private void AddPairedPeakList(MS3XcorrItem ms3, ZedGraphControl zgc, int scan1, int scan2)
{
zgc.GraphPane.ClearData();
var s1 = GetPeakList(scan1);
var s2 = GetPeakList(scan2);
var ppl1 = new PointPairList();
foreach (var m in s1)
{
ppl1.Add(new PointPair(m.Mz, m.Intensity));
}
zgc.GraphPane.AddIndividualLine(ms3.Sequence1 + ":" + scan1.ToString(), ppl1, Color.Red);
var ppl2 = new PointPairList();
foreach (var m in s2)
{
ppl2.Add(new PointPair(m.Mz, -m.Intensity));
}
zgc.GraphPane.AddIndividualLine(ms3.Sequence2 + ":" + scan2.ToString(), ppl2, Color.Blue);
if (ms3.MS2Scan1 == scan1)
{
zgc.GraphPane.Title.Text = "MS2: " + ms3.Sequence1 + " ~ " + ms3.Sequence2;
}
else
{
zgc.GraphPane.Title.Text = string.Format("MS3: m/z = {0:0.####}, Xcorr = {1:0.####} ~ {2:0.####} = {3:0.####}", ms3.MS3Precursor1, SpectrumXcorr.CalculateUnnormalized(s1, s1), SpectrumXcorr.CalculateUnnormalized(s2, s2), ms3.Xcorr);
}
zgc.UpdateGraph();
}
private void DrawSpectrum(IIdentifiedSpectrum spectrum)
{
if (spectrum.Annotations.ContainsKey("PepMutation"))
{
zgcPeaks.MasterPane.PaneList[0].Title.Text = string.Format("MH={0:0.00000},PPM={1:0.0},SEQ={2},MUT={3},COUNT={4}",
spectrum.TheoreticalMH,
PrecursorUtils.mz2ppm(spectrum.TheoreticalMH, spectrum.TheoreticalMinusExperimentalMass),
spectrum.Sequence,
spectrum.Annotations["PepMutation"],
(from a in spectrum.Annotations
where a.Key.EndsWith("_PepCount")
select Convert.ToInt32(a.Value)).Sum());
}
else
{
zgcPeaks.MasterPane.PaneList[0].Title.Text = string.Format("MH={0:0.00000},PPM={1:0.0},SEQ={2}",
spectrum.TheoreticalMH,
PrecursorUtils.mz2ppm(spectrum.TheoreticalMH, spectrum.TheoreticalMinusExperimentalMass),
spectrum.Sequence);
}
var mass = aas.MonoPeptideMass(PeptideUtils.GetMatchedSequence(spectrum.Sequence));
if (Math.Abs(mass - spectrum.TheoreticalMass) > 0.1)
{
MessageBox.Show(string.Format("Error : {0} - {1}", mass, spectrum.TheoreticalMass));
return;
}
var name = string.Format("{0}_{1}", spectrum.Query.FileScan.Experimental, spectrum.Query.FileScan.FirstScan);
var peakPane = zgcPeaks.MasterPane.PaneList[0];
peakPane.ClearData();
var ppmPane = zgcPeaks.MasterPane.PaneList[1];
ppmPane.ClearData();
if (!mgfMap.ContainsKey(name))
{
MessageBox.Show("Cannot find peak list {0}", name);
return;
}
var mgf = mgfMap[name];
var maxIntensity = mgf.Max(m => m.Intensity);
var maxMz = Math.Min(2000, mgf.Max(m => m.Mz));
var productTolerance = productIonPPM;
var minIntensity = maxIntensity * 0.05;
AddIonSeries(peakPane, ppmPane, mgf, productTolerance, minIntensity, yBuilder, spectrum.Sequence, Color.Red);
AddIonSeries(peakPane, ppmPane, mgf, productTolerance, minIntensity, bBuilder, spectrum.Sequence, Color.Blue);
if (spectrum.Charge > 2)
{
AddIonSeries(peakPane, ppmPane, mgf, productTolerance, minIntensity, y2Builder, spectrum.Sequence, Color.Brown);
AddIonSeries(peakPane, ppmPane, mgf, productTolerance, minIntensity, b2Builder, spectrum.Sequence, Color.GreenYellow);
}
AddUnmatchedIons(peakPane, mgf);
foreach (var pane in zgcPeaks.MasterPane.PaneList)
{
pane.XAxis.Scale.Min = 0;
pane.XAxis.Scale.Max = maxMz;
}
zgcPeaks.UpdateGraph();
var targetpngfile = GetTargetFile(targetDir, spectrum);
zgcPeaks.GetImage().Save(targetpngfile, ImageFormat.Png);
}