private static int?CalcProductCharge(double productMassH, double productMz, double tolerance, bool isCustomIon,
int maxCharge, MassShiftType massShiftType, out int massShift, out int nearestCharge)
{
return(CalcCharge(productMassH, productMz, tolerance, isCustomIon,
Transition.MIN_PRODUCT_CHARGE,
Math.Min(maxCharge, Transition.MAX_PRODUCT_CHARGE),
Transition.MassShifts,
massShiftType,
out massShift,
out nearestCharge));
}
/// <summary>
/// Calculates the matching charge within a tolerance for a mass, assuming (de)protonation.
/// </summary>
/// <param name="mass">The mass to calculate charge for (actually massH if !IsCustomIon)</param>
/// <param name="mz">The desired m/z value the charge should produce</param>
/// <param name="tolerance">How far off the actual m/z is allowed to be</param>
/// <param name="isCustomIon">Is this a custom ion formula?</param>
/// <param name="minCharge">Minimum charge to consider</param>
/// <param name="maxCharge">Maximum charge to consider</param>
/// <param name="massShifts">Possible mass shifts that may have been applied to decoys</param>
/// <param name="massShiftType"></param>
/// <param name="massShift">Mass shift required to to achieve this charge state or zero</param>
/// <param name="nearestCharge">closest matching charge, useful when return value is null</param>
/// <returns>A matching charge or null, in which case the closest non-matching charge can be found in the nearestCharge value.</returns>
public static Adduct CalcCharge(TypedMass mass, double mz, double tolerance, bool isCustomIon, int minCharge, int maxCharge,
ICollection <int> massShifts, MassShiftType massShiftType, out int massShift, out int nearestCharge)
{
Assume.IsTrue(minCharge <= maxCharge);
massShift = 0;
nearestCharge = 0;
double nearestDelta = double.MaxValue;
for (int i = minCharge; i <= maxCharge; i++)
{
if (i != 0) // Avoid z=0 if we're entertaining negative charge states
{
double calculatedMz = isCustomIon
? Adduct.FromChargeProtonated(i).MzFromNeutralMass(mass)
: SequenceMassCalc.GetMZ(mass, i);
double delta = mz - calculatedMz;
double deltaAbs = Math.Abs(delta);
int potentialShift = (int)Math.Round(deltaAbs);
double fractionalDelta = deltaAbs - potentialShift;
if (MatchMz(fractionalDelta, tolerance) && MatchMassShift(potentialShift, massShifts, massShiftType))
{
massShift = potentialShift;
if (delta < 0)
{
massShift = -massShift;
}
var result = i;
nearestCharge = i;
return(Adduct.FromCharge(result, isCustomIon ? Adduct.ADDUCT_TYPE.non_proteomic : Adduct.ADDUCT_TYPE.proteomic));
}
if (deltaAbs < nearestDelta)
{
nearestDelta = deltaAbs;
nearestCharge = i;
}
// If the charge is positive and the calculated m/z is smaller than the desired m/z
// increasing the charge further cannot possibly produce a match
if (massShiftType == MassShiftType.none && minCharge > 0 && delta > 0)
{
break;
}
}
}
Debug.Assert(nearestCharge != 0); // Could only happen if min > max
return(Adduct.EMPTY);
}
/// <summary>
/// Calculates the matching charge within a tolerance for a mass.
/// </summary>
/// <param name="massH">The mass to calculate charge for</param>
/// <param name="mz">The desired m/z value the charge should produce</param>
/// <param name="tolerance">How far off the actual m/z is allowed to be</param>
/// <param name="isCustomIon">Is this a custom ion formula?</param>
/// <param name="minCharge">Minimum charge to consider</param>
/// <param name="maxCharge">Maximum charge to consider</param>
/// <param name="massShifts">Possible mass shifts that may have been applied to decoys</param>
/// <param name="massShiftType"></param>
/// <param name="massShift">Mass shift required to to achieve this charge state or zero</param>
/// <param name="nearestCharge">closest matching charge, useful when return value is null</param>
/// <returns>A matching charge or null, in which case the closest non-matching charge can be found in the nearestCharge value.</returns>
public static int?CalcCharge(double massH, double mz, double tolerance, bool isCustomIon, int minCharge, int maxCharge,
ICollection <int> massShifts, MassShiftType massShiftType, out int massShift, out int nearestCharge)
{
Assume.IsTrue(minCharge <= maxCharge);
massShift = 0;
nearestCharge = 0;
double nearestDelta = double.MaxValue;
for (int i = minCharge; i <= maxCharge; i++)
{
if (i != 0) // Avoid z=0 if we're entertaining negative charge states
{
double delta = mz - (isCustomIon ? BioMassCalc.CalculateIonMz(massH, i) : SequenceMassCalc.GetMZ(massH, i));
double deltaAbs = Math.Abs(delta);
int potentialShift = (int)Math.Round(deltaAbs);
double fractionalDelta = deltaAbs - potentialShift;
if (MatchMz(fractionalDelta, tolerance) && MatchMassShift(potentialShift, massShifts, massShiftType))
{
massShift = potentialShift;
if (delta < 0)
{
massShift = -massShift;
}
int?result = i;
nearestCharge = i;
return(result);
}
if (deltaAbs < nearestDelta)
{
nearestDelta = deltaAbs;
nearestCharge = i;
}
}
}
Debug.Assert(nearestCharge != 0); // Could only happen if min > max
return(null);
}
/// <summary>
/// Calculates the matching charge within a tolerance for a mass.
/// </summary>
/// <param name="massH">The mass to calculate charge for</param>
/// <param name="mz">The desired m/z value the charge should produce</param>
/// <param name="tolerance">How far off the actual m/z is allowed to be</param>
/// <param name="isCustomIon">Is this a custom ion formula?</param>
/// <param name="minCharge">Minimum charge to consider</param>
/// <param name="maxCharge">Maximum charge to consider</param>
/// <param name="massShifts">Possible mass shifts that may have been applied to decoys</param>
/// <param name="massShiftType"></param>
/// <param name="massShift">Mass shift required to to achieve this charge state or zero</param>
/// <param name="nearestCharge">closest matching charge, useful when return value is null</param>
/// <returns>A matching charge or null, in which case the closest non-matching charge can be found in the nearestCharge value.</returns>
public static int? CalcCharge(double massH, double mz, double tolerance, bool isCustomIon, int minCharge, int maxCharge,
ICollection<int> massShifts, MassShiftType massShiftType, out int massShift, out int nearestCharge)
{
Assume.IsTrue(minCharge <= maxCharge);
massShift = 0;
nearestCharge = 0;
double nearestDelta = double.MaxValue;
for (int i = minCharge; i <= maxCharge; i++)
{
if (i != 0) // Avoid z=0 if we're entertaining negative charge states
{
double delta = mz - ( isCustomIon ? BioMassCalc.CalculateIonMz(massH, i) : SequenceMassCalc.GetMZ(massH, i) );
double deltaAbs = Math.Abs(delta);
int potentialShift = (int) Math.Round(deltaAbs);
double fractionalDelta = deltaAbs - potentialShift;
if (MatchMz(fractionalDelta, tolerance) && MatchMassShift(potentialShift, massShifts, massShiftType))
{
massShift = potentialShift;
if (delta < 0)
massShift = -massShift;
int? result = i;
nearestCharge = i;
return result;
}
