private AcetylationParams GetParamsFromGUI()
{
double mediumMarker = double.Parse(textBoxMediumMarker.Text);
double heavyMarker = double.Parse(textBoxHeavyMarker.Text);
if (mediumMarker > heavyMarker)
{
throw new Exception("Heavy marker should be heavier than medium marker");
}
if (!Directory.Exists(textBoxMS1SEProDirectory.Text))
{
throw new Exception("MS1 directory does not exist");
}
AcetylationParams myParams = new AcetylationParams(
textBoxMS1SEProDirectory.Text,
mediumMarker,
heavyMarker,
(int)numericUpDownSearchSpace.Value
);
return(myParams);
}
private void buttonGO_Click(object sender, EventArgs e)
{
double ppmTolerance = 65;
AcetylationParams myParams = GetParamsFromGUI();
string [] seproFiles = Directory.GetFiles(myParams.MS1SEProDirectory, "*.sepr");
foreach (string seproFile in seproFiles)
{
Console.WriteLine("Loading SEPro File: " + seproFile);
ResultPackage sepro = ResultPackage.Load(seproFile);
Console.WriteLine("Done loading SEPro File");
//Lets sort sqt scans by their file name and then load an ms1 file at a time
List <string> files = Directory.GetFiles(myParams.MS1SEProDirectory, "*.ms1").ToList();
foreach (string file in files)
{
Console.WriteLine("Loading " + file);
List <MSLight> theMS1Spectra = PatternTools.MSParserLight.ParserLight.ParseLightMS2(file);
List <SQTScan> scans = sepro.MyProteins.AllSQTScans.FindAll(a => file.Contains(Regex.Replace(a.FileName, "sqt", "ms1")));
foreach (SQTScan scan in scans)
{
//theMS1Spectra.Sort((a, b) => Math.Abs(scan.ScanNumber - a.ScanNumber).CompareTo(Math.Abs(scan.ScanNumber - b.ScanNumber)));
List <MSLight> mstmp = theMS1Spectra.FindAll(a => a.ScanNumber < scan.ScanNumber);
mstmp.Sort((a, b) => Math.Abs(a.ScanNumber - scan.ScanNumber).CompareTo(Math.Abs(scan.ScanNumber - b.ScanNumber)));
//theMS1Spectra.Sort((a, b) => Math.Abs(a.ScanNumber - scan.ScanNumber).CompareTo(Math.Abs(scan.ScanNumber - b.ScanNumber)));
//Check if we are dealing with a medium or heavy peptide
bool isMedium = false;
if (scan.PeptideSequenceCleaned.StartsWith("(" + textBoxMediumMarker.Text + ")"))
{
isMedium = true;
}
//Find the delta
int noMods = Regex.Matches(scan.PeptideSequenceCleaned, Regex.Escape("(")).Count;
double delta = ((double)noMods * myParams.DeltaHighMedium) / (double)scan.ChargeState;
//scan.PeptideSequenceCleaned
double chargedPrecursor = (scan.MeasuredMH + ((double)(scan.ChargeState - 1) * 1.0078)) / (double)(scan.ChargeState);
scan.Quantitation = new List <List <double> >();
Console.WriteLine("Scan: " + scan.ScanNumber + " +" + scan.ChargeState + " " + scan.PeptideSequence);
for (int i = 0; i < myParams.SearchSpaceSize; i++)
{
//Obtain ratios from MS1
double mediumIntensity = -1;
double heavyIntensity = -1;
if (isMedium)
{
mediumIntensity = mstmp[i].Ions.FindAll(a => Math.Abs(pTools.PPM(a.MZ, chargedPrecursor)) < ppmTolerance).Sum(a => a.Intensity);
heavyIntensity = mstmp[i].Ions.FindAll(a => Math.Abs(pTools.PPM(a.MZ, chargedPrecursor + delta)) < ppmTolerance).Sum(a => a.Intensity);
}
else
{
mediumIntensity = mstmp[i].Ions.FindAll(a => Math.Abs(pTools.PPM(a.MZ, chargedPrecursor - delta)) < ppmTolerance).Sum(a => a.Intensity);
heavyIntensity = mstmp[i].Ions.FindAll(a => Math.Abs(pTools.PPM(a.MZ, chargedPrecursor)) < ppmTolerance).Sum(a => a.Intensity);
}
double summed = mediumIntensity + heavyIntensity;
scan.Quantitation.Add(new List <double>()
{
mediumIntensity, heavyIntensity
});
Console.WriteLine("\tRatio: " + scan.ScanNumber + ": " + Math.Round(mediumIntensity / heavyIntensity, 2));
Console.WriteLine("\tIntensities: " + mediumIntensity + " " + heavyIntensity);
}
Console.WriteLine("");
}
}
Console.WriteLine("Patching Sepro File, " + seproFile + " with quantitative data");
sepro.Save(seproFile);
}
Console.WriteLine("Done!");
}