/// <summary>
/// This will take the input of a peptide sequence and a bool for the fragmentation mode (false = CID, true = ETD).
/// </summary>
/// <param name="peptide">This is the peptide sequence.</param>
/// <param name="fragmentationModeETD">True when the fragmentation mode is CID</param>
/// <returns>List of theoretical ions as key/value pairs (key is ion abbreviation, value is m/z value)</returns>
public List <KeyValuePair <string, double> > GetTheoreticalDataByPeptideSequence(string peptide, bool fragmentationModeETD)
{
// Set the element mode
m_mMwtWin.SetElementMode(MwtWinDll.MWElementAndMassRoutines.emElementModeConstants.emIsotopicMass);
// Initialize the options
MwtWinDll.MWPeptideClass.udtFragmentationSpectrumOptionsType udtFragSpectrumOptions = default(MwtWinDll.MWPeptideClass.udtFragmentationSpectrumOptionsType);
udtFragSpectrumOptions.Initialize();
// Initialize udtFragSpectrumOptions with the defaults
udtFragSpectrumOptions = m_mMwtWin.Peptide.GetFragmentationSpectrumOptions();
// The entire list of value will be retirved without any filtering
udtFragSpectrumOptions.DoubleChargeIonsShow = true;
udtFragSpectrumOptions.TripleChargeIonsShow = true;
udtFragSpectrumOptions.DoubleChargeIonsThreshold = 1;
udtFragSpectrumOptions.TripleChargeIonsThreshold = 1;
// Each label begins with "b", "y", "c", or "z"
char modeString1;
if (fragmentationModeETD)
{
modeString1 = 'c';
udtFragSpectrumOptions.IonTypeOptions[(int)MwtWinDll.MWPeptideClass.itIonTypeConstants.itBIon].ShowIon = false;
udtFragSpectrumOptions.IonTypeOptions[(int)MwtWinDll.MWPeptideClass.itIonTypeConstants.itYIon].ShowIon = false;
udtFragSpectrumOptions.IonTypeOptions[(int)MwtWinDll.MWPeptideClass.itIonTypeConstants.itCIon].ShowIon = true;
udtFragSpectrumOptions.IonTypeOptions[(int)MwtWinDll.MWPeptideClass.itIonTypeConstants.itZIon].ShowIon = true;
udtFragSpectrumOptions.IonTypeOptions[(int)MwtWinDll.MWPeptideClass.itIonTypeConstants.itAIon].ShowIon = false;
}
else
{
modeString1 = 'b';
udtFragSpectrumOptions.IonTypeOptions[(int)MwtWinDll.MWPeptideClass.itIonTypeConstants.itBIon].ShowIon = true;
udtFragSpectrumOptions.IonTypeOptions[(int)MwtWinDll.MWPeptideClass.itIonTypeConstants.itYIon].ShowIon = true;
udtFragSpectrumOptions.IonTypeOptions[(int)MwtWinDll.MWPeptideClass.itIonTypeConstants.itCIon].ShowIon = false;
udtFragSpectrumOptions.IonTypeOptions[(int)MwtWinDll.MWPeptideClass.itIonTypeConstants.itZIon].ShowIon = false;
udtFragSpectrumOptions.IonTypeOptions[(int)MwtWinDll.MWPeptideClass.itIonTypeConstants.itAIon].ShowIon = false;
}
// MolecularWeightTool allowed modification symbols.
// 33 !
// 35 #
// 36 $
// 37 %
// 38 &
// 39 '
// 42 *
// 43 +
// 63 ?
