private Ion GetPrecursor(string filter, MSLight lastMS1)
{
Match precursorM = capturePrecursor.Match(filter);
double chargedPrecursor = double.Parse(precursorM.Groups[1].ToString());
double intensity = -1;
double mz = -1;
//now we need to get the closest peak to the MS1 peaks
for (int i = 0; i < lastMS1.MZ.Count; i++)
{
if (Math.Abs(PatternTools.pTools.PPM(lastMS1.MZ[i], chargedPrecursor)) <= MyParams.PPMToleranceForInferingPrecursorMZ)
{
if (lastMS1.Intensity[i] > intensity)
{
intensity = lastMS1.Intensity[i];
mz = lastMS1.MZ[i];
}
}
}
if (mz == -1)
{
mz = chargedPrecursor;
intensity = 0;
}
return(new Ion(mz, intensity, lastMS1.CromatographyRetentionTime, lastMS1.ScanNumber));
}
private void ButtonLoadExample_Click(object sender, RoutedEventArgs e)
{
string peptide = TextBoxPeptide.Text;
//Get the experimental
string[] lines = Regex.Split(SpectrumViewer2.Properties.Resources.ExampleSpectrum, "\n");
MSLight msExperimental = new MSLight();
List <double> mz = new List <double>();
List <double> intensities = new List <double>();
foreach (string l in lines)
{
string[] mzI = Regex.Split(l, "\t");
mz.Add(double.Parse(mzI[0]));
intensities.Add(double.Parse(mzI[1]));
}
msExperimental.MZ = mz;
msExperimental.Intensity = intensities;
MainViewer1.PlotAnotatedSpectrum(msExperimental, 500, peptide);
}
public MultiNotchMS3Item(MSLight scn)
{
string precursorScan = scn.ILines.Find(a => a.Contains("PrecursorScan"));
string[] cols = Regex.Split(precursorScan, "\t");
MyIons = scn.Ions;
MS2PrecursorScan = int.Parse(cols[2]);
}
public static string PrintSpectrumMS2(MSLight ms)
{
StringBuilder sw = new StringBuilder();
bool isFullScan = false;
if (ms.ActivationType.Equals(""))
{
isFullScan = true;
}
sw.Append("S\t" + ms.ScanNumber.ToString("000000") + "\t" + ms.ScanNumber.ToString("000000"));
if (isFullScan)
{
sw.Append("\n");
}
else
{
sw.Append("\t" + ms.ChargedPrecursor + "\n");
}
sw.Append("I\tRetTime\t" + ms.CromatographyRetentionTime + "\n");
sw.Append("I\tIonInjectionTime\t" + ms.IonInjectionTime + "\n");
if (!isFullScan)
{
sw.Append("I\tActivationType\t" + ms.ActivationType + "\n");
}
sw.Append("I\tInstrumentType\t" + ms.InstrumentType + "\n");
if (!isFullScan)
{
foreach (string s in ms.ILines)
{
sw.Append(s + "\n");
}
foreach (string zLine in ms.ZLines)
{
//Write the Z Lines
sw.Append(zLine + "\n");
}
}
List <Ion> myIons = ms.Ions;
myIons.Sort((a, b) => a.MZ.CompareTo(b.MZ));
for (int i = 0; i < myIons.Count; i++)
{
sw.Append(myIons[i].MZ + " " + myIons[i].Intensity + "\n");
}
return(sw.ToString());
}
private List <Ion> GetIonsFromSpectrum(MSLight ms)
{
List <Ion> theIons = new List <Ion>(ms.MZ.Count);
for (int i = 0; i < ms.MZ.Count; i++)
{
theIons.Add(new Ion(ms.MZ[i], ms.Intensity[i], 0, 0));
}
return(theIons);
}
public void PlotAnotatedSpectrum(MSLight msExperimental, double ppm, string peptide)
{
//Predict the spectrum
//Find PTMs
List <ModificationItem> mods = SpectraPredictor.GetVMods(peptide);
SpectralPredictionParameters spp = new SpectralPredictionParameters(false, true, false, false, true, false, true, true, 2, true, mods);
SpectraPredictor sp = new SpectraPredictor(spp);
List <PredictedIon> theoreticalSpectrum = sp.PredictPeaks(peptide, 2, 1950, msExperimental, 500);
