public PeptideSpectrumMatch(TandemMassSpectrum spectrum, Peptide peptide, MassTolerance productMassTolerance)
{
Spectrum = spectrum;
Peptide = peptide;
PrecursorMassErrorDa = spectrum.PrecursorMass - (precursorMassType == MassType.Average ? peptide.AverageMass : peptide.MonoisotopicMass);
PrecursorMassErrorPpm = PrecursorMassErrorDa / (precursorMassType == MassType.Average ? peptide.AverageMass : peptide.MonoisotopicMass) * 1e6;
ScoreMatch(productMassTolerance);
}
private Peptide(Peptide peptide) : this(peptide.Parent, peptide.StartResidueNumber, peptide.EndResidueNumber, peptide.MissedCleavages)
{
}
public IEnumerable <Peptide> GetVariablyModifiedPeptides(IEnumerable <Modification> variableModifications, int maximumVariableModificationIsoforms)
{
Dictionary <int, List <Modification> > possible_modifications = new Dictionary <int, List <Modification> >(Length + 4);
foreach (Modification variable_modification in variableModifications)
{
if (variable_modification.Type == ModificationType.ProteinNTerminus && (StartResidueNumber == 1 || (StartResidueNumber == 2 && Parent[0] == 'M')) &&
(variable_modification.AminoAcid == char.MinValue || this[0] == variable_modification.AminoAcid))
{
List <Modification> prot_n_term_variable_mods;
if (!possible_modifications.TryGetValue(0, out prot_n_term_variable_mods))
{
prot_n_term_variable_mods = new List <Modification>();
prot_n_term_variable_mods.Add(variable_modification);
possible_modifications.Add(0, prot_n_term_variable_mods);
}
else
{
prot_n_term_variable_mods.Add(variable_modification);
}
}
if (variable_modification.Type == ModificationType.PeptideNTerminus && (variable_modification.AminoAcid == char.MinValue || this[0] == variable_modification.AminoAcid))
{
List <Modification> pep_n_term_variable_mods;
if (!possible_modifications.TryGetValue(1, out pep_n_term_variable_mods))
{
pep_n_term_variable_mods = new List <Modification>();
pep_n_term_variable_mods.Add(variable_modification);
possible_modifications.Add(1, pep_n_term_variable_mods);
}
else
{
pep_n_term_variable_mods.Add(variable_modification);
}
}
for (int r = 0; r < Length; r++)
{
if (variable_modification.Type == ModificationType.AminoAcidResidue && this[r] == variable_modification.AminoAcid)
{
List <Modification> residue_variable_mods;
if (!possible_modifications.TryGetValue(r + 2, out residue_variable_mods))
{
residue_variable_mods = new List <Modification>();
residue_variable_mods.Add(variable_modification);
possible_modifications.Add(r + 2, residue_variable_mods);
}
else
{
residue_variable_mods.Add(variable_modification);
}
}
}
if (variable_modification.Type == ModificationType.PeptideCTerminus && (variable_modification.AminoAcid == char.MinValue || this[Length - 1] == variable_modification.AminoAcid))
{
List <Modification> pep_c_term_variable_mods;
if (!possible_modifications.TryGetValue(Length + 2, out pep_c_term_variable_mods))
{
pep_c_term_variable_mods = new List <Modification>();
pep_c_term_variable_mods.Add(variable_modification);
possible_modifications.Add(Length + 2, pep_c_term_variable_mods);
}
else
{
pep_c_term_variable_mods.Add(variable_modification);
}
}
if (variable_modification.Type == ModificationType.ProteinCTerminus && (EndResidueNumber == Parent.Length - 1) &&
(variable_modification.AminoAcid == char.MinValue || this[Length - 1] == variable_modification.AminoAcid))
{
List <Modification> prot_c_term_variable_mods;
if (!possible_modifications.TryGetValue(Length + 3, out prot_c_term_variable_mods))
{
prot_c_term_variable_mods = new List <Modification>();
prot_c_term_variable_mods.Add(variable_modification);
possible_modifications.Add(Length + 3, prot_c_term_variable_mods);
}
else
{
prot_c_term_variable_mods.Add(variable_modification);
}
}
}
int variable_modification_isoforms = 0;
foreach (Dictionary <int, Modification> kvp in GetVariableModificationPatterns(possible_modifications))
{
Peptide peptide = new Peptide(this);
peptide.FixedModifications = FixedModifications;
peptide.VariableModifications = kvp;
yield return(peptide);
variable_modification_isoforms++;
if (variable_modification_isoforms == maximumVariableModificationIsoforms)
{
yield break;
}
}
}
// This Init method needs to be called before this object can be used.
// For more info, see how we use these objects in DatabaseSearcher.
//
// We copy the peptide parameter deeply (because these sometimes come
// from reusable buffers) but not the spectrum parameter (because these
// are not reused).
//
// The array product_masses_buf is used for temporary internal storage
// and may be resized. It needs to be local to the current thread; no
// locking is performed. Its contents are not of interest to the
// caller.
//
// The fast_q_sorter object also need to be local to the current
// thread, as its internal state will be modified.
public void Init(TandemMassSpectrum spectrum, Peptide peptide, MassTolerance productMassTolerance,
ref double[] product_masses_buf, FastQSorter fast_q_sorter)
{
Spectrum = spectrum;
if(Peptide == null)
Peptide = new Peptide();
Peptide.CopyFrom(peptide);
PrecursorMassErrorDa = spectrum.PrecursorMass - (precursorMassType == MassType.Average ? peptide.AverageMass : peptide.MonoisotopicMass);
PrecursorMassErrorPpm = PrecursorMassErrorDa / (precursorMassType == MassType.Average ? peptide.AverageMass : peptide.MonoisotopicMass) * 1e6;
ScoreMatch(productMassTolerance, ref product_masses_buf, fast_q_sorter);
}
// Copy all of this objects data members from the other object's data
// members. We copy other.Peptide deeply (because these sometimes come
// from reusable buffers) but not other.Spectrum (because these are not
// reused).
public void CopyFrom(PeptideSpectrumMatch other)
{
Spectrum = other.Spectrum;
if(Peptide == null)
Peptide = new Peptide();
Peptide.CopyFrom(other.Peptide);
PrecursorMassErrorDa = other.PrecursorMassErrorDa;
PrecursorMassErrorPpm = other.PrecursorMassErrorPpm;
MatchingProducts = other.MatchingProducts;
TotalProducts = other.TotalProducts;
MatchingProductsFraction = other.MatchingProductsFraction;
MatchingIntensity = other.MatchingIntensity;
MatchingIntensityFraction = other.MatchingIntensityFraction;
MorpheusScore = other.MorpheusScore;
}
private Peptide(Peptide peptide)
: this(peptide.Parent, peptide.StartResidueNumber, peptide.EndResidueNumber, peptide.MissedCleavages)
{
}
public IEnumerable<Peptide> GetVariablyModifiedPeptides(IEnumerable<Modification> variableModifications, int maximumVariableModificationIsoforms)
{
Dictionary<int, List<Modification>> possible_modifications = new Dictionary<int, List<Modification>>(Length + 4);
foreach(Modification variable_modification in variableModifications)
{
if(variable_modification.Type == ModificationType.ProteinNTerminus && (StartResidueNumber == 1 || (StartResidueNumber == 2 && Parent[0] == 'M'))
&& (variable_modification.AminoAcid == char.MinValue || this[0] == variable_modification.AminoAcid))
{
List<Modification> prot_n_term_variable_mods;
if(!possible_modifications.TryGetValue(0, out prot_n_term_variable_mods))
{
prot_n_term_variable_mods = new List<Modification>();
prot_n_term_variable_mods.Add(variable_modification);
possible_modifications.Add(0, prot_n_term_variable_mods);
}
else
{
prot_n_term_variable_mods.Add(variable_modification);
}
}
if(variable_modification.Type == ModificationType.PeptideNTerminus && (variable_modification.AminoAcid == char.MinValue || this[0] == variable_modification.AminoAcid))
{
List<Modification> pep_n_term_variable_mods;
if(!possible_modifications.TryGetValue(1, out pep_n_term_variable_mods))
{
pep_n_term_variable_mods = new List<Modification>();
pep_n_term_variable_mods.Add(variable_modification);
possible_modifications.Add(1, pep_n_term_variable_mods);
}
else
{
pep_n_term_variable_mods.Add(variable_modification);
}
}
for(int r = 0; r < Length; r++)