// 64 @
// 94 ^
// 95 _
// 96 `
// 126 ~
string allowedSymbols = "!#$%&'*+?@^_`~";
string usedSymbols = new string(m_modificationList.Keys.ToArray());
string availableSymbols = "";
foreach (char c in allowedSymbols)
{
if (!usedSymbols.Contains(c))
{
availableSymbols += c;
}
}
Dictionary <char, char> badSymbolMap = new Dictionary <char, char>();
//Add the modifications if needed.
if (m_modificationList != null)
{
m_mMwtWin.Peptide.RemoveAllModificationSymbols(); // Remove the default MWT modification symbols
foreach (KeyValuePair <char, double> modPair in m_modificationList)
{
// Key is symbol, value is mzValue
string modComment = string.Empty;
bool indicatesPhospho = Math.Abs(modPair.Value - 79.9663326) < 0.005;
int modResult = m_mMwtWin.Peptide.SetModificationSymbol(modPair.Key.ToString(), modPair.Value, indicatesPhospho,
modComment);
if (modResult != 0) // A symbol that is not allowed, most likely
{
modResult = m_mMwtWin.Peptide.SetModificationSymbol(availableSymbols[0].ToString(), modPair.Value, indicatesPhospho,
modComment);
badSymbolMap.Add(modPair.Key, availableSymbols[0]); // Add it to the dictionary
availableSymbols = availableSymbols.Substring(1); // Remove it from the available symbols.
}
//if modresult = 0 symbol add is successful, useful spot for breakpoint
//modResult = modResult + 0;
}
}
string peptideFix = peptide;
foreach (KeyValuePair <char, char> symfix in badSymbolMap)
{
peptideFix = peptideFix.Replace(symfix.Key, symfix.Value);
}
// Obtain the fragmentation spectrum for a peptide
// First define the peptide sequence
// Need to pass "false" to parameter blnIs3LetterCode since "peptide" is in one-letter notation
m_mMwtWin.Peptide.SetSequence(peptideFix,
MwtWinDll.MWPeptideClass.ntgNTerminusGroupConstants.ntgHydrogen,
MwtWinDll.MWPeptideClass.ctgCTerminusGroupConstants.ctgHydroxyl,
false);
// Update the options
m_mMwtWin.Peptide.SetFragmentationSpectrumOptions(udtFragSpectrumOptions);
// Get the fragmentation masses
MwtWinDll.MWPeptideClass.udtFragmentationSpectrumDataType[] udtFragSpectrum = null;
m_mMwtWin.Peptide.GetFragmentationMasses(ref udtFragSpectrum);
var cleanPeptide = m_mMwtWin.Peptide.GetSequence(false, false, false, false, false);
if (string.IsNullOrWhiteSpace(cleanPeptide))
{
// No valid residues
return(new List <KeyValuePair <string, double> >());
}
// Obtain the list of ions
List <KeyValuePair <string, double> > theoryList = GetTheoryList(cleanPeptide, fragmentationModeETD, modeString1, udtFragSpectrum);
return(theoryList);
}
private void TestAccessFunctions(string sequence)//public or private
{
string strNewSeq = sequence;
// Set the element mode (average, monoisotopic, or integer)
mMwtWin.SetElementMode(MwtWinDll.MWElementAndMassRoutines.emElementModeConstants.emIsotopicMass);
MwtWinDll.MWPeptideClass.udtFragmentationSpectrumOptionsType udtFragSpectrumOptions = default(MwtWinDll.MWPeptideClass.udtFragmentationSpectrumOptionsType);
udtFragSpectrumOptions.Initialize();
// Initialize udtFragSpectrumOptions with the defaults
udtFragSpectrumOptions = mMwtWin.Peptide.GetFragmentationSpectrumOptions();
// Customize the options
udtFragSpectrumOptions.DoubleChargeIonsShow = false; //false
udtFragSpectrumOptions.TripleChargeIonsShow = false;
udtFragSpectrumOptions.IonTypeOptions[(int)MwtWinDll.MWPeptideClass.itIonTypeConstants.itAIon].ShowIon = false;