if (deltaAbs < nearestDelta)
{
nearestDelta = deltaAbs;
nearestCharge = i;
}
}
}
Debug.Assert(nearestCharge != 0); // Could only happen if min > max
return null;
}
private static bool MatchMassShift(int potentialShift, ICollection<int> massShifts, MassShiftType massShiftType)
{
return (massShiftType != MassShiftType.shift_only && potentialShift == 0) ||
(massShiftType != MassShiftType.none && massShifts.Contains(potentialShift));
}
private static int? CalcProductCharge(double productMassH, double productMz, double tolerance, bool isCustomIon,
int maxCharge, MassShiftType massShiftType, out int massShift, out int nearestCharge)
{
return CalcCharge(productMassH, productMz, tolerance, isCustomIon,
Transition.MIN_PRODUCT_CHARGE,
Math.Min(maxCharge, Transition.MAX_PRODUCT_CHARGE),
Transition.MassShifts,
massShiftType,
out massShift,
out nearestCharge);
}
public static int CalcProductCharge(double productPrecursorMass,
int precursorCharge,
double[,] productMasses,
IList<IList<ExplicitLoss>> potentialLosses,
double productMz,
double tolerance,
MassType massType,
MassShiftType massShiftType,
out IonType? ionType,
out int? ordinal,
out TransitionLosses losses,
out int massShift)
{
// Get length of fragment ion mass array
int len = productMasses.GetLength(1);
// Check all possible ion types and offsets
double minDelta = double.MaxValue, minDeltaNs = double.MaxValue;
int bestCharge = 0, bestChargeNs = 0;
IonType? bestIonType = null, bestIonTypeNs = null;
int? bestOrdinal = null, bestOrdinalNs = null;
TransitionLosses bestLosses = null, bestLossesNs = null;
int bestMassShift = 0;
// Check to see if it is the precursor
foreach (var lossesTrial in TransitionGroup.CalcTransitionLosses(IonType.precursor, 0, massType, potentialLosses))
{
double productMass = productPrecursorMass - (lossesTrial != null ? lossesTrial.Mass : 0);
int potentialMassShift;
int nearestCharge;
int? charge = CalcProductCharge(productMass, productMz, tolerance, false, precursorCharge,
massShiftType, out potentialMassShift, out nearestCharge);
if (charge.HasValue && charge.Value == precursorCharge)
{
double potentialMz = SequenceMassCalc.GetMZ(productMass, charge.Value) + potentialMassShift;
double delta = Math.Abs(productMz - potentialMz);
if (potentialMassShift == 0 && minDeltaNs > delta)
{
bestChargeNs = charge.Value;
bestIonTypeNs = IonType.precursor;
bestOrdinalNs = len + 1;
bestLossesNs = lossesTrial;
minDeltaNs = delta;
}
else if (potentialMassShift != 0 && minDelta > delta)
{
bestCharge = charge.Value;
bestIonType = IonType.precursor;
bestOrdinal = len + 1;
bestLosses = lossesTrial;
bestMassShift = potentialMassShift;
minDelta = delta;
}
}
}
foreach (IonType type in Transition.ALL_TYPES)
{
// Types have priorities. If moving to a lower priority type, and there is already a
// suitable answer stop looking.
if ((type == Transition.ALL_TYPES[2] || type == Transition.ALL_TYPES[2]) &&
(MatchMz(minDelta, tolerance) || MatchMz(minDeltaNs, tolerance)))
break;
for (int offset = 0; offset < len; offset++)
{
foreach (var lossesTrial in TransitionGroup.CalcTransitionLosses(type, offset, massType, potentialLosses))
{
// Look for the closest match.
double productMass = productMasses[(int) type, offset];
if (lossesTrial != null)
productMass -= lossesTrial.Mass;
int potentialMassShift;
int nearestCharge;
int? chargeFound = CalcProductCharge(productMass, productMz, tolerance, false, precursorCharge,
massShiftType, out potentialMassShift, out nearestCharge);
if (chargeFound.HasValue)
{
int charge = chargeFound.Value;
double potentialMz = SequenceMassCalc.GetMZ(productMass, charge) + potentialMassShift;
double delta = Math.Abs(productMz - potentialMz);
if (potentialMassShift == 0 && minDeltaNs > delta)
{
bestChargeNs = charge;
bestIonTypeNs = type;
// The peptide length is 1 longer than the mass array
bestOrdinalNs = Transition.OffsetToOrdinal(type, offset, len + 1);
bestLossesNs = lossesTrial;
minDeltaNs = delta;
}
else if (potentialMassShift != 0 && minDelta > delta)
{
bestCharge = charge;
bestIonType = type;
// The peptide length is 1 longer than the mass array
bestOrdinal = Transition.OffsetToOrdinal(type, offset, len + 1);
bestLosses = lossesTrial;
bestMassShift = potentialMassShift;
minDelta = delta;
}
}
}
}
}
// Pefer no-shift to shift, even if the shift value is closer
if (MatchMz(minDelta, tolerance) && !MatchMz(minDeltaNs, tolerance))
{
ionType = bestIonType;
ordinal = bestOrdinal;
losses = bestLosses;
massShift = bestMassShift;
return bestCharge;
}
ionType = bestIonTypeNs;
ordinal = bestOrdinalNs;
losses = bestLossesNs;
massShift = 0;
return bestChargeNs;
}
private static bool MatchMassShift(int potentialShift, ICollection <int> massShifts, MassShiftType massShiftType)
{
return((massShiftType != MassShiftType.shift_only && potentialShift == 0) ||
(massShiftType != MassShiftType.none && massShifts.Contains(potentialShift)));
}
public static int CalcProductCharge(double productPrecursorMass,
int precursorCharge,
double[,] productMasses,
IList <IList <ExplicitLoss> > potentialLosses,
double productMz,
double tolerance,
MassType massType,
MassShiftType massShiftType,
out IonType?ionType,
out int?ordinal,
out TransitionLosses losses,
out int massShift)
{
// Get length of fragment ion mass array
int len = productMasses.GetLength(1);
// Check all possible ion types and offsets
double minDelta = double.MaxValue, minDeltaNs = double.MaxValue;
int bestCharge = 0, bestChargeNs = 0;
IonType? bestIonType = null, bestIonTypeNs = null;
int? bestOrdinal = null, bestOrdinalNs = null;
TransitionLosses bestLosses = null, bestLossesNs = null;
int bestMassShift = 0;
// Check to see if it is the precursor
foreach (var lossesTrial in TransitionGroup.CalcTransitionLosses(IonType.precursor, 0, massType, potentialLosses))
{
double productMass = productPrecursorMass - (lossesTrial != null ? lossesTrial.Mass : 0);
int potentialMassShift;
int nearestCharge;
int? charge = CalcProductCharge(productMass, productMz, tolerance, false, precursorCharge,
massShiftType, out potentialMassShift, out nearestCharge);
if (charge.HasValue && charge.Value == precursorCharge)
{
double potentialMz = SequenceMassCalc.GetMZ(productMass, charge.Value) + potentialMassShift;
double delta = Math.Abs(productMz - potentialMz);
if (potentialMassShift == 0 && minDeltaNs > delta)
{
bestChargeNs = charge.Value;
bestIonTypeNs = IonType.precursor;
bestOrdinalNs = len + 1;
bestLossesNs = lossesTrial;
minDeltaNs = delta;
}
else if (potentialMassShift != 0 && minDelta > delta)
{
bestCharge = charge.Value;
bestIonType = IonType.precursor;
bestOrdinal = len + 1;
bestLosses = lossesTrial;
bestMassShift = potentialMassShift;
minDelta = delta;
}
}
}
foreach (IonType type in Transition.ALL_TYPES)
{
// Types have priorities. If moving to a lower priority type, and there is already a
// suitable answer stop looking.
if ((type == Transition.ALL_TYPES[2] || type == Transition.ALL_TYPES[2]) &&
(MatchMz(minDelta, tolerance) || MatchMz(minDeltaNs, tolerance)))
{
break;
}
for (int offset = 0; offset < len; offset++)
{
foreach (var lossesTrial in TransitionGroup.CalcTransitionLosses(type, offset, massType, potentialLosses))
{
// Look for the closest match.
double productMass = productMasses[(int)type, offset];
if (lossesTrial != null)
{
productMass -= lossesTrial.Mass;
}
int potentialMassShift;
int nearestCharge;
int?chargeFound = CalcProductCharge(productMass, productMz, tolerance, false, precursorCharge,
massShiftType, out potentialMassShift, out nearestCharge);
if (chargeFound.HasValue)
{
int charge = chargeFound.Value;
double potentialMz = SequenceMassCalc.GetMZ(productMass, charge) + potentialMassShift;
double delta = Math.Abs(productMz - potentialMz);
if (potentialMassShift == 0 && minDeltaNs > delta)
{
bestChargeNs = charge;
bestIonTypeNs = type;
// The peptide length is 1 longer than the mass array
bestOrdinalNs = Transition.OffsetToOrdinal(type, offset, len + 1);
bestLossesNs = lossesTrial;
minDeltaNs = delta;
}
else if (potentialMassShift != 0 && minDelta > delta)
{
bestCharge = charge;
bestIonType = type;
// The peptide length is 1 longer than the mass array
bestOrdinal = Transition.OffsetToOrdinal(type, offset, len + 1);
bestLosses = lossesTrial;
bestMassShift = potentialMassShift;
minDelta = delta;
}
}
}
}
}
// Pefer no-shift to shift, even if the shift value is closer
if (MatchMz(minDelta, tolerance) && !MatchMz(minDeltaNs, tolerance))
{
ionType = bestIonType;
ordinal = bestOrdinal;
losses = bestLosses;
massShift = bestMassShift;
return(bestCharge);
}
ionType = bestIonTypeNs;
ordinal = bestOrdinalNs;
losses = bestLossesNs;
massShift = 0;
return(bestChargeNs);
}
public static Adduct CalcProductCharge(TypedMass productPrecursorMass,
int?productZ,
Adduct precursorCharge,
IList <IonType> acceptedIonTypes,
IonTable <TypedMass> productMasses,
IList <IList <ExplicitLoss> > potentialLosses,
double productMz,
double tolerance,
MassType massType,
MassShiftType massShiftType,
out IonType?ionType,
out int?ordinal,
out TransitionLosses losses,
out int massShift)
{
// Get length of fragment ion mass array
int len = productMasses.GetLength(1);
// Check all possible ion types and offsets
double?minDelta = null;
double?minFragmentMass = null, maxFragmentMass = null, maxLoss = null;
if (massShiftType == MassShiftType.none)
{
if (!productZ.HasValue)
{
minFragmentMass = productMz - tolerance;
}
else
{
minFragmentMass = SequenceMassCalc.GetMH(productMz - tolerance, productZ.Value);
maxFragmentMass = SequenceMassCalc.GetMH(productMz + tolerance, productZ.Value);
}
}
var bestCharge = Adduct.EMPTY;
IonType? bestIonType = null;
int? bestOrdinal = null;
TransitionLosses bestLosses = null;
int bestMassShift = 0;
// Check to see if it is the precursor
foreach (var lossesTrial in TransitionGroup.CalcTransitionLosses(IonType.precursor, 0, massType, potentialLosses))
{
var productMass = productPrecursorMass;
if (lossesTrial != null)
{
productMass -= lossesTrial.Mass;
maxLoss = Math.Max(maxLoss ?? 0, lossesTrial.Mass);
}
int potentialMassShift;
int nearestCharge;
var charge = CalcProductCharge(productMass, productZ, productMz, tolerance, false, precursorCharge,
massShiftType, out potentialMassShift, out nearestCharge);
if (Equals(charge, precursorCharge))
{
double potentialMz = SequenceMassCalc.GetMZ(productMass, charge) + potentialMassShift;
double delta = Math.Abs(productMz - potentialMz);
if (CompareIonMatch(delta, lossesTrial, potentialMassShift, minDelta, bestLosses, bestMassShift) < 0)
{
bestCharge = charge;
bestIonType = IonType.precursor;
bestOrdinal = len + 1;
bestLosses = lossesTrial;
bestMassShift = potentialMassShift;
minDelta = delta;
}
}
}
if (maxLoss.HasValue)
{
maxFragmentMass += maxLoss.Value;
}
var categoryLast = -1;
foreach (var typeAccepted in GetIonTypes(acceptedIonTypes))
{
var type = typeAccepted.IonType;
var category = typeAccepted.IonCategory;
// Types have priorities. If changing type category, and there is already a
// suitable answer stop looking.
if (category != categoryLast && minDelta.HasValue && MatchMz(minDelta.Value, tolerance))
{
break;
}
categoryLast = category;
// The peptide length is 1 longer than the mass array
for (int ord = len; ord > 0; ord--)
{
int offset = Transition.OrdinalToOffset(type, ord, len + 1);
var productMassBase = productMasses[type, offset];
// Until below the maximum fragment mass no possible matches
if (maxFragmentMass.HasValue && productMassBase > maxFragmentMass.Value)
{
continue;
}
// Once below the minimum fragment mass no more possible matches, so stop
if (minFragmentMass.HasValue && productMassBase < minFragmentMass.Value)
{
break;
}
foreach (var lossesTrial in TransitionGroup.CalcTransitionLosses(type, offset, massType, potentialLosses))
{
// Look for the closest match.
var productMass = productMassBase;
if (lossesTrial != null)
{
productMass -= lossesTrial.Mass;
}
int potentialMassShift;
int nearestCharge;
var chargeFound = CalcProductCharge(productMass, productZ, productMz, tolerance, false, precursorCharge,
massShiftType, out potentialMassShift, out nearestCharge);
if (!chargeFound.IsEmpty)
{
var charge = chargeFound;
double potentialMz = SequenceMassCalc.GetMZ(productMass, charge) + potentialMassShift;
double delta = Math.Abs(productMz - potentialMz);
if (CompareIonMatch(delta, lossesTrial, potentialMassShift, minDelta, bestLosses, bestMassShift) < 0)
{
bestCharge = charge;
bestIonType = type;
bestOrdinal = ord;
bestLosses = lossesTrial;
bestMassShift = potentialMassShift;
minDelta = delta;
}
}
}
}
}
ionType = bestIonType;
ordinal = bestOrdinal;
losses = bestLosses;
massShift = bestMassShift;
return(bestCharge);
}
public static Adduct CalcProductCharge(TypedMass productPrecursorMass,
Adduct precursorCharge,
IList <IonType> acceptedIonTypes,
IonTable <TypedMass> productMasses,
IList <IList <ExplicitLoss> > potentialLosses,
double productMz,
double tolerance,
MassType massType,
MassShiftType massShiftType,
out IonType?ionType,
out int?ordinal,
out TransitionLosses losses,
out int massShift)
{
// Get length of fragment ion mass array
int len = productMasses.GetLength(1);
// Check all possible ion types and offsets
double? minDelta = null;
var bestCharge = Adduct.EMPTY;
IonType? bestIonType = null;
int? bestOrdinal = null;
TransitionLosses bestLosses = null;
int bestMassShift = 0;
// Check to see if it is the precursor
foreach (var lossesTrial in TransitionGroup.CalcTransitionLosses(IonType.precursor, 0, massType, potentialLosses))
{
var productMass = productPrecursorMass - (lossesTrial != null ? lossesTrial.Mass : 0);
int potentialMassShift;
int nearestCharge;
var charge = CalcProductCharge(productMass, productMz, tolerance, false, precursorCharge,
massShiftType, out potentialMassShift, out nearestCharge);
if (Equals(charge, precursorCharge))
{
double potentialMz = SequenceMassCalc.GetMZ(productMass, charge) + potentialMassShift;
double delta = Math.Abs(productMz - potentialMz);
if (CompareIonMatch(delta, lossesTrial, potentialMassShift, minDelta, bestLosses, bestMassShift) < 0)
{
bestCharge = charge;
bestIonType = IonType.precursor;
bestOrdinal = len + 1;
bestLosses = lossesTrial;
bestMassShift = potentialMassShift;
minDelta = delta;
}
}
}
var categoryLast = -1;
foreach (var typeAccepted in GetIonTypes(acceptedIonTypes))
{
var type = typeAccepted.IonType;
var category = typeAccepted.IonCategory;
// Types have priorities. If changing type category, and there is already a
// suitable answer stop looking.
if (category != categoryLast && minDelta.HasValue && MatchMz(minDelta.Value, tolerance))
{
break;
}
categoryLast = category;
for (int offset = 0; offset < len; offset++)
{
foreach (var lossesTrial in TransitionGroup.CalcTransitionLosses(type, offset, massType, potentialLosses))
{
// Look for the closest match.
var productMass = productMasses[type, offset];
if (lossesTrial != null)
{
productMass -= lossesTrial.Mass;
}
int potentialMassShift;
int nearestCharge;
var chargeFound = CalcProductCharge(productMass, productMz, tolerance, false, precursorCharge,
massShiftType, out potentialMassShift, out nearestCharge);
if (!chargeFound.IsEmpty)
{
var charge = chargeFound;
double potentialMz = SequenceMassCalc.GetMZ(productMass, charge) + potentialMassShift;
double delta = Math.Abs(productMz - potentialMz);
if (CompareIonMatch(delta, lossesTrial, potentialMassShift, minDelta, bestLosses, bestMassShift) < 0)
{
bestCharge = charge;
bestIonType = type;
// The peptide length is 1 longer than the mass array
bestOrdinal = Transition.OffsetToOrdinal(type, offset, len + 1);
bestLosses = lossesTrial;
bestMassShift = potentialMassShift;
minDelta = delta;
}
}
}
}
}
ionType = bestIonType;
ordinal = bestOrdinal;
losses = bestLosses;
massShift = bestMassShift;
return(bestCharge);
}
