/// <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 complementary arginine spectra.
/// </summary>
/// <param name="error">The maximum parent mass error allowed.</param>
internal static void FindComplementaryArginineSpectra(double error)
{
// Set the mass change
double mChange = 0.984;
// Set the validation results
var vResultList = citValResults;
// Loop through the validation results
foreach (ValResult result in vResultList)
{
// Create a temporary dictionary of complementary spectra
Dictionary <XTSpectrum, List <XTSpectrum> > compPepDic = new Dictionary <XTSpectrum, List <XTSpectrum> >();
// Loop through all of the modified spectra
foreach (XTSpectrum specMod in result.ModifiedSpectra)
{
// Create an temporary list of complementary spectra
var compPeptides = new List <XTSpectrum>();
// Loop through all of the complementary validation result
foreach (ValResult compResult in vResultList)
{
// TODO: Understand Can be taken out of compResult loop if necessary:??
// Loop through al of the spectra in the complementary result's parent
foreach (XTSpectrum spec in compResult.ParentResult.XSpectrums)
{
// Calculate the parent mass error
double delta = Math.Abs(spec.ParentMass - (specMod.ParentMass - mChange));
// Check if the parent mass error is less than the max allowed error AND the peptide sequence match
if (delta <= error & spec.Proteins[0].DoaminSeq == specMod.Proteins[0].DoaminSeq)
{
// Calculate the ions
XTSpectrum scanMS2 = IonCalculation.CalculateAllIons(spec);
// Get the original filename
scanMS2 = ReturnOriginalFileNameSpectrum(scanMS2, compResult);
// Get the original scan ID
scanMS2 = GetOriginalScanID(scanMS2);
// Find the original MS1 information
scanMS2 = FindMS1.FindOriginalMS1Info(scanMS2);
// Handle the orphan spetra
scanMS2 = FindMS1.HandleOrphanSpecs(scanMS2);
// Add the complementary spectra to the temporary list
compPeptides.Add(scanMS2);
}
}
}
// If no complementary spectra has been found, continue
if (compPeptides.Count() == 0)
{
continue;
}
else
{
// If the dictionary of compmentary spectra does not have the modified spectra, add it to the dictionary
if (compPepDic.ContainsKey(specMod) == false)
{
compPepDic.Add(specMod, compPeptides);
}
}
}
// Set the complementary spectra dictionary to the result's spectra dicitonary
result.CitSpectraDictionary = compPepDic;
}
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 complementary citrullinated scans.
/// </summary>
/// <param name="error">The maximum parent mass error allowed.</param>
internal static void FindComplimentaryCitrullinationScans(double error)
{
// Get the list of used citrullination spectra
List <int> usedIDList = GetListOfUsedIDs();
// Set the proton mass
double pMass = 1.007276470;
// Set the arginine validation result list to list of validation results
var vResultList = argValResults;
// Loop through all of the vlaidation results
foreach (ValResult result in vResultList)
{
// Get the name of the inpput file
string inputFileName = result.ParentResult.OriginalInputFile;
// Loop through all of the input results
foreach (Input input in FileReader.inputFiles)
{
// TODO: Can be inserted into if statement if it needs only to work on single results
// Create a temporary dictionary of spectra and their complementary scans
Dictionary <XTSpectrum, List <RawScan> > compPepDic = new Dictionary <XTSpectrum, List <RawScan> >();
// Loop through all of the arginine spectra
foreach (XTSpectrum specArg in result.ArginineSpectra)
{
// If the arginine spectra is already used, continue
if (usedIDList.Contains(specArg.ID))
{
continue;
}
else
{
// If not.
// Create a tmeporary list of complementary scans
var compPeptides = new List <RawScan>();
// Calculate the ions
XTSpectrum scanArg = IonCalculation.CalculateAllIons(specArg);
// Loop through all of the MS2 scans
foreach (RawScan mgfScan in input.MS2Scans)
{
// Calculate the parent mass error
double delta = Math.Abs(scanArg.ParentMass - ((mgfScan.PreCursorMz * mgfScan.Charge) - ((mgfScan.Charge - 1) * pMass) - 0.984));
// Check if the parent mass error is less than the allowed parent mass error
if (delta <= error)
{
// If so.
// Calculate the relative intenties values
RawScan normMgfScan = CalcRelativeIntVals(mgfScan);
// Calculate all potential citrullination ions
normMgfScan = IonCalculation.CalculateAllPotentialCitrullinationIons(scanArg, normMgfScan);
// Get the original filename
normMgfScan = ReturnOriginalFileNameScan(normMgfScan, input);
// Find the potential citrullinated parent in MS1
normMgfScan = FindMS1.FindPotCitParentMS1Scan(normMgfScan);
// Handle orphan scans
normMgfScan = FindMS1.HandleOrphanScans(normMgfScan);
// Add the scan to the list
compPeptides.Add(normMgfScan);
}
}
// If no complementary scan has been found, continue.
if (compPeptides.Count() == 0)
{
continue;
}
else
{
// If the dictionary of complementary scans does not already contains the arginine spectra, add it
if (compPepDic.ContainsKey(scanArg) == false)
{
compPepDic.Add(scanArg, compPeptides);
}
}
}
}
// Set the dictionary to the result
result.ArgSpectraDictionary = compPepDic;
}
}
// Set the result list
ReturnValResultArg(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);
}