public static double ComputeMonoisotopicMass(string pepSeqWithMods)
{
double mass = Constants.WATER_MONOISOTOPIC_MASS;
bool cumulMod = false;
string strMod = "";
for (int i = 0; i < pepSeqWithMods.Length; i++)
{
if (pepSeqWithMods[i] == '(')
{
strMod = "";
cumulMod = true;
}
else if (pepSeqWithMods[i] == ')')
{
cumulMod = false;
mass += ModificationDictionary.Instance[strMod].MonoisotopicMassShift;
}
else if (cumulMod)
{
strMod += pepSeqWithMods[i];
}
else
{
mass += AminoAcidMasses.GetMonoisotopicMass(pepSeqWithMods[i]);
}
}
return(mass);
}
public double[] GetMasses()
{
double cumul = Proteomics.Utilities.Constants.WATER_MONOISOTOPIC_MASS;
double[] array = new double[BaseSequence.Length];
for (int r = 1; r <= BaseSequence.Length; r++)
{
double tmp = 0;
if (FixedModifications != null && FixedModifications.ContainsKey(r + 1))
{
foreach (Modification mod in FixedModifications[r + 1])
{
tmp += mod.MonoisotopicMassShift;
}
}
if (VariableModifications != null && VariableModifications.ContainsKey(r + 1))
{
tmp += VariableModifications[r + 1].MonoisotopicMassShift;
}
array[r - 1] = AminoAcidMasses.GetMonoisotopicMass(BaseSequence[r - 1]) + tmp;
cumul += array[r - 1];
}
return(array);
}
public static double[] GetMasses(string sequence)
{
double[] proteinMasses = new double[sequence.Length];
for (int i = 0; i < sequence.Length; i++)
{
proteinMasses[i] = AminoAcidMasses.GetMonoisotopicMass(sequence[i]);
}
return(proteinMasses);
}
private void InitializeProductArrays()
{
double mass_shift;
cumulativeNTerminalMass = new double[Length];
mass_shift = 0.0;
// fixed modifications on protein N-terminus
if (fixedModifications != null)
{
List <Modification> prot_n_term_fixed_mods;
if (fixedModifications.TryGetValue(0, out prot_n_term_fixed_mods))
{
foreach (Modification fixed_modification in prot_n_term_fixed_mods)
{
mass_shift += fixed_modification.MonoisotopicMassShift;
}
}
}
// variable modification on the protein N-terminus
if (variableModifications != null)
{
Modification protein_n_term_variable_mod;
if (variableModifications.TryGetValue(0, out protein_n_term_variable_mod))
{
mass_shift += protein_n_term_variable_mod.MonoisotopicMassShift;
}
}
// fixed modifications on peptide N-terminus
if (fixedModifications != null)
{
List <Modification> pep_n_term_fixed_mods;
if (fixedModifications.TryGetValue(1, out pep_n_term_fixed_mods))
{
foreach (Modification fixed_modification in pep_n_term_fixed_mods)
{
mass_shift += fixed_modification.MonoisotopicMassShift;
}
}
}
// variable modification on peptide N-terminus
if (variableModifications != null)
{
Modification pep_n_term_variable_mod;
if (variableModifications.TryGetValue(1, out pep_n_term_variable_mod))
{
mass_shift += pep_n_term_variable_mod.MonoisotopicMassShift;
}
}
cumulativeNTerminalMass[0] = mass_shift;
for (int r = 1; r < Length; r++)
{
mass_shift = 0.0;
// fixed modifications on this residue
if (fixedModifications != null)
{
List <Modification> residue_fixed_mods;
if (fixedModifications.TryGetValue(r + 1, out residue_fixed_mods))
{
foreach (Modification fixed_modification in residue_fixed_mods)
{
mass_shift += fixed_modification.MonoisotopicMassShift;
}
}
}
// variable modification on this residue
if (variableModifications != null)
{
Modification residue_variable_mod;
if (variableModifications.TryGetValue(r + 1, out residue_variable_mod))
{
mass_shift += residue_variable_mod.MonoisotopicMassShift;
}
}
cumulativeNTerminalMass[r] = cumulativeNTerminalMass[r - 1] + (productMassType == MassType.Average ? AminoAcidMasses.GetAverageMass(this[r - 1]) : AminoAcidMasses.GetMonoisotopicMass(this[r - 1])) + mass_shift;
}
cumulativeCTerminalMass = new double[Length];
mass_shift = 0.0;
// fixed modifications on protein C-terminus
if (fixedModifications != null)
{
List <Modification> prot_c_term_fixed_mods;
if (fixedModifications.TryGetValue(Length + 3, out prot_c_term_fixed_mods))
{
foreach (Modification fixed_modification in prot_c_term_fixed_mods)
{
mass_shift += fixed_modification.MonoisotopicMassShift;
}
}
}
// variable modification on protein C-terminus
if (variableModifications != null)
{
Modification prot_c_term_variable_mod;
if (variableModifications.TryGetValue(Length + 3, out prot_c_term_variable_mod))
{
mass_shift += prot_c_term_variable_mod.MonoisotopicMassShift;
}
}
// fixed modifications on peptide C-terminus
if (fixedModifications != null)
{
List <Modification> pep_c_term_fixed_mods;
if (fixedModifications.TryGetValue(Length + 2, out pep_c_term_fixed_mods))
{