{
if(variable_modification.Type == ModificationType.AminoAcidResidue && this[r] == variable_modification.AminoAcid)
{
List<Modification> residue_variable_mods;
if(!possible_modifications.TryGetValue(r + 2, out residue_variable_mods))
{
residue_variable_mods = new List<Modification>();
residue_variable_mods.Add(variable_modification);
possible_modifications.Add(r + 2, residue_variable_mods);
}
else
{
residue_variable_mods.Add(variable_modification);
}
}
}
if(variable_modification.Type == ModificationType.PeptideCTerminus && (variable_modification.AminoAcid == char.MinValue || this[Length - 1] == variable_modification.AminoAcid))
{
List<Modification> pep_c_term_variable_mods;
if(!possible_modifications.TryGetValue(Length + 2, out pep_c_term_variable_mods))
{
pep_c_term_variable_mods = new List<Modification>();
pep_c_term_variable_mods.Add(variable_modification);
possible_modifications.Add(Length + 2, pep_c_term_variable_mods);
}
else
{
pep_c_term_variable_mods.Add(variable_modification);
}
}
if(variable_modification.Type == ModificationType.ProteinCTerminus && (EndResidueNumber == Parent.Length - 1)
&& (variable_modification.AminoAcid == char.MinValue || this[Length - 1] == variable_modification.AminoAcid))
{
List<Modification> prot_c_term_variable_mods;
if(!possible_modifications.TryGetValue(Length + 3, out prot_c_term_variable_mods))
{
prot_c_term_variable_mods = new List<Modification>();
prot_c_term_variable_mods.Add(variable_modification);
possible_modifications.Add(Length + 3, prot_c_term_variable_mods);
}
else
{
prot_c_term_variable_mods.Add(variable_modification);
}
}
}
int variable_modification_isoforms = 0;
foreach(Dictionary<int, Modification> kvp in GetVariableModificationPatterns(possible_modifications))
{
Peptide peptide = new Peptide(this);
peptide.FixedModifications = FixedModifications;
peptide.VariableModifications = kvp;
yield return peptide;
variable_modification_isoforms++;
if(variable_modification_isoforms == maximumVariableModificationIsoforms)
{
yield break;
}
}
}
private void ScoreMatch(MassTolerance productMassTolerance)
{
double[] theoretical_product_masses = Peptide.CalculateProductMasses(PRODUCT_TYPES[Spectrum.FragmentationMethod]).ToArray();
TotalProducts = theoretical_product_masses.Length;
// speed optimizations
int num_theoretical_products = theoretical_product_masses.Length;
double[] experimental_masses = Spectrum.Masses;
double[] experimental_intensities = Spectrum.Intensities;
int num_experimental_peaks = experimental_masses.Length;
double product_mass_tolerance_value = productMassTolerance.Value;
MassToleranceUnits product_mass_tolerance_units = productMassTolerance.Units;
MatchingProducts = 0;
int t = 0;
int e = 0;
while (t < num_theoretical_products && e < num_experimental_peaks)
{
double mass_difference = experimental_masses[e] - theoretical_product_masses[t];
if (product_mass_tolerance_units == MassToleranceUnits.ppm)
{
mass_difference = mass_difference / theoretical_product_masses[t] * 1e6;
}
if (Math.Abs(mass_difference) <= product_mass_tolerance_value)
{
MatchingProducts++;
t++;
}
else if (mass_difference < 0)
{
e++;
}
else if (mass_difference > 0)
{
t++;
}
}
MatchingProductsFraction = (double)MatchingProducts / TotalProducts;
MatchingIntensity = 0.0;
int e2 = 0;
int t2 = 0;
while (e2 < num_experimental_peaks && t2 < num_theoretical_products)
{
double mass_difference = experimental_masses[e2] - theoretical_product_masses[t2];
if (product_mass_tolerance_units == MassToleranceUnits.ppm)
{
mass_difference = mass_difference / theoretical_product_masses[t2] * 1e6;
