpectrum> scan in mm)
//{
// MSLight m = new MSLight();
// Spectrum<MZPeak, MZSpectrum> spec = scan.MassSpectrum;
// m.MZ = spec.GetMasses().Select(a => Math.Round(a, 5)).ToList();
// m.Intensity = spec.GetIntensities().Select(a => Math.Round(a, 5)).ToList();
// m.ScanNumber = scan.SpectrumNumber;
// m.CromatographyRetentionTime = scan.RetentionTime;
// m.IonInjectionTime = scan.InjectionTime;
// //"1000511 MS level 1";
// Console.WriteLine("\tMS level :" + scan.MsnOrder);
// int msLevel = scan.MsnOrder;
// m.ILines.Add("I\tms_level\t" + msLevel);
// if (msLevel > 1)
// {
// //Precursor info
// m.ChargedPrecursor = Math.Round(mm.GetPrecursorMz(scan.SpectrumNumber), 5);
// double z = (double)mm.GetPrecusorCharge(scan.SpectrumNumber);
// double mh = Math.Round(PatternTools.pTools.DechargeMSPeakToPlus1(m.ChargedPrecursor, z), 5);
// m.ZLines.Add("Z\t" + z + "\t" + mh);
// m.MHPrecursor.Add(mh);
// //Not working
// //m.ILines.Add("I\tPrecursorScan\t" + mm.GetParentSpectrumNumber(ds.SpectrumNumber));
// DissociationType dt = mm.GetDissociationType(scan.SpectrumNumber);
// if (dt == DissociationType.CID)
// m.ActivationType = "CID";
// else if (dt == CSMSL.Proteomics.DissociationType.ETD)
// m.ActivationType = "ETD";
// else if (dt == CSMSL.Proteomics.DissociationType.ECD)
// m.ActivationType = "ECD";
// else if (dt == CSMSL.Proteomics.DissociationType.HCD)
// m.ActivationType = "HCD";
// else if (dt == CSMSL.Proteomics.DissociationType.MPD)
// m.ActivationType = "MPD";
// else if (dt == CSMSL.Proteomics.DissociationType.NPTR)
// m.ActivationType = "NF";
// else if (dt == CSMSL.Proteomics.DissociationType.PQD)
// m.ActivationType = "PQD";
// else
// m.ActivationType = null;
// }
// MZAnalyzerType mzat = mm.GetMzAnalyzer(m.ScanNumber);
// if (mzat == MZAnalyzerType.FTICR)
// {
// m.InstrumentType = "FTICR";
// }
// else if (mzat == MZAnalyzerType.IonTrap2D)
// {
// m.InstrumentType = "Ion Trap 2D";
// }
// else if (mzat == MZAnalyzerType.IonTrap3D)
// {
// m.InstrumentType = "ITMS";
// }
// else if (mzat == MZAnalyzerType.Orbitrap)
// {
// m.InstrumentType = "FTMS";
// }
// else if (mzat == MZAnalyzerType.Quadrupole)
// {
// m.InstrumentType = "Quadrupole";
// }
// else if (mzat == MZAnalyzerType.Sector)
// {
// m.InstrumentType = "Sector";
// }
// else if (mzat == MZAnalyzerType.TOF)
// {
// m.InstrumentType = "TOF";
// }
// else if (mzat == MZAnalyzerType.Unknown)
// {
// m.InstrumentType = "Unknown";
// }
// theSpectra.Add(m);
// Console.WriteLine(m.ScanNumber);
//}
//return theSpectra;
return(null);
}
else
{
throw new Exception(fi.Extension + " is not an acceptable extendion");
}
}
