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; }