private bool AddModificationsAndComputeMass(SearchResultsBaseClass searchResult, bool updateModOccurrenceCounts)
{
const bool ALLOW_DUPLICATE_MOD_ON_TERMINUS = true;
bool success;
try
{
// Assume success for now
success = true;
// If any modifications of type IsotopicMod are defined, add them to the Search Result Mods now
searchResult.SearchResultAddIsotopicModifications(updateModOccurrenceCounts);
// Parse .PeptideSequenceWithMods to determine the modified residues present
if (!AddDynamicAndStaticResidueMods(searchResult, updateModOccurrenceCounts))
{
success = false;
}
// Add the protein and peptide terminus static mods (if defined and if the peptide is at a protein terminus)
// Since Sequest allows a terminal peptide residue to be modified twice, we'll allow that to happen,
// even though, biologically, that's typically not possible
// However, there are instances where this is possible, e.g. methylation of D or E on the C-terminus
// (where two COOH groups are present)
searchResult.SearchResultAddStaticTerminusMods(ALLOW_DUPLICATE_MOD_ON_TERMINUS, updateModOccurrenceCounts);
// Compute the monoisotopic mass for this peptide
searchResult.ComputeMonoisotopicMass();
// Populate .PeptideModDescription
searchResult.UpdateModDescription();
}
catch (Exception)
{
success = false;
}
return(success);
}
private bool AddDynamicAndStaticResidueMods(
SearchResultsBaseClass searchResult,
bool updateModOccurrenceCounts)
{
// Step through .PeptideSequenceWithMods
// For each residue, check if a static mod is defined that affects that residue
// For each mod symbol, determine the modification and add to searchResult
var mostRecentLetter = '-';
var residueLocInPeptide = 0;
// Assume success for now
var success = true;
var sequenceWithMods = searchResult.PeptideSequenceWithMods;
for (var index = 0; index <= sequenceWithMods.Length - 1; index++)
{
var character = sequenceWithMods[index];
if (StringUtilities.IsLetterAtoZ(character))
{
mostRecentLetter = character;
residueLocInPeptide++;
for (var modIndex = 0; modIndex <= mPeptideMods.ModificationCount - 1; modIndex++)
{
if (mPeptideMods.GetModificationTypeByIndex(modIndex) == ModificationDefinition.ResidueModificationType.StaticMod)
{
var modificationDefinition = mPeptideMods.GetModificationByIndex(modIndex);
if (modificationDefinition.TargetResiduesContain(character))
{
// Match found; add this modification
var residueTerminusState = searchResult.DetermineResidueTerminusState(residueLocInPeