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);
}
public LFPeptide psmToLFPeptide(PSM psm, ThermoRawFile rawFile)
{
var pep = new LFPeptide
{
ms2ScanNumber = psm.scanNumber,
sequence = psm.peptide.Sequence,
charge = psm.charge,
TheoreticalMZ = psm.mzCalc
};
pep.parentMS1 = rawFile.GetParentSpectrumNumber(pep.ms2ScanNumber);
pep.parentMS1Time = rawFile.GetRetentionTime(pep.parentMS1);
//pep.UserMZ = psm.mzObs;
pep.UserMZ = rawFile.GetPrecursorMz(pep.ms2ScanNumber);
return(pep);
}
public void crunch(string rawFilePath, string byonicResultsPath, string outputFolderPath)
{
List <PSM> allPsmsQuant = new List <PSM>();
OnUpdateProgress(0.25);
ThermoRawFile rawFile = new ThermoRawFile(@rawFilePath);
rawFile.Open();
String file = Path.GetFileNameWithoutExtension(byonicResultsPath);
StreamReader byonicFile = new StreamReader(byonicResultsPath);
StreamWriter outputSummary = new StreamWriter(@outputFolderPath + "\\" + file + "_summary.csv");
//StreamWriter outputList = new StreamWriter(@outputFolderPath + "\\" + file + "_list.txt");
//Write Headers
//outputList.WriteLine("Prot.Rank\tSequence\tPeptideParseFriendly\tPeptide\tPos.\tMods(variable)\tGlycans\t"+
// "PEP2D\tPEP1D\t|Log Prob|\tScore\tDeltaScore\tDelta Mod.Score\tCharge\tObs.m/z\t"+
// "Precursor Theoretical m/z (Th)\tppmerr.\tObs.MH\tCalc.MH\tCleavage\tGlycansPos.\tProteinName" +
// "\tProt.Id\tScanTime\tSpectrum Number\tMods(fixed)\tFDR2D\tFDR1D\t"+
// "FDR uniq.2D\tFDR uniq.1D\tq-value2D\tq-value1D\tisGlycoPeptide\tmodsPassedCheck" +
// "\tpositionPassedCheck\tfragmentation\tMasterScan");
List <int> HCDscans = new List <int>();
List <int> ETDscans = new List <int>();
int totalMSMSscans = 0;
//these will have decoys and targets, so only use is for FDR calc (FDR calc will be at PSM level)
List <PSM> allPSMs = new List <PSM>();
List <PSM> hcdPSMs = new List <PSM>();
List <PSM> etdPSMs = new List <PSM>();
List <PSM> allGlycoPSMs = new List <PSM>();
List <PSM> hcdGlycoPSMs = new List <PSM>();
List <PSM> etdGlycoPSMs = new List <PSM>();
//use this to print file to use in next program
//List<PSM> masterListPSMs = new List<PSM>();
//these will have no decoys, so use for counts and other processing
Dictionary <string, List <PSM> > allPSMsNODECOY = new Dictionary <string, List <PSM> >();
Dictionary <string, List <PSM> > hcdPSMsNODECOY = new Dictionary <string, List <PSM> >();
Dictionary <string, List <PSM> > etdPSMsNODECOY = new Dictionary <string, List <PSM> >();
Dictionary <string, List <PSM> > allGlycoPSMsNODECOY = new Dictionary <string, List <PSM> >();
Dictionary <string, List <PSM> > hcdGlycoPSMsNODECOY = new Dictionary <string, List <PSM> >();