DataGridResultTable.ItemsSource = theoreticalSpectrum;
SpectrumEye1.Plot(msExperimental.Ions, msExperimental.Ions[0].MZ, msExperimental.Ions.Last().MZ, ppm, theoreticalSpectrum);
}
/// <summary>
///
/// </summary>
/// <param name="rawFile">The Thermo RAW File</param>
/// <param name="scanNumbers">If no scan numbers are in the array the filter will search for all scan numbers</param>
/// <returns></returns>
public List <MSLight> GetSpectra(string rawFile, List <int> scanNumbers, bool onlyMS1)
{
Console.WriteLine("Parsing " + rawFile);
MSFileReaderLib.MSFileReader_XRawfile m2 = new MSFileReaderLib.MSFileReader_XRawfile();
m2.Open(rawFile);
m2.SetCurrentController(0, 1);
//string filter2 = "";
//m2.GetFilterForScanNum(50, ref filter2);
int noSpectra = 0;
m2.GetNumSpectra(ref noSpectra);
MSLight lastMS1 = new MSLight();
List <MSLight> mySpectra = new List <MSLight>(noSpectra);
for (int i = 1; i <= noSpectra; i++)
{
string filter = null;
if (scanNumbers.Count == 0 || scanNumbers.Contains(i))
{
m2.GetFilterForScanNum(i, ref filter);
MSLight thisMS = new MSLight();
Ion precursor = new Ion(-1, -1, -1, -1);
if (isMS1.IsMatch(filter))
{
lastMS1 = thisMS;
}
else
{
if (onlyMS1)
{
continue;
}
if (!MyParams.UseThermoMonoIsotopicPrediction)
{
precursor = GetPrecursor(filter, lastMS1);
}
}
//-------------
double retentionTime = 0;
m2.RTFromScanNum(i, ref retentionTime);
string thisFilter = null;
m2.GetFilterForScanNum(i, ref thisFilter);
string flags = null;
m2.GetFlags(ref flags);
//------------
double scanCentroidPeakWidth = 0.005;
int arraySize = maxNoPeaks;
object massList = null;
object peakFlags = null;
m2.GetMassListFromScanNum(
ref i,
filter,
scanIntensityCutoffType,
scanIntensityCutoffValue,
maxNoPeaks,
scanCentroidResult,
ref scanCentroidPeakWidth,
ref massList,
ref peakFlags,
ref arraySize);
thisMS.ScanNumber = i;
object trailerLabels = null;
object trailerValues = null;
int cc = 0;
m2.GetTrailerExtraForScanNum(i, ref trailerLabels, ref trailerValues, ref cc);
object chargeStateObject = null;
m2.GetTrailerExtraValueForScanNum(i, "Charge State:", ref chargeStateObject);
double chargeState = double.Parse(chargeStateObject.ToString());
string[] theStringValues = (string[])trailerValues;
if (theStringValues[1].Contains("="))
{
string [] split = Regex.Split(theStringValues[1], "=");
string [] correction = Regex.Split(split[1], ";");
thisMS.IonInjectionTime = double.Parse(correction[0]);
}
else
{
thisMS.IonInjectionTime = double.Parse(theStringValues[2]);
}
Match instrument = captureInstrumentType.Match(filter);
thisMS.InstrumentType = instrument.Groups[1].ToString();
thisMS.ILines.Add("I\tFilter\t" + filter);
Match activationType = captureActivationType.Match(filter);
thisMS.ActivationType = activationType.Groups[1].ToString().ToUpper();
if (!thisMS.ActivationType.Equals(""))
{
if (MyParams.UseThermoMonoIsotopicPrediction)
{
object monoisotopicObject = null;
m2.GetTrailerExtraValueForScanNum(i, "Monoisotopic M/Z:", ref monoisotopicObject);
double objectValue = Math.Round(double.Parse(monoisotopicObject.ToString()), 4);
if (objectValue == 0)
{
//Thermo was unable to determine precursor so we will try to get it.