udtFragSpectrumOptions.IonTypeOptions[(int)MwtWinDll.MWPeptideClass.itIonTypeConstants.itBIon].ShowIon = true;
udtFragSpectrumOptions.IonTypeOptions[(int)MwtWinDll.MWPeptideClass.itIonTypeConstants.itYIon].ShowIon = true;
udtFragSpectrumOptions.IonTypeOptions[(int)MwtWinDll.MWPeptideClass.itIonTypeConstants.itBIon].NeutralLossAmmonia = false;
udtFragSpectrumOptions.IonTypeOptions[(int)MwtWinDll.MWPeptideClass.itIonTypeConstants.itYIon].NeutralLossAmmonia = false;
udtFragSpectrumOptions.IonTypeOptions[(int)MwtWinDll.MWPeptideClass.itIonTypeConstants.itBIon].NeutralLossPhosphate = false;
udtFragSpectrumOptions.IonTypeOptions[(int)MwtWinDll.MWPeptideClass.itIonTypeConstants.itYIon].NeutralLossPhosphate = false;
udtFragSpectrumOptions.IonTypeOptions[(int)MwtWinDll.MWPeptideClass.itIonTypeConstants.itBIon].NeutralLossWater = false;
udtFragSpectrumOptions.IonTypeOptions[(int)MwtWinDll.MWPeptideClass.itIonTypeConstants.itYIon].NeutralLossWater = false;
udtFragSpectrumOptions.IonTypeOptions[(int)MwtWinDll.MWPeptideClass.itIonTypeConstants.itCIon].ShowIon = false;
udtFragSpectrumOptions.IonTypeOptions[(int)MwtWinDll.MWPeptideClass.itIonTypeConstants.itZIon].ShowIon = false;
// Obtain the fragmentation spectrum for a peptide
// First define the peptide sequence
// Need to pass "false" to parameter blnIs3LetterCode since strNewSeq is in one-letter notation
mMwtWin.Peptide.SetSequence(strNewSeq,
MwtWinDll.MWPeptideClass.ntgNTerminusGroupConstants.ntgHydrogen,
MwtWinDll.MWPeptideClass.ctgCTerminusGroupConstants.ctgHydroxyl,
false);
// Update the options
mMwtWin.Peptide.SetFragmentationSpectrumOptions(ref udtFragSpectrumOptions);
// Get the fragmentation masses
MwtWinDll.MWPeptideClass.udtFragmentationSpectrumDataType[] udtFragSpectrum = null;
mMwtWin.Peptide.GetFragmentationMasses(ref udtFragSpectrum);
//store b and y ions in separate lists
List <double> bList = new List <double>();
List <double> yList = new List <double>();
for (int i = 0; i < udtFragSpectrum.Length; i++)
{
if (udtFragSpectrum[i].Symbol != null && udtFragSpectrum[i].Symbol.Contains("y"))
{
yList.Add(Convert.ToDouble(udtFragSpectrum[i].Mass.ToString("0.0000")));
}
else
{
bList.Add(Convert.ToDouble(udtFragSpectrum[i].Mass.ToString("0.0000")));
}
//byPeakList.Add(Convert.ToDouble(udtFragSpectrum[i].Mass.ToString("0.0000")));
}
bPeakHolder = bList.ToArray();
yPeakHolder = yList.ToArray();
}
public void TestAccessFunctions()
{
// Set the element mode (average, monoisotopic, or integer)
mMwtWin.SetElementMode(MwtWinDll.MWElementAndMassRoutines.emElementModeConstants.emIsotopicMass);
MwtWinDll.MWPeptideClass.udtFragmentationSpectrumOptionsType udtFragSpectrumOptions = default(MwtWinDll.MWPeptideClass.udtFragmentationSpectrumOptionsType);
udtFragSpectrumOptions.Initialize();
// Initialize udtFragSpectrumOptions with the defaults
udtFragSpectrumOptions = mMwtWin.Peptide.GetFragmentationSpectrumOptions();
// Customize the options
udtFragSpectrumOptions.DoubleChargeIonsShow = true;
udtFragSpectrumOptions.TripleChargeIonsShow = true;
udtFragSpectrumOptions.DoubleChargeIonsThreshold = 400;
udtFragSpectrumOptions.TripleChargeIonsThreshold = 400;
udtFragSpectrumOptions.IonTypeOptions[(int)MwtWinDll.MWPeptideClass.itIonTypeConstants.itAIon].ShowIon = false;
udtFragSpectrumOptions.IonTypeOptions[(int)MwtWinDll.MWPeptideClass.itIonTypeConstants.itBIon].ShowIon = false;
udtFragSpectrumOptions.IonTypeOptions[(int)MwtWinDll.MWPeptideClass.itIonTypeConstants.itYIon].ShowIon = true;
udtFragSpectrumOptions.IonTypeOptions[(int)MwtWinDll.MWPeptideClass.itIonTypeConstants.itYIon].NeutralLossAmmonia = false;
udtFragSpectrumOptions.IonTypeOptions[(int)MwtWinDll.MWPeptideClass.itIonTypeConstants.itYIon].NeutralLossPhosphate = false;
udtFragSpectrumOptions.IonTypeOptions[(int)MwtWinDll.MWPeptideClass.itIonTypeConstants.itYIon].NeutralLossWater = false;
udtFragSpectrumOptions.IonTypeOptions[(int)MwtWinDll.MWPeptideClass.itIonTypeConstants.itCIon].ShowIon = false;
udtFragSpectrumOptions.IonTypeOptions[(int)MwtWinDll.MWPeptideClass.itIonTypeConstants.itZIon].ShowIon = false;
udtFragSpectrumOptions.IntensityOptions.BYIonShoulder = 0;
// Customize the modification symbols
mMwtWin.Peptide.SetModificationSymbol("!", 57.02146, false, "Carbamidomethylation");
mMwtWin.Peptide.SetModificationSymbol("+", 10.0, false, "Heavy Arg");
string strNewSeq = "C!ETQNPVSAR+";
// Obtain the fragmentation spectrum for a peptide
// First define the peptide sequence
// Need to pass "false" to parameter blnIs3LetterCode since strNewSeq is in one-letter notation
mMwtWin.Peptide.SetSequence1LetterSymbol(strNewSeq);
// Update the options
mMwtWin.Peptide.SetFragmentationSpectrumOptions(udtFragSpectrumOptions);
// Get the fragmentation masses
MwtWinDll.MWPeptideClass.udtFragmentationSpectrumDataType[] udtFragSpectrum = null;
mMwtWin.Peptide.GetFragmentationMasses(ref udtFragSpectrum);
// Print the results to the console
Console.WriteLine("Fragmentation spectrum for " + mMwtWin.Peptide.GetSequence(false, true, false, false));
Console.WriteLine();
Console.WriteLine("Mass Intensity \tSymbol");
for (int i = 0; i < udtFragSpectrum.Length; i++)
{
Console.WriteLine(udtFragSpectrum[i].Mass.ToString("0.000") + " " + udtFragSpectrum[i].Intensity.ToString("###0") + " \t" + udtFragSpectrum[i].Symbol);
// For debugging purposes, stop after displaying 20 ions
if (i >= 30)
{
Console.WriteLine("...");
break;
}
}
Console.WriteLine();
short intSuccess = 0;
string strResults = null;
double[,] ConvolutedMSData2D = null;
int ConvolutedMSDataCount = 0;
// Compute the Isotopic distribution for the peptide
// Need to first convert to an empirical formula
// To do this, first obtain the peptide sequence in 3-letter notation
string strSeq3Letter = mMwtWin.Peptide.GetSequence(true, false, false, true, false);
// Now assing to the Compound class
mMwtWin.Compound.SetFormula(strSeq3Letter);
// Now convert to an empirical formula
string s = mMwtWin.Compound.ConvertToEmpirical();
bool blnAddProtonChargeCarrier = true;
short intChargeState = 1;
Console.WriteLine("Isotopic abundance test with Charge=" + intChargeState);
intSuccess = mMwtWin.ComputeIsotopicAbundances(ref s, intChargeState, ref strResults, ref ConvolutedMSData2D, ref ConvolutedMSDataCount);
Console.WriteLine(strResults);
blnAddProtonChargeCarrier = false;
intChargeState = 1;
Console.WriteLine("Isotopic abundance test with Charge=" + intChargeState + "; do not add a proton charge carrier");
intSuccess = mMwtWin.ComputeIsotopicAbundances(ref s, intChargeState, ref strResults, ref ConvolutedMSData2D, ref ConvolutedMSDataCount, blnAddProtonChargeCarrier);
Console.WriteLine(strResults);
}