Dictionary <string, List <PSM> > etdGlycoPSMsNODECOY = new Dictionary <string, List <PSM> >();
for (int i = rawFile.FirstSpectrumNumber; i <= rawFile.LastSpectrumNumber; i++)
{
if (rawFile.GetMsnOrder(i) == 2)
{
if (rawFile.GetDissociationType(i).ToString().Equals("HCD"))
{
HCDscans.Add(i);
}
if (rawFile.GetDissociationType(i).ToString().Equals("ETD"))
{
ETDscans.Add(i);
}
totalMSMSscans++;
}
}
//Added to accomodate PRM exps
bool isPRM = false;
using (var csv = new CsvReader(byonicFile, true, '\t'))
{
while (csv.ReadNextRecord())
{
try
{
List <int> glycanPositionsList = new List <int>();
string PID = "NA";//csv["PID"];
string protRank = csv["ProtRank"];
string byonicSequence = csv["Sequence"];
string peptidesToBeParsed = csv["PeptideParseFriendly"];
// NEW
string aminoAcidSequence = peptidesToBeParsed.Split(',')[0];
string byonicIntensity = "NA"; //csv["Intensity"];
int peptideStartPosition = int.Parse(csv["Pos."]);
string modsToBeParsed = csv["Mods(variable)"];
string glycansToBeParsed = csv["Glycans"];
double PEP2D = double.Parse(csv["PEP2D"]);
double PEP1D = double.Parse(csv["PEP1D"]);
double logProb = 0; // double.Parse(csv["|Log Prob|"]);
double score = double.Parse(csv["Score"]);
double deltaScore = double.Parse(csv["DeltaScore"]);
double deltaModScore = double.Parse(csv["Delta Mod.Score"]);
int charge = int.Parse(csv["z"]);
double mzObs = double.Parse(csv["Obs.m/z"]);
double mzCalc = double.Parse(csv["Calc.m/z"]);
//double ppmError = double.Parse(csv["ppmerr."]);
string ppmError = csv["ppmerr."];
double obsMH = double.Parse(csv["Obs.MH"]);
double calcMH = double.Parse(csv["Calc.MH"]);
string cleavage = csv["Cleavage"];
string glycanPositions = csv["GlycansPos."];
string proteinName = csv["ProteinName"];
int protID = int.Parse(csv["Prot.Id"]);
double scanTime = double.Parse(csv["ScanTime"]);
int scanNumber = int.Parse(csv["Scan #"]);
string modsFixed = csv["Mods(fixed)"];
double FDR2D = double.Parse(csv["FDR2D"]);
double FDR1D = double.Parse(csv["FDR1D"]);
double FDR2Dunique = double.Parse(csv["FDR uniq.2D"]);
double FDR1Dunique = double.Parse(csv["FDR uniq.1D"]);
double qvalue2D = double.Parse(csv["q-value2D"]);
double qvalue1D = double.Parse(csv["q-value1D"]);
// Flags to be used
bool isGlycoPeptide = false;
bool modsPassedCheck = false;
bool positionsPassedCheck = false;
if (modsToBeParsed.Contains("Glycan"))
{
isGlycoPeptide = true;
}
string fragmentation = rawFile.GetDissociationType(scanNumber).ToString();
//ThermoSpectrum spectrum = rawFile.GetSpectrum(scanNumber);
string[] parsedPeptide = peptidesToBeParsed.Split(',');
Peptide peptide = new Peptide(parsedPeptide[0]);
//string[] parsedSequenceWithMods = sequence.Split('.');
//string uniqueSequence = parsedSequenceWithMods[1];
string uniqueSequence = byonicSequence.Substring(2, byonicSequence.Length - 4);
//Console.WriteLine(uniqueSequence);
//Console.WriteLine(newSequence);
//Console.ReadKey();
//add to master list here
if (!String.IsNullOrEmpty(modsToBeParsed))
{
string[] modsParsedArrary = modsToBeParsed.Split(';');
for (int i = 0; i < modsParsedArrary.Length; i++)
{
string mod = modsParsedArrary[i];
//Console.WriteLine(mod);
//Console.ReadKey();
if (mod[0].Equals(' '))
{
mod = mod.Substring(1);
}
if (mod.Contains("NGlycan") && !mod[0].Equals('N'))
{
modsPassedCheck = false;
}
if (mod.Contains("NGlycan") && mod[0].Equals('N'))
{
modsPassedCheck = true;
}
if (mod.Contains("OGlycan") && mod[0].Equals('S'))
{
modsPassedCheck = true;
}
if (mod.Contains("OGlycan") && mod[0].Equals('T'))
{
modsPassedCheck = true;
}
}
}
if (!String.IsNullOrEmpty(glycanPositions))
{
string[] glycansPosParsedArray = glycanPositions.Split(';');
for (int i = 0; i < glycansPosParsedArray.Length; i++)
{
int glycanPos = Convert.ToInt32(glycansPosParsedArray[i]);
glycanPositionsList.Add(glycanPos);
}
}
OnUpdateProgress(0.5);
if (glycanPositionsList.Count != glycanPositionsList.Distinct().Count())
{
positionsPassedCheck = false;
}
else
{
positionsPassedCheck = true;
}
int masterScan = 0;
try
{
masterScan = rawFile.GetParentSpectrumNumber(scanNumber);
}catch (Exception e)
{
// Included for PRM (MS2 has not master scan)
isPRM = true;
}
PSM psm = new PSM(peptide, PID, protRank, peptidesToBeParsed, peptideStartPosition, modsToBeParsed, glycansToBeParsed,
PEP2D, PEP1D, logProb, score, deltaScore, deltaModScore, charge, mzObs, mzCalc, ppmError,
obsMH, calcMH, cleavage, glycanPositions, proteinName, protID, scanTime, scanNumber, modsFixed, FDR2D, FDR1D,
FDR2Dunique, FDR1Dunique, qvalue2D, qvalue1D, isGlycoPeptide, fragmentation, byonicSequence,
modsPassedCheck, masterScan, positionsPassedCheck, byonicIntensity);//, spectrum);
allPSMs.Add(psm);
if (fragmentation.Equals("HCD"))
{
hcdPSMs.Add(psm);
}
if (fragmentation.Equals("ETD"))
{
etdPSMs.Add(psm);
}
if (isGlycoPeptide)
{
allGlycoPSMs.Add(psm);
if (fragmentation.Equals("HCD"))
{
hcdGlycoPSMs.Add(psm);
}
if (fragmentation.Equals("ETD"))
{
etdGlycoPSMs.Add(psm);
}
}
if (!proteinName.Contains("DECOY") && !proteinName.Contains("Reverse") && modsPassedCheck && positionsPassedCheck)
{
if (!allPSMsNODECOY.ContainsKey(uniqueSequence))
{
allPSMsNODECOY.Add(uniqueSequence, new List <PSM>());
}
allPSMsNODECOY[uniqueSequence].Add(psm);
if (fragmentation.Equals("HCD"))
{
if (!hcdPSMsNODECOY.ContainsKey(uniqueSequence))
{
hcdPSMsNODECOY.Add(uniqueSequence, new List <PSM>());
}
hcdPSMsNODECOY[uniqueSequence].Add(psm);
}
if (fragmentation.Equals("ETD"))
{
if (!etdPSMsNODECOY.ContainsKey(uniqueSequence))
{
etdPSMsNODECOY.Add(uniqueSequence, new List <PSM>());
}
etdPSMsNODECOY[uniqueSequence].Add(psm);
}
if (isGlycoPeptide)
{
if (!allGlycoPSMsNODECOY.ContainsKey(uniqueSequence))
{
allGlycoPSMsNODECOY.Add(uniqueSequence, new List <PSM>());
}
allGlycoPSMsNODECOY[uniqueSequence].Add(psm);
if (fragmentation.Equals("HCD"))
{
if (!hcdGlycoPSMsNODECOY.ContainsKey(uniqueSequence))
{
hcdGlycoPSMsNODECOY.Add(uniqueSequence, new List <PSM>());
}
hcdGlycoPSMsNODECOY[uniqueSequence].Add(psm);
}
if (fragmentation.Equals("ETD"))
{
if (!etdGlycoPSMsNODECOY.ContainsKey(uniqueSequence))
{
etdGlycoPSMsNODECOY.Add(uniqueSequence, new List <PSM>());
}
etdGlycoPSMsNODECOY[uniqueSequence].Add(psm);
}
}
}
/**
* psm.Peak126 = GetPeak(psm, 126.055, rawFile);
* psm.Peak138 = GetPeak(psm, 138.055, rawFile);
* psm.Peak144 = GetPeak(psm, 144.065, rawFile);
* psm.Peak168 = GetPeak(psm, 168.066, rawFile);
* psm.Peak186 = GetPeak(psm, 186.076, rawFile);
* psm.Peak204 = GetPeak(psm, 204.087, rawFile);
* psm.Peak274 = GetPeak(psm, 274.092, rawFile);
* psm.Peak292 = GetPeak(psm, 292.103, rawFile);
* psm.Peak366 = GetPeak(psm, 366.140, rawFile);
**/
double GlcNAcToGalNAcratio = 0;
/*
* outputList.Write("PID\tProt.Rank\tSequence\tPeptideParseFriendly\tPos.\tMods(variable)\tGlycans\tPEP2D\tPEP1D\t|Log Prob|\tScore\tDeltaScore\tDelta Mod.Score\tz\tObs.m/z\t");
* outputList.Write("Calc.m/z\tppmerr.\tObs.m/z\tCalc.m/z\tCleavage\tGlycansPos.\tProteinName\tProt.Id\tScanTime\tScan #\tMods(fixed)\tFDR2D\tFDR1D\t");
* outputList.WriteLine("FDR uniq.2D\tFDR uniq.1D\tq-value2D\tq-value1D\tisGlycoPeptide\tmodsPassedCheck\tpositionPassedCheck\tfragmentation\tPeak126\tPeak138\tPeak144\tPeak168\tPeak186\tPeak204\tPeak274\tPeak292\tPeak366");
*/
//outputList.WriteLine(protRank + "\t" + byonicSequence + "\t" + peptidesToBeParsed + "\t" + aminoAcidSequence + "\t" +
// peptideStartPosition + "\t" + modsToBeParsed + "\t" + glycansToBeParsed + "\t" + PEP2D + "\t" + PEP1D + "\t" +
// logProb + "\t" + score + "\t" + deltaScore + "\t" + deltaModScore + "\t" + charge + "\t" + mzObs + "\t" + mzCalc +
// "\t" + ppmError + "\t" + obsMH + "\t" + calcMH + "\t" + cleavage + "\t" + glycanPositions + "\t" + proteinName + "\t" +
// protID + "\t" + scanTime + "\t" + scanNumber + "\t" + modsFixed + "\t" + FDR2D + "\t" + FDR1D + "\t" + FDR2Dunique +
// "\t" + FDR1Dunique + "\t" + qvalue2D + "\t" + qvalue1D + "\t" + isGlycoPeptide + "\t" + modsPassedCheck + "\t" +
// positionsPassedCheck + "\t" + fragmentation + "\t" + masterScan);
} catch (Exception e)
{
Console.WriteLine();
}
}
}
//24 7,Console.ReadKey();
//For Nick's LFQ
if (!isPRM)