precursor = GetPrecursor(filter, lastMS1);
thisMS.ChargedPrecursor = precursor.MZ;
}
else
{
precursor = new Ion(objectValue, 1, 1, i);
//Console.WriteLine("Monoisotopic Thermo: " + precursor.MZ);
thisMS.ChargedPrecursor = precursor.MZ;
}
}
else
{
thisMS.ChargedPrecursor = precursor.MZ;
}
if (chargeState == 0)
{
thisMS.ZLines.Add("Z\t2\t" + Math.Round(PatternTools.pTools.DechargeMSPeakToPlus1(precursor.MZ, 2), 4));
thisMS.ZLines.Add("Z\t3\t" + Math.Round(PatternTools.pTools.DechargeMSPeakToPlus1(precursor.MZ, 3), 4));
}
else
{
thisMS.ZLines.Add("Z\t" + int.Parse(chargeState.ToString()).ToString() + "\t" + Math.Round(PatternTools.pTools.DechargeMSPeakToPlus1(precursor.MZ, chargeState), 4));
}
thisMS.ILines.Add("I\tPrecursorScan\t" + lastMS1.ScanNumber);
thisMS.ILines.Add("I\tPrecursorInt\t" + precursor.Intensity);
}
double[,] thisMassList = (double[, ])massList;
int l = thisMassList.GetLength(1);
double[] mz = new double[thisMassList.GetLength(1)];
double[] intensity = new double[thisMassList.GetLength(1)];
for (int counter = 0; counter < thisMassList.GetLength(1); counter++)
{
if (thisMassList[1, counter] > 0.5) //check if we have a minimum intensity
{
mz[counter] = Math.Round(thisMassList[0, counter], 5);
intensity[counter] = Math.Round(thisMassList[1, counter], 1);
//thisMS.MZ.Add(Math.Round(thisMassList[0, counter], 5));
//thisMS.Intensity.Add(Math.Round(thisMassList[1, counter], 1));
}
}
if (mz.Length == 0) //There is no use in saving an empty MS
{
continue;
}
thisMS.MZ = mz.ToList();
thisMS.Intensity = intensity.ToList();
thisMS.CromatographyRetentionTime = Math.Round(retentionTime, 3);
//----------------------------
mySpectra.Add(thisMS);
}
}
Console.WriteLine(".");
m2.Close();
//Some final cleanup
mySpectra.RemoveAll(a => a.MZ.Count < 5);
if (MyParams.ActivateSpectraCleaner)
{
CleanSpectra(mySpectra);
}
return(mySpectra);
}
public List <PredictedIon> PredictPeaks(string iPeptide, double precursorCharge, double theoreticalMassMH, MSLight ms, double ppm)
{
List <PredictedIon> result = PredictPeaks(iPeptide, precursorCharge, theoreticalMassMH);
foreach (PredictedIon pi in result)
{
if (ms.MZ.Exists(a => Math.Abs(PatternTools.pTools.PPM(a, pi.MZ)) <= ppm))
{
pi.Matched = true;
}
}
return(result);
}
public void PlotSpectrum(MSLight msExperimental)
{
SpectrumEye1.Plot(msExperimental.Ions, msExperimental.Ions[0].MZ, msExperimental.Ions.Last().MZ, 0);
}
static void Main(string[] args)
{
// Generate DTA
string dtaDir = @"C:\Users\pcarvalho\Desktop\Juli_fosfo\DTA\out";
string inputSQT = @"C:\Users\pcarvalho\Desktop\Colaborations\Juli_fosfo\DTA\20140410_JF_HAP50mmmS2.sqt";
string inputMS2 = @"C:\Users\pcarvalho\Desktop\Colaborations\Juli_fosfo\DTA\20140410_jf_hap50mmms2.ms2";
if (true) //Remove MSMS from a file
{
int targetNoSpectra = 9917;
List <MSLight> theMS = PatternTools.MSParserLight.ParserLight.ParseLightMS2(inputMS2);
string outputMS2 = @"C:\Users\pcarvalho\Desktop\Colaborations\Juli_fosfo\DTA\Removed3_20140410_jf_hap50mmms2.ms2";
while (theMS.Count > targetNoSpectra)
{
int scnRemove = PatternTools.pTools.getRandomNumber(theMS.Count - 1);
theMS.RemoveAt(scnRemove);
}
PatternTools.MSParser.MSPrinter.PrintMSListToFile(theMS, outputMS2, "", MSFileFormat.ms2);
Console.WriteLine("Done!");
}
//Generate a side by side table of XDScores and AScores
if (false) //Generate a side by side table of XDScores and AScores
{
XDScore.XDScore xdScore = new XDScore.XDScore(new List <string>()
{
inputSQT
}, true);
SQTParser2 sqtParser = new SQTParser2();
List <SQTScan2> theSQT = sqtParser.Parse(inputSQT);
//Parse the aScore File
StreamReader sr = new StreamReader(@"C:\Users\pcarvalho\Desktop\Juli_fosfo\DTA\AllResults.txt");
string line;
StreamWriter sw = new StreamWriter(@"C:\Users\pcarvalho\Desktop\Juli_fosfo\DTA\AScoreXDScoreGoodScores.txt");
while ((line = sr.ReadLine()) != null)
{
string[] cols = Regex.Split(line, "[-|\t]");
double aScore = double.Parse(cols[2]);
