/// <summary>
/// Find citrullinated spectra.
/// </summary>
internal static void FindCitrullinatedSpectra()
{
// Create an empty list of validation results
var vResultList = new List <ValResult>();
// Set the search parameters. Amino acid and mass change
string residue = "R";
double mChange = 0.984;
// Loop through the list of X!Tandem search results
foreach (XTResult res in FileReader.XTandemSearchResults)
{
// Create an empty instance of validation result
ValResult vResult = new ValResult();
// Create a empty list of spectra
var specModPeptides = new List <XTSpectrum>();
// Set the current X!Tandem result as the parent result of the validation result
vResult.ParentResult = res;
// Loop through each of the spectra in the result
foreach (XTSpectrum spec in res.XSpectrums)
{
// Loop through each of the proteins in the spectrum
foreach (XTProtein prot in spec.Proteins)
{
// Loop through each of the modification in the protein
foreach (XTModification mod in prot.Modifications)
{
// Check that the modification matches the citrullination
if (mod.AminoAcid == residue & mod.MassChange == mChange)
{
// If so.
// Calculate the ions
XTSpectrum scanMS2 = IonCalculation.CalculateAllIons(spec);
// Get the original filename
scanMS2 = ReturnOriginalFileNameSpectrum(scanMS2, vResult);
// Get the original scan ID
scanMS2 = GetOriginalScanID(scanMS2);
// Find the original MS1 informaton
scanMS2 = FindMS1.FindOriginalMS1Info(scanMS2);
// Handle orphan spectra
scanMS2 = FindMS1.HandleOrphanSpecs(scanMS2);
// Add the spectra to the list of modified spectra
specModPeptides.Add(scanMS2);
}
}
}
}
// Set the modified spectra to the temporary list filled with data
vResult.ModifiedSpectra = specModPeptides;
// Add the result to the result list
vResultList.Add(vResult);
}
// Set the result
ReturnVResultCit(vResultList);
}
/// <summary>
/// Find lonely citrullinated spectra.
/// </summary>
internal static void FindLonelyCitrullinatedSpectra()
{
// Create an temporary list of results
var vResultList = new List <ValResult>();
// Get a list of ids of already used citrullinated spectra
var usedIDList = GetListOfUsedCitIDs();
// Set the residue and mass change for the citrullination
var residue = "R";
double mChange = 0.984;
// Loop through all of the X!Tandem results
foreach (XTResult res in FileReader.XTandemSearchResults)
{
// Create an empty validation result
ValResult vResult = new ValResult();
// Create a temporary list of spectra
var specModPeptides = new List <XTSpectrum>();
// Set the X!Tandem result as the parent result of the validation
vResult.ParentResult = res;
// Loop through all of the spectra in the result
foreach (XTSpectrum spec in res.XSpectrums)
{
// Loop through all of the proteins in the spectra
foreach (XTProtein prot in spec.Proteins)
{
// Loop through all of the protein modification
foreach (XTModification mod in prot.Modifications)
{
// Check if the modification matches a citrulination
if (mod.AminoAcid == residue & mod.MassChange == mChange)
{
// If so, check if the spectra is already used. If so, continue
if (usedIDList.Contains(spec.ID))
{
continue;
}
else
{
// If not.
// Calculate the ions
XTSpectrum scanMS2 = IonCalculation.CalculateAllIons(spec);
// Get the original filename
scanMS2 = ReturnOriginalFileNameSpectrum(scanMS2, vResult);
// Get the original scan ID
scanMS2 = GetOriginalScanID(scanMS2);
// Find the original MS1 informaton
scanMS2 = FindMS1.FindOriginalMS1Info(scanMS2);
// Handle orpah spectra
scanMS2 = FindMS1.HandleOrphanSpecs(scanMS2);
// If the list does not already contain the spectra, add it.
if (specModPeptides.Contains(scanMS2) == false)
{
specModPeptides.Add(scanMS2);
}
}
}
}
}
}
// Set the list of found modified spectra to the result's list of modified spectra
vResult.ModifiedSpectra = specModPeptides;
// Add the result to the result list
vResultList.Add(vResult);
}
// Set the results
ReturnValResultLoneCit(vResultList);
}
/// <summary>
/// Find the arginine spectra.
/// </summary>
internal static void FindArginineSpectra()
{
// Create a temporary list of validation results
var vResultList = new List <ValResult>();
// Set the residue and mass change for the citrullination
var residue = "R";
double mChange = 0.984;
// Loop through all of the X!Tandem results
foreach (XTResult res in FileReader.XTandemSearchResults)
{
// Create an empty validation result
ValResult vResult = new ValResult();
// Create an temporary list of arginine spectra
var specArgPeptides = new List <XTSpectrum>();
// Set the X!Tandem result as the parent result of the validation
vResult.ParentResult = res;
Console.WriteLine("Spectras of result: {0}", res.XSpectrums.Count());
// Loop through all of the spectra in the X!Tandem result
foreach (XTSpectrum spec in res.XSpectrums)
{
Console.WriteLine("Proteins of Spectrum: {0}", spec.Proteins.Count());
// Loop through all of the proteins in the spectrum
foreach (XTProtein prot in spec.Proteins)
{
// Create an indicator for weather or not the spectrum contains a citrullination. Default: False
bool containsCit = false;
// Loop through all of the protein modifications
foreach (XTModification mod in prot.Modifications)
{
// Check if the modification matches the citrullination. If so set the citrullination indicator to true
if (mod.AminoAcid == residue & mod.MassChange == mChange)
{
containsCit = true;
}
}
// Check if the protein has an arginine, but does not contain a citrulline.
if (prot.DoaminSeq.Contains(residue) & containsCit == false)
{
// Get the spectrum with the original filename
XTSpectrum specMS2 = ReturnOriginalFileNameSpectrum(spec, vResult);
// Get the original filename
specMS2 = GetOriginalScanID(specMS2);
// Find the original MS1 data
specMS2 = FindMS1.FindOriginalMS1Info(specMS2);
// Handle the orphan spectra
specMS2 = FindMS1.HandleOrphanSpecs(specMS2);
// Add the spectrum to the list of arginine spectra
specArgPeptides.Add(specMS2);
}
}
}
// Set the list of arginine spectra to the results list
vResult.ArginineSpectra = specArgPeptides;
// Add the result to the result list
vResultList.Add(vResult);
Console.WriteLine("Number of Citrullinations in Result: {0}", vResult.ArginineSpectra.Count());
}
// Set the result
ReturnValResultArg(vResultList);
}
/// <summary>
/// Set the original filename to the MS2 spectrum.
/// </summary>
/// <param name="specMS2">The MS2 spectrum.</param>
/// <param name="result">The validation result.</param>
/// <returns>The MS2 spectrum with the original filename.</returns>
private static XTSpectrum ReturnOriginalFileNameSpectrum(XTSpectrum specMS2, ValResult result)
{
specMS2.OriginalFileName = result.ParentResult.OriginalInputFile;
return(specMS2);
}