{
try
{
LFQProcessor lfqs = new LFQProcessor(@rawFilePath);
allPsmsQuant = lfqs.crunch(allPSMs);
}
catch (Exception e)
{
System.Windows.Forms.MessageBox.Show(e.ToString());
}
}
else
{
allPsmsQuant = allPSMs;
}
// Start LFQ Writer
StreamWriter quantWriter = new StreamWriter(@outputFolderPath + "\\" + file + "_list_Quant.txt");
quantWriter.WriteLine("Prot.Rank\tSequence\tPeptideParseFriendly\tPeptide\tPos.\tMods(variable)\tGlycans" +
"\tPEP2D\tPEP1D\t|Log Prob|\tScore\tDeltaScore\tDelta Mod.Score\tCharge\tObs.m/z\t" +
"Precursor Theoretical m/z (Th)\tppmerr.\tObs.MH\tCalc.MH\tCleavage\tGlycansPos.\tProteinName" +
"\tProt.Id\tScanTime\tSpectrum Number\tMods(fixed)\tFDR2D\tFDR1D\t" +
"FDR uniq.2D\tFDR uniq.1D\tq-value2D\tq-value1D\tisGlycoPeptide\tmodsPassedCheck" +
"\tpositionPassedCheck\tfragmentation\tMasterScan\tLFQ Intensity");
foreach (PSM psmQ in allPsmsQuant)
{
//if(psmQ.logProb > 1 && psmQ.score > 150 && psmQ.deltaModScore > 10)
if (psmQ.score > 50)
{
quantWriter.WriteLine(psmQ.protRank + "\t" + psmQ.byonicSequence + "\t" + psmQ.peptidesToBeParsed + "\t" + psmQ.peptide.Sequence + "\t" +
psmQ.peptideStartPosition + "\t" + psmQ.modsToBeParsed + "\t" + psmQ.glycansToBeParsed + "\t" + psmQ.PEP2D + "\t" + psmQ.PEP1D + "\t" + psmQ.logProb +
"\t" + psmQ.score + "\t" + psmQ.deltaScore + "\t" + psmQ.deltaModScore + "\t" + psmQ.charge + "\t" + psmQ.mzObs + "\t" + psmQ.mzCalc + "\t" + psmQ.ppmError +
"\t" + psmQ.obsMH + "\t" + psmQ.calcMH + "\t" + psmQ.cleavage + "\t" + psmQ.glycanPositions + "\t" + psmQ.proteinName + "\t" + psmQ.protID + "\t" + psmQ.scanTime +
"\t" + psmQ.scanNumber + "\t" + psmQ.modsFixed + "\t" + psmQ.FDR2D + "\t" + psmQ.FDR1D + "\t" + psmQ.FDR2Dunique + "\t" + psmQ.FDR1Dunique + "\t" +
psmQ.qvalue2D + "\t" + psmQ.qvalue1D + "\t" + psmQ.isGlycoPeptide + "\t" + psmQ.modsPassedCheck + "\t" + psmQ.positionPassedCheck + "\t" + psmQ.fragmentation
+ "\t" + psmQ.masterScan + "\t" + psmQ.intensity);
}
}
quantWriter.Close();
// End LFQ Writer
OnUpdateProgress(0.75);
double allPSMsFDR = CalculateFDR(allPSMs);
double hcdPSMsFDR = CalculateFDR(hcdPSMs);
double etdPSMsFDR = CalculateFDR(etdPSMs);
double allGlycoPSMsFDR = CalculateFDR(allGlycoPSMs);
double hcdGlycoPSMsFDR = CalculateFDR(hcdGlycoPSMs);
double etdGlycoPSMsFDR = CalculateFDR(etdGlycoPSMs);
int allPSMCount = GetPSMcount(allPSMsNODECOY);
int hcdPSMCount = GetPSMcount(hcdPSMsNODECOY);
int etdPSMCount = GetPSMcount(etdPSMsNODECOY);
int allGlycoPSMCount = GetPSMcount(allGlycoPSMsNODECOY);
int hcdGlycoPSMCount = GetPSMcount(hcdGlycoPSMsNODECOY);
int etdGlycoPSMCount = GetPSMcount(etdGlycoPSMsNODECOY);
int allPeptideCount = allPSMsNODECOY.Count;
int hcdPeptideCount = hcdPSMsNODECOY.Count;