int scanNo = int.Parse(cols[0]);
SQTScan2 theScan = theSQT.Find(a => a.ScanNumber == scanNo);
if (theScan.Matches[0].PrimaryScore > 2 && theScan.ChargeState == 2)
{
double xd = xdScore.GetDeltaScore(theScan, false);
sw.WriteLine(scanNo + "\t" + aScore + "\t" + xd);
}
}
sr.Close();
sw.Close();
}
if (false)
{
SQTParser2 sqtParser = new SQTParser2();
List <SQTScan2> myScans = sqtParser.Parse(inputSQT);
List <MSLight> theMS2 = PatternTools.MSParserLight.ParserLight.ParseLightMS2(inputMS2);
myScans.RemoveAll(a => a.Matches.Count == 0);
myScans.RemoveAll(a => !a.Matches[0].PeptideSequence.Contains("79"));
foreach (SQTScan2 scn in myScans)
{
try
{
Console.Write(".");
MSLight thems = theMS2.Find(a => a.ScanNumber == (int)scn.ScanNumber);
string pepSeq = scn.Matches[0].PeptideSequence;
pepSeq = Regex.Replace(pepSeq, @"\(\+79\.966300\)", "Z");
StreamWriter sw = new StreamWriter(dtaDir + "/" + scn.ScanNumber + "-" + pepSeq + ".dta");
sw.WriteLine(thems.MHPrecursor[0] + " " + thems.Zs[0].ToString());
foreach (Ion i in thems.Ions)
{
sw.WriteLine(i.MZ + " " + i.Intensity);
}
sw.Close();
} catch
{
Console.Write("P");
}
}
}
if (false)
{
DirectoryInfo di = new DirectoryInfo(dtaDir);
FileInfo[] theFiles = di.GetFiles("*.dta");
StreamWriter sw = new StreamWriter(@"C:\Users\pcarvalho\Desktop\Juli_fosfo\DTA\result.txt");
foreach (FileInfo fi in theFiles)
{
// Read file data
FileStream fs = new FileStream(fi.FullName, FileMode.Open, FileAccess.Read);
byte[] data = new byte[fs.Length];
fs.Read(data, 0, data.Length);
fs.Close();
// Generate post objects
Dictionary <string, object> postParameters = new Dictionary <string, object>();
postParameters.Add("fileformat", "txt");
postParameters.Add("userfile", new FormUpload.FileParameter(data, fi.Name, "application/msword"));
postParameters.Add("mods", "1"); //Cystein
postParameters.Add("MAX_FILE_SIZE", "40000");
string [] cols = Regex.Split(fi.Name, "[-|.]");
string pepS = Regex.Replace(cols[1], "Z", "*");
postParameters.Add("sequence", pepS);
postParameters.Add("submit", "Calculate Ascore");
HttpWebResponse webResponse = FormUpload.MultipartFormDataPost(@"http://ascore.med.harvard.edu/trim/trim-single.php", "PhosphoPeptide", postParameters);
// Process response
StreamReader responseReader = new StreamReader(webResponse.GetResponseStream());
string fullResponse = responseReader.ReadToEnd();
webResponse.Close();
string[] cols2 = Regex.Split(fullResponse, "\n");
Regex getNo = new Regex("[0-9]+.[0-9]+");
try
{
foreach (var m in getNo.Matches(cols2[39]))
{
sw.WriteLine(fi.Name + "\t" + m.ToString());
Console.WriteLine(m.ToString());
sw.Flush();
}
}
catch { Console.Write("f"); }
fi.Delete();
}
sw.Close();
}
if (false)
{
// Read file data
string file = @"C:\Users\pcarvalho\Desktop\Juli_fosfo\ToMSAorNotToMSA\test.txt";
FileStream fs = new FileStream(file, FileMode.Open, FileAccess.Read);
byte[] data = new byte[fs.Length];
fs.Read(data, 0, data.Length);
fs.Close();
// Generate post objects
Dictionary <string, object> postParameters = new Dictionary <string, object>();
//postParameters.Add("fileformat", "txt");
postParameters.Add("userfile", new FormUpload.FileParameter(data, file, "application/msword"));
postParameters.Add("mods", "1"); //Cystein
postParameters.Add("MAX_FILE_SIZE", "40000");
postParameters.Add("sequence", "IEDVGS*DEEDDSGK");
postParameters.Add("submit", "Calculate Ascore");
HttpWebResponse webResponse = FormUpload.MultipartFormDataPost(@"http://ascore.med.harvard.edu/trim/trim-single.php", "PhosphoPeptide", postParameters);
// Process response
StreamReader responseReader = new StreamReader(webResponse.GetResponseStream());
string fullResponse = responseReader.ReadToEnd();
webResponse.Close();
string[] cols = Regex.Split(fullResponse, "\n");
Regex getNo = new Regex("[0-9]+.[0-9]+");
foreach (var m in getNo.Matches(cols[39]))
{
Console.WriteLine(m.ToString());
}
Console.WriteLine("Done");
}
}
