public static double[] GetYSeries(string sequence, PeptideModificationState fixedMods,
PeptideModificationState varMods)
{
double m = MolUtil.YIonMassOffset;
if (fixedMods.GetCTermModification() != ushort.MaxValue)
{
Modification mod = Tables.modificationList[fixedMods.GetCTermModification()];
m += mod.DeltaMass;
}
if (varMods.GetCTermModification() != ushort.MaxValue)
{
Modification mod = Tables.modificationList[varMods.GetCTermModification()];
m += mod.DeltaMass;
}
int n = sequence.Length - 1;
double[] masses = new double[n];
for (int i = 0; i < masses.Length; i++)
{
m += AminoAcid.aaMonoMasses[sequence[n - i]];
if (fixedMods.GetModificationAt(n - i) != ushort.MaxValue)
{
Modification mod = Tables.modificationList[fixedMods.GetModificationAt(n - i)];
m += mod.DeltaMass;
}
if (varMods.GetModificationAt(n - i) != ushort.MaxValue)
{
Modification mod = Tables.modificationList[varMods.GetModificationAt(n - i)];
m += mod.DeltaMass;
}
masses[i] = m;
}
return(masses);
}
public static double[] GetPhosphoXSeries(string sequence, PeptideModificationState fixedMods,
PeptideModificationState varMods,
out MsmsPeakAnnotation[] descriptions, bool includeNeutralLoss)
{
List <double> masses = new List <double>();
List <MsmsPeakAnnotation> descr = new List <MsmsPeakAnnotation>();
double[] y = GetYSeries(sequence, fixedMods, varMods);
for (int i = 0; i < y.Length; i++)
{
int index = sequence.Length - 1 - i;
if (varMods.GetModificationAt(index) != ushort.MaxValue)
{
if (Tables.modificationList[varMods.GetModificationAt(index)].IsPhosphorylation)
{
double x = y[i] + MolUtil.MassO + MolUtil.MassC;
masses.Add(x);
descr.Add(new MsmsPeakAnnotation(MsmsSeriesType.X, i + 1, 1, false));
if (sequence[index] != 'Y' && includeNeutralLoss)
{
double xn = x - 97.976896;
masses.Add(xn);
descr.Add(new MsmsPeakAnnotation(MsmsSeriesType.X, i + 1, 1, true));
}
}
}
}
descriptions = descr.ToArray();
return(masses.ToArray());
}
public static double[] GetNeutralLossBSeries(string sequence, PeptideModificationState fixedMods,
PeptideModificationState varMods)
{
double[] result = new double[sequence.Length - 1];
int neutralLossIndex = -1;
for (int i = 0; i < sequence.Length - 1; i++)
{
if (varMods.GetModificationAt(i) != ushort.MaxValue)
{
if (Tables.modificationList[varMods.GetModificationAt(i)].HasNeutralLoss)
{
if (Tables.modificationList[varMods.GetModificationAt(i)].IsPhosphorylation && sequence[i] == 'Y')
{
continue;
}
neutralLossIndex = i;
break;
}
}
}
if (neutralLossIndex != -1)
{
double[] b = GetBSeries(sequence, fixedMods, varMods);
Modification mod = Tables.modificationList[varMods.GetModificationAt(neutralLossIndex)];
double loss = mod.GetNeutralLoss()[0];
for (int i = neutralLossIndex; i < sequence.Length - 1; i++)
{
result[i] = b[i] - loss;
}
}
return(result);
}
public static double[] GetNeutralLossXSeries(string sequence, PeptideModificationState fixedMods,
PeptideModificationState varMods)
{
double[] result = new double[sequence.Length - 1];
int neutralLossIndex = -1;
for (int i = result.Length - 1; i >= 0; i--)
{
if (varMods.GetModificationAt(i) != ushort.MaxValue)
{
if (Tables.modificationList[varMods.GetModificationAt(i)].HasNeutralLoss)