int etdPeptideCount = etdPSMsNODECOY.Count;
int allGlycoPeptideCount = allGlycoPSMsNODECOY.Count;
int hcdGlycoPeptideCount = hcdGlycoPSMsNODECOY.Count;
int etdGlycoPeptideCount = etdGlycoPSMsNODECOY.Count;
int hcdWithHexNAcOxonium = GetSpectraCountOxonium(HCDscans, 204.087, 0, rawFile);
int hcdWithHexNAcHexOxonium = GetSpectraCountOxonium(HCDscans, 366.14, 0, rawFile);
int hcdWithHexNAcHex2Oxonium = GetSpectraCountOxonium(HCDscans, 528.19, 0, rawFile);
int hcdWithHexNAcHex3Oxonium = GetSpectraCountOxonium(HCDscans, 690.245, 0, rawFile);
int hcdWithHexNAc2Hex3Oxonium = GetSpectraCountOxonium(HCDscans, 893.325, 0, rawFile);
int hcdWithHexNAcHexNeuAcOxonium = GetSpectraCountOxonium(HCDscans, 657.235, 0, rawFile);
int hcdWithHexoseOxonium = GetSpectraCountOxonium(HCDscans, 163.060, 0, rawFile);
int hcdWithFucOxonium = GetSpectraCountOxonium(HCDscans, 147.065, 0, rawFile);
int hcdWithNeuAcOxonium = GetSpectraCountOxonium(HCDscans, 274.092, 292.103, rawFile);
int hcdWithNeuAcAcetylOxonium = GetSpectraCountOxonium(HCDscans, 316.103, 334.113, rawFile);
int hcdWithHexNAcNeuAcOxonium = GetSpectraCountOxonium(HCDscans, 495.182, 0, rawFile);
int hcdWithNeuGcOxonium = GetSpectraCountOxonium(HCDscans, 290.087, 308.098, rawFile);
int hcdWithNeuGcAcetylOxonium = GetSpectraCountOxonium(HCDscans, 332.098, 350.108, rawFile);
int hcdWithPhosphoHexOxonium = GetSpectraCountOxonium(HCDscans, 243.0264, 0, rawFile);
int etdWithHexNAcOxonium = GetSpectraCountOxonium(ETDscans, 204.087, 0, rawFile);
int etdWithHexNAcHexOxonium = GetSpectraCountOxonium(ETDscans, 366.14, 0, rawFile);
int etdWithHexNAcHex2Oxonium = GetSpectraCountOxonium(ETDscans, 528.19, 0, rawFile);
int etdWithHexNAcHex3Oxonium = GetSpectraCountOxonium(ETDscans, 690.245, 0, rawFile);
int etdWithHexNAc2Hex3Oxonium = GetSpectraCountOxonium(ETDscans, 893.325, 0, rawFile);
int etdWithHexNAcHexNeuAcOxonium = GetSpectraCountOxonium(ETDscans, 657.235, 0, rawFile);
int etdWithHexoseOxonium = GetSpectraCountOxonium(ETDscans, 163.060, 0, rawFile);
int etdWithFucOxonium = GetSpectraCountOxonium(ETDscans, 147.065, 0, rawFile);
int etdWithNeuAcOxonium = GetSpectraCountOxonium(ETDscans, 274.092, 292.103, rawFile);
int etdWithNeuAcAcetylOxonium = GetSpectraCountOxonium(ETDscans, 316.103, 334.113, rawFile);
int etdWithHexNAcNeuAcOxonium = GetSpectraCountOxonium(ETDscans, 495.182, 0, rawFile);
int etdWithNeuGcOxonium = GetSpectraCountOxonium(ETDscans, 290.087, 308.098, rawFile);
int etdWithNeuGcAcetylOxonium = GetSpectraCountOxonium(ETDscans, 332.098, 350.108, rawFile);
int etdWithPhosphoHexOxonium = GetSpectraCountOxonium(ETDscans, 243.0264, 0, rawFile);
OnUpdateProgress(1.0);