}
if (Math.Abs(mass_difference) <= product_mass_tolerance_value)
{
MatchingIntensity += experimental_intensities[e2];
e2++;
}
else if (mass_difference < 0)
{
e2++;
}
else if (mass_difference > 0)
{
t2++;
}
}
MatchingIntensityFraction = MatchingIntensity / Spectrum.TotalIntensity;
MorpheusScore = MatchingProducts + MatchingIntensityFraction;
}
public IEnumerable <Peptide> Digest(Protease protease, int maximumMissedCleavages, InitiatorMethionineBehavior initiatorMethionineBehavior,
int?minimumPeptideLength, int?maximumPeptideLength)
{
if (Length > 0)
{
if (protease.CleavageSpecificity != CleavageSpecificity.None)
{
// these are the 0-based residue indices the protease cleaves AFTER
List <int> indices = protease.GetDigestionSiteIndices(this);
indices.Insert(0, -1);
indices.Add(Length - 1);
if (protease.CleavageSpecificity == CleavageSpecificity.Full)
{
for (int missed_cleavages = 0; missed_cleavages <= maximumMissedCleavages; missed_cleavages++)
{
for (int i = 0; i < indices.Count - missed_cleavages - 1; i++)
{
if (initiatorMethionineBehavior != InitiatorMethionineBehavior.Cleave || indices[i] + 1 != 0 || this[0] != 'M')
{
int length = indices[i + missed_cleavages + 1] - indices[i];
if ((!minimumPeptideLength.HasValue || length >= minimumPeptideLength.Value) && (!maximumPeptideLength.HasValue || length <= maximumPeptideLength.Value))
{
// start residue number: +1 for starting at the next residue after the cleavage, +1 for 0->1 indexing
// end residue number: +1 for 0->1 indexing
Peptide peptide = new Peptide(this, indices[i] + 1 + 1, indices[i + missed_cleavages + 1] + 1, missed_cleavages);
yield return(peptide);
}
}
if (initiatorMethionineBehavior != InitiatorMethionineBehavior.Retain && indices[i] + 1 == 0 && this[0] == 'M')
{
int length = indices[i + missed_cleavages + 1] - indices[i] - 1;
if (length > 0 && (!minimumPeptideLength.HasValue || length >= minimumPeptideLength.Value) && (!maximumPeptideLength.HasValue || length <= maximumPeptideLength.Value))
{
// start residue number: +1 for skipping initiator methionine, +1 for starting at the next residue after the cleavage, +1 for 0->1 indexing
// end residue number: +1 for 0->1 indexing
Peptide peptide_without_initiator_methionine = new Peptide(this, indices[i] + 1 + 1 + 1, indices[i + missed_cleavages + 1] + 1, missed_cleavages);
yield return(peptide_without_initiator_methionine);
}
}
}
}
}
else // protease.CleavageSpecificity == CleavageSpecificity.Semi || protease.CleavageSpecificity == CleavageSpecificity.SemiN || protease.CleavageSpecificity == CleavageSpecificity.SemiC
{
if (protease.CleavageSpecificity == CleavageSpecificity.Semi || protease.CleavageSpecificity == CleavageSpecificity.SemiN)
{
for (int missed_cleavages = 0; missed_cleavages <= maximumMissedCleavages; missed_cleavages++)
{
for (int i = 0; i < indices.Count - missed_cleavages - 1; i++)
{
if (initiatorMethionineBehavior != InitiatorMethionineBehavior.Cleave || indices[i] + 1 != 0 || this[0] != 'M')
{
// conditional ensures that we are generating peptides at their lowest missed cleavage state
for (int length = indices[i + missed_cleavages + 1] - indices[i]; length > (indices[i + missed_cleavages + 1] - indices[i]) - (indices[i + missed_cleavages + 1] - indices[(i + missed_cleavages + 1) - 1]); length--)
{
if ((indices[i] + 1 + 1) + length - 1 <= Length)
{
if ((!minimumPeptideLength.HasValue || length >= minimumPeptideLength.Value) && (!maximumPeptideLength.HasValue || length <= maximumPeptideLength.Value))
{
// start residue number: +1 for starting at the next residue after the cleavage, +1 for 0->1 indexing