{
neutralLossIndex = i;
break;
}
}
}
if (neutralLossIndex != -1)
{
double[] x = GetXSeries(sequence, fixedMods, varMods);
Modification mod = Tables.modificationList[varMods.GetModificationAt(neutralLossIndex)];
double loss = mod.GetNeutralLoss()[0];
for (int i = neutralLossIndex; i >= 0; i--)
{
result[i] = x[i] - loss;
}
}
return(result);
}
public override bool Equals(object anObject)
{
if (this == anObject)
{
return(true);
}
if (anObject is PeptideModificationState)
{
PeptideModificationState other = (PeptideModificationState)anObject;
if (other.GetNTermModification() != GetNTermModification())
{
return(false);
}
if (other.GetCTermModification() != GetCTermModification())
{
return(false);
}
if (other.Length != Length)
{
return(false);
}
for (int i = 0; i < Length; i++)
{
if (other.GetModificationAt(i) != GetModificationAt(i))
{
return(false);
}
}
return(true);
}
return(false);
}
private static int CalcSilacIndex(char aa, PeptideModificationState labelMods, string sequence, SilacType type,
SilacLabel[] labels1, SilacLabel[] labels2)
{
for (int i = 0; i < sequence.Length; i++)
{
if (sequence[i] != aa)
{
continue;
}
ushort m = labelMods.GetModificationAt(i);
if (type == SilacType.Doublets)
{
if (m != ushort.MaxValue)
{
return(1);
}
return(0);
}
if (type == SilacType.Triplets)
{
int ind1 = -1;
for (int j = 0; j < labels1.Length; j++)
{
if (AminoAcid.GetAminoAcidFromLabel(labels1[j]).Letter == aa)
{
ind1 = j;
}
}
int ind2 = -1;
for (int j = 0; j < labels2.Length; j++)
{
if (AminoAcid.GetAminoAcidFromLabel(labels2[j]).Letter == aa)
{
ind2 = j;
}
}
if (ind1 == -1 && ind2 == -1)
{
return(-1);
}
if (ind1 == -1)
{
if (m != ushort.MaxValue)
{
return(2);
}
return(-1);
}
if (ind2 == -1)
{
if (m != ushort.MaxValue)
{
return(1);
}
return(-1);
}
SilacLabel l1 = labels1[ind1];
SilacLabel l2 = labels2[ind2];
if (l1 == l2)
{
if (m == ushort.MaxValue)
{
return(0);
}
return(-1);
}
if (m == ushort.MaxValue)
{
return(0);
}
if (Tables.modifications[AminoAcid.GetMascotModificationStringForLabel(l1)].Index == m)
{
return(1);
}
if (Tables.modifications[AminoAcid.GetMascotModificationStringForLabel(l2)].Index == m)
{
return(2);
}
throw new Exception("Never get here.");
}
throw new Exception("Should never happen.");
}
return(-1);
}
private int GetSilacIndex(char aa, SilacType type, SilacLabel[] labels1, SilacLabel[] labels2)
{
if (type == SilacType.Singlets)
{
return(0);
}
int index = -1;
string seq = sequence;
for (int i = 0; i < seq.Length; i++)
{
if (seq[i] == aa)
{
index = i;
break;
}
}
if (index == -1)
{
return(-1);
}
Modification[] mods = T07SearchEngineEnhancement.GetModifiedVersions(aa, type, labels1, labels2);
ushort mod = modifications.GetModificationAt(index);
if (mod == ushort.MaxValue)
{
for (int i = 1; i < mods.Length; i++)
{
if (mods[i] == null)
{
return(-1);
}
}
return(0);
}
if (type == SilacType.Doublets)
{
if (mods[1] == null)
{
return(-1);
}
if (mods[1].Index == mod)
{
return(1);
}
return(-1);
}
if (mods[1] == mods[2])
{
return(-1);
}
if (mods[1] != null && mods[1].Index == mod)
{
return(1);
}
if (mods[2] != null && mods[2].Index == mod)
{
return(2);
}
return(-1);
}