foreach (Modification fixed_modification in pep_c_term_fixed_mods)
{
mass_shift += fixed_modification.MonoisotopicMassShift;
}
}
}
// variable modification on peptide C-terminus
if (variableModifications != null)
{
Modification pep_c_term_variable_mod;
if (variableModifications.TryGetValue(Length + 2, out pep_c_term_variable_mod))
{
mass_shift += pep_c_term_variable_mod.MonoisotopicMassShift;
}
}
cumulativeCTerminalMass[0] = mass_shift;
for (int r = 1; r < Length; r++)
{
mass_shift = 0.0;
// fixed modifications on this residue
if (fixedModifications != null)
{
List <Modification> residue_fixed_mods;
if (fixedModifications.TryGetValue(Length - r + 2, out residue_fixed_mods))
{
foreach (Modification fixed_modification in residue_fixed_mods)
{
mass_shift += fixed_modification.MonoisotopicMassShift;
}
}
}
// variable modification on this residue
if (variableModifications != null)
{
Modification residue_variable_mod;
if (variableModifications.TryGetValue(Length - r + 2, out residue_variable_mod))
{
mass_shift += residue_variable_mod.MonoisotopicMassShift;
}
}
cumulativeCTerminalMass[r] = cumulativeCTerminalMass[r - 1] + (productMassType == MassType.Average ? AminoAcidMasses.GetAverageMass(this[Length - r]) : AminoAcidMasses.GetMonoisotopicMass(this[Length - r])) + mass_shift;
}
initializeProductArrays = false;
}
public IEnumerable <ProductMatch> ComputeFragments(Peptide peptide, int precursorKnownCharge, DBOptions dbOptions)
{
int maxCharge;
if (precursorKnownCharge > 1)
{
maxCharge = precursorKnownCharge - 1;
}
else
{
maxCharge = precursorKnownCharge;
}
string sequence = peptide.BaseSequence;
ProductMatch match = new ProductMatch();
double cumulativeNTerminalMass = 0; // 1.007276 + 15.9949;//TODO Add NTerminal modifications here
double cumulativeCTerminalMass = 0; // 1.007276;//TODO Add CTerminal modifications here
string cumulSeq = "";
string cumulRevSeq = "";
for (int r = 1; r <= sequence.Length; r++)
{
match.fragmentPos = r;
//Peptide mods, computed during digestion
//TODO Only search for modifications that were seen in the spectrum
double tmp = 0;
cumulSeq += sequence[r - 1];
if (peptide.FixedModifications != null && peptide.FixedModifications.ContainsKey(r + 1))
{
foreach (Modification mod in peptide.FixedModifications[r + 1])
{
tmp += mod.MonoisotopicMassShift;
}
}
if (peptide.VariableModifications != null && peptide.VariableModifications.ContainsKey(r + 1))
{
tmp += peptide.VariableModifications[r + 1].MonoisotopicMassShift;
}
cumulativeNTerminalMass += AminoAcidMasses.GetMonoisotopicMass(sequence[r - 1]) + tmp;
tmp = 0;
cumulRevSeq += sequence[sequence.Length - r];
if (peptide.FixedModifications != null && peptide.FixedModifications.ContainsKey(sequence.Length + 2 - r))
{
foreach (Modification mod in peptide.FixedModifications[sequence.Length + 2 - r])
{
tmp += mod.MonoisotopicMassShift;
}
}
if (peptide.VariableModifications != null && peptide.VariableModifications.ContainsKey(sequence.Length + 2 - r))
{
tmp += peptide.VariableModifications[sequence.Length + 2 - r].MonoisotopicMassShift;
}
cumulativeCTerminalMass += AminoAcidMasses.GetMonoisotopicMass(sequence[sequence.Length - r]) + tmp;
for (int c = maxCharge; c > 0; c--)
{
match.charge = c;
foreach (FragmentClass fragment in this)
{
if (fragment.IsReverse)
{
match.fragmentPos = 1 + sequence.Length - r;
}
else
{
match.fragmentPos = r;
}
match.Fragment = fragment;
foreach (double product_mass in fragment.ComputeFragment(cumulativeCTerminalMass, cumulativeNTerminalMass))
{
match.weight = fragment.Distribution;//TODO Adjust this value by computing overall impact (times 10?)
//ModLess
match.theoMz = Numerics.MZFromMass(product_mass, c);
yield return(match);
//Added mods
if (dbOptions.addFragmentMods)
{
foreach (Modification mod in FragmentDictionary.Fragments.Values)
{
if ((fragment.IsReverse ? cumulRevSeq : cumulSeq).Contains(mod.AminoAcid))
{
//!!!!match.Fragment = mod;
match.weight = fragment.Distribution * mod.Probability;
match.theoMz = Numerics.MZFromMass(product_mass + mod.MonoisotopicMassShift, c);
yield return(match);
}
}
}
}
}
}
}
if (dbOptions.addFragmentLoss)
{
match.charge = 1;
match.Fragment = FragLossObject;
foreach (Modification mod in FragmentDictionary.AAFragments.Values)
{
if (peptide.BaseSequence.Contains(mod.AminoAcid))
{
match.fragmentPos = peptide.BaseSequence.IndexOf(mod.AminoAcid);
match.theoMz = mod.MonoisotopicMassShift;// Numerics.MZFromMass(mod.MonoisotopicMassShift, 1);
match.weight = mod.Probability;
yield return(match);
}
}
}
}
