public SrmTransition GetModel(PepV01 peptide)
{
int offset = FragmentIon.OrdinalToOffset(FragmentType,
FragmentOrdinal, peptide.Length);
double mh = NeutralMass + BioMassCalc.MassProton;
FragmentIon fragment = new FragmentIon(peptide, FragmentType, offset, mh);
double start = StartRT ?? 0;
double stop = StopRT ?? 0;
return(new SrmTransition(fragment, CollisionEnergy,
DeclusteringPotential, start - stop,
PrecursorCharge, ProductCharge));
}
public override bool Equals(object obj)
{
if (ReferenceEquals(this, obj))
{
return(true);
}
PepV01 pep = obj as PepV01;
return(pep != null &&
pep.Begin == Begin &&
pep.End == End &&
Equals(pep._fastaSequence, _fastaSequence));
}
public XmlPeptide(PepV01 peptide, XmlTransition[] transitions)
{
Begin = peptide.Begin;
End = peptide.End;
Sequence = peptide.Sequence;
PrevAA = peptide.PrevAA;
NextAA = peptide.NextAA;
NeutralMass = SequenceMassCalc.PersistentNeutral(peptide.MassH);
MissedCleavages = peptide.MissedCleavages;
if (peptide.PredictedRetentionTime.HasValue)
{
PredictedRetentionTime = Math.Round(peptide.PredictedRetentionTime.Value, 2);
}
Transitions = transitions;
}
public FragmentIon(PepV01 peptide, IonType type, int offset, double mh)
{
_peptide = peptide;
IType = type;
CleavageOffset = offset;
MassH = mh;
// Derived values
if (IsNTerminal())
{
Ordinal = offset + 1;
AA = peptide.Sequence[offset];
}
else
{
Ordinal = _peptide.Length - offset - 1;
AA = peptide.Sequence[offset + 1];
}
}
public FragmentIon(PepV01 peptide, IonType type, int offset, double mh)
{
_peptide = peptide;
IType = type;
CleavageOffset = offset;
MassH = new TypedMass(mh, MassType.MonoisotopicMassH);
// Derived values
if (IsNTerminal())
{
Ordinal = offset + 1;
AA = peptide.Target.Sequence[offset];
}
else
{
Ordinal = _peptide.Length - offset - 1;
AA = peptide.Target.Sequence[offset + 1];
}
}
public XmlTransition(SrmTransition transition)
{
FragmentType = transition.Fragment.IType;
FragmentOrdinal = transition.Fragment.Ordinal;
NeutralMass = SequenceMassCalc.PersistentNeutral(transition.Fragment.MassH);
PrecursorCharge = transition.PrecursorCharge;
ProductCharge = transition.Charge;
PrecursorMz = SequenceMassCalc.PersistentMZ(transition.PrecursorMZ);
ProductMz = SequenceMassCalc.PersistentMZ(transition.MZ);
CollisionEnergy = Math.Round(transition.CollisionEnergy, 6);
if (transition.DeclusteringPotential.HasValue)
{
DeclusteringPotential = Math.Round(transition.DeclusteringPotential.Value, 6);
}
PepV01 peptide = transition.Fragment.Peptide;
if (peptide.PredictedRetentionTime.HasValue && transition.RetentionTimeWindow > 0)
{
double start = Math.Round(peptide.PredictedRetentionTime.Value - transition.RetentionTimeWindow / 2, 2);
StartRT = start;
StopRT = Math.Round(start + transition.RetentionTimeWindow, 2);
}
}
public FragmentIon(PepV01 peptide, IonType type, int offset, double mh)
{
_peptide = peptide;
IType = type;
CleavageOffset = offset;
MassH = mh;
// Derived values
if (IsNTerminal())
{
Ordinal = offset + 1;
AA = peptide.Sequence[offset];
}
else
{
Ordinal = _peptide.Length - offset - 1;
AA = peptide.Sequence[offset + 1];
}
}
public SrmTransition GetModel(PepV01 peptide)
{
int offset = FragmentIon.OrdinalToOffset(FragmentType,
FragmentOrdinal, peptide.Length);
double mh = NeutralMass + BioMassCalc.MassProton;
FragmentIon fragment = new FragmentIon(peptide, FragmentType, offset, mh);
double start = StartRT ?? 0;
double stop = StopRT ?? 0;
return new SrmTransition(fragment, CollisionEnergy,
DeclusteringPotential, start - stop,
PrecursorCharge, ProductCharge);
}
public XmlPeptide(PepV01 peptide, XmlTransition[] transitions)
{
Begin = peptide.Begin;
End = peptide.End;
Sequence = peptide.Sequence;
PrevAA = peptide.PrevAA;
NextAA = peptide.NextAA;
NeutralMass = SequenceMassCalc.PersistentNeutral(peptide.MassH);
MissedCleavages = peptide.MissedCleavages;
if (peptide.PredictedRetentionTime.HasValue)
PredictedRetentionTime = Math.Round(peptide.PredictedRetentionTime.Value, 2);
Transitions = transitions;
}
