public void GeneratePrmInfo(string resultFilePath, string outputFilePath)
{
Console.Write("Processing {0}", Path.GetFileName(resultFilePath));
Console.Out.Flush();
var rawFilePath =
@"D:\Research\Data\EDRN\DDA\raw\" + Path.GetFileNameWithoutExtension(resultFilePath) + ".raw";
var reader = new XCaliburReader(rawFilePath);
var run = InMemoryLcMsRun.GetLcMsRun(rawFilePath);
var tolerance = new Tolerance(10, ToleranceUnit.Ppm);
const string spikedInPeptideFile = @"D:\Research\Data\EDRN\SpikedPeptides.txt";
var spikedInPeptides = File.ReadAllLines(spikedInPeptideFile);
var spikedInPepSet = new HashSet<string>();
foreach (var p in spikedInPeptides)
{
spikedInPepSet.Add(p);
}
// const string resultFilePath = @"D:\Research\Data\EDRN\DDA\Frac7_NTT2.tsv";
//const string resultFilePath = @"D:\Research\Data\EDRN\DDA\Heavy\342865_EDRN_Serum_07_DDA_1_12Nov13_Samwise_13-07-28.tsv";
// const string resultFilePath = @"D:\Research\Data\EDRN\DDA\NTT1_NoMod\342865_EDRN_Serum_07_DDA_1_12Nov13_Samwise_13-07-28.tsv";
const double qValueThreshold = 0.01;
var pepSet = new HashSet<string>();
MsGfPlusHeaderInformation headerInfo = null;
//var prefix = new HashSet<string>();
//var suffix = new HashSet<string>();
var numPeptides = 0;
var prevScanNum = -1;
using (var writer = new StreamWriter(outputFilePath))
{
writer.WriteLine("Peptide\tCharge\tMonoMz\tMostAbundantMz\tMs2ScanNum\tRtMs2\tRtApex\tRtStart\tRtEnd\tSpecEValue\tPepQValue");
foreach (var line in File.ReadLines(resultFilePath))
{
if (line.StartsWith("#"))
{
headerInfo = new MsGfPlusHeaderInformation(line);
continue;
}
var match = new MsGfMatch(line, headerInfo);
if (match.ScanNum == prevScanNum) continue;
prevScanNum = match.ScanNum;
if (!match.IsValid || match.Protein.StartsWith(FastaDatabase.DecoyProteinPrefix)) continue;
if (match.PepQValue > qValueThreshold) continue;
var peptide = match.Peptide.Replace("C+57.021", "C").Replace("K+8.014", "K").Replace("R+10.008", "R");
if (pepSet.Contains(peptide)) continue;
pepSet.Add(peptide);
if (spikedInPepSet.Contains(peptide))
{
var ion = new Ion(match.Formula, match.Charge);
var mostAbundantIonMz = ion.GetMostAbundantIsotopeMz();
var xic = run.GetPrecursorExtractedIonChromatogram(mostAbundantIonMz, tolerance, match.ScanNum);
if (xic.Count == 0) continue;
var minScan = xic.Min().ScanNum;
var maxScan = xic.Max().ScanNum;
writer.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}\t{9}\t{10}",
peptide,
match.Charge,
ion.GetMonoIsotopicMz(),
mostAbundantIonMz,
match.ScanNum,
reader.RtFromScanNum(match.ScanNum),
reader.RtFromScanNum(xic.GetApexScanNum()), // Rt apex
reader.RtFromScanNum(minScan), // Rt start
reader.RtFromScanNum(maxScan), // Rt end
match.SpecEValue,
match.PepQValue);
++numPeptides;
}
//else
//{
// foreach (var spikedInPeptide in spikedInPeptides)
// {
// if (spikedInPeptide.StartsWith(peptide)) prefix.Add(spikedInPeptide + "\t" + peptide + "\t" + match.ScanNum);
// else if (spikedInPeptide.EndsWith(peptide)) suffix.Add(spikedInPeptide + "\t" + peptide + "\t" + match.ScanNum);
// }
//}
}
}
//Console.WriteLine("*********Prefix");
//foreach(var p in prefix) Console.WriteLine(p);
//Console.WriteLine("*********Suffix");
//foreach (var p in suffix) Console.WriteLine(p);
Console.WriteLine("\t{0}", numPeptides);
}