// end residue number: start residue number + length - 1
Peptide peptide = new Peptide(this, indices[i] + 1 + 1, (indices[i] + 1 + 1) + length - 1, missed_cleavages);
yield return(peptide);
}
}
}
}
if (initiatorMethionineBehavior != InitiatorMethionineBehavior.Retain && indices[i] + 1 == 0 && this[0] == 'M')
{
// conditional ensures that we are generating peptides at their lowest missed cleavage state
for (int length = indices[i + missed_cleavages + 1] - indices[i]; length > (indices[i + missed_cleavages + 1] - indices[i]) - (indices[i + missed_cleavages + 1] - indices[(i + missed_cleavages + 1) - 1]); length--)
{
if ((indices[i] + 1 + 1 + 1) + length - 1 <= Length)
{
if ((!minimumPeptideLength.HasValue || length >= minimumPeptideLength.Value) && (!maximumPeptideLength.HasValue || length <= maximumPeptideLength.Value))
{
// start residue number: +1 for skipping initiator methionine, +1 for starting at the next residue after the cleavage, +1 for 0->1 indexing
// end residue number: start residue number + length - 1
Peptide peptide_without_initiator_methionine = new Peptide(this, indices[i] + 1 + 1 + 1, (indices[i] + 1 + 1 + 1) + length - 1, missed_cleavages);
yield return(peptide_without_initiator_methionine);
}
}
}
}
}
}
}
if (protease.CleavageSpecificity == CleavageSpecificity.Semi || protease.CleavageSpecificity == CleavageSpecificity.SemiC)
{
for (int missed_cleavages = 0; missed_cleavages <= maximumMissedCleavages; missed_cleavages++)
{
for (int i = 0; i < indices.Count - missed_cleavages - 1; i++)
{
// handling for initiator methionine not required
// - (protease.CleavageSpecificity == CleavageSpecificity.Semi ? 1 : 0) ensures that we don't repeat the same peptides we generated above in the SemiN digestion
// conditional ensures that we are generating peptides at their lowest missed cleavage state
for (int length = indices[i + missed_cleavages + 1] - indices[i] - (protease.CleavageSpecificity == CleavageSpecificity.Semi ? 1 : 0); length > (indices[i + missed_cleavages + 1] - indices[i]) - (indices[i + 1] - indices[i]); length--)
{
if ((indices[i + missed_cleavages + 1] + 1) - length + 1 >= 1)
{
if ((!minimumPeptideLength.HasValue || length >= minimumPeptideLength.Value) && (!maximumPeptideLength.HasValue || length <= maximumPeptideLength.Value))
{
// start residue number: end residue number - length + 1
// end residue number: +1 for 0->1 indexing
Peptide peptide = new Peptide(this, (indices[i + missed_cleavages + 1] + 1) - length + 1, indices[i + missed_cleavages + 1] + 1, missed_cleavages);
yield return(peptide);
}
}
}
}
}
}
}
}
else // protease.CleavageSpecificity == CleavageSpecificity.None
{
if (initiatorMethionineBehavior != InitiatorMethionineBehavior.Cleave || this[0] != 'M')
{
if ((!minimumPeptideLength.HasValue || Length >= minimumPeptideLength.Value) && (!maximumPeptideLength.HasValue || Length <= maximumPeptideLength.Value))
{
Peptide peptide = new Peptide(this, 1, Length, -1);
yield return(peptide);
}
}
if (initiatorMethionineBehavior != InitiatorMethionineBehavior.Retain && this[0] == 'M')
{
if (Length > 1 && (!minimumPeptideLength.HasValue || Length - 1 >= minimumPeptideLength.Value) && (!maximumPeptideLength.HasValue || Length - 1 <= maximumPeptideLength.Value))
{
Peptide peptide_without_initiator_methionine = new Peptide(this, 2, Length, -1);
yield return(peptide_without_initiator_methionine);
}
}
}
}
}
public void CopyFrom(Peptide peptide)
{
Init(peptide.Parent, peptide.StartResidueNumber, peptide.EndResidueNumber, peptide.MissedCleavages);
}