outputSummary.WriteLine(",Total,HCD,ETD");
outputSummary.WriteLine("MS/MS Scans," + totalMSMSscans + "," + HCDscans.Count + "," + ETDscans.Count);
outputSummary.WriteLine("PSMs (all)," + allPSMCount + "," + hcdPSMCount + "," + etdPSMCount);
outputSummary.WriteLine("Unique Peptides (all)," + allPeptideCount + "," + hcdPeptideCount + "," + etdPeptideCount);
outputSummary.WriteLine("FDR PSM level," + allPSMsFDR + "," + hcdPSMsFDR + "," + etdPSMsFDR);
outputSummary.WriteLine("GlycoPSMs," + allGlycoPSMCount + "," + hcdGlycoPSMCount + "," + etdGlycoPSMCount);
outputSummary.WriteLine("Unique GlycoPeptides," + allGlycoPeptideCount + "," + hcdGlycoPeptideCount + "," + etdGlycoPeptideCount);
outputSummary.WriteLine("FDR GlycoPSM level," + allGlycoPSMsFDR + "," + hcdGlycoPSMsFDR + "," + etdGlycoPSMsFDR);
outputSummary.WriteLine("Oxonium Ions /////,/////////,/////////,/////////");
outputSummary.WriteLine("HexNAc (204.09),," + hcdWithHexNAcOxonium + "," + etdWithHexNAcOxonium);
outputSummary.WriteLine("HexNAcHex (366.14),," + hcdWithHexNAcHexOxonium + "," + etdWithHexNAcHexOxonium);
outputSummary.WriteLine("HexNAcHex(2) (528.19),," + hcdWithHexNAcHex2Oxonium + "," + etdWithHexNAcHex2Oxonium);
outputSummary.WriteLine("HexNAcHex(3) (690.245),," + hcdWithHexNAcHex3Oxonium + "," + etdWithHexNAcHex3Oxonium);
outputSummary.WriteLine("HexNAc(2)Hex(3) (893.325),," + hcdWithHexNAc2Hex3Oxonium + "," + etdWithHexNAc2Hex3Oxonium);
outputSummary.WriteLine("HexNAcHexNeuAc (657.23),," + hcdWithHexNAcHexNeuAcOxonium + "," + etdWithHexNAcHexNeuAcOxonium);
outputSummary.WriteLine("Hexose (163.06),," + hcdWithHexoseOxonium + "," + etdWithHexoseOxonium);
outputSummary.WriteLine("Fucose (147.065),," + hcdWithFucOxonium + "," + etdWithFucOxonium);
outputSummary.WriteLine("NeuAc (272.09/292.103),," + hcdWithNeuAcOxonium + "," + etdWithNeuAcOxonium);
outputSummary.WriteLine("NeuAcAcetyl (316.103/334.113),," + hcdWithNeuAcAcetylOxonium + "," + etdWithNeuAcAcetylOxonium);
outputSummary.WriteLine("HexNAcNeuAc (495.1382),," + hcdWithHexNAcNeuAcOxonium + "," + etdWithHexNAcNeuAcOxonium);
outputSummary.WriteLine("NeuGc (290.087/308.098),," + hcdWithNeuGcOxonium + "," + etdWithNeuGcOxonium);
outputSummary.WriteLine("NeuGcAcetyl (332.098/350.108),," + hcdWithNeuGcAcetylOxonium + "," + etdWithNeuGcAcetylOxonium);
outputSummary.WriteLine("PhosphoHex (243.0264),," + hcdWithPhosphoHexOxonium + "," + etdWithPhosphoHexOxonium);
outputSummary.Close();
//outputList.Close();
var glycoFragmentFinder = new glycoFragmentFinder(rawFile, "1", @outputFolderPath + "\\" + file + "_list.txt", uniprotGlycoDBFile, outputFolderPath);
glycoFragmentFinder.crunch();
rawFile.Dispose();
OnUpdateProgress(0.0);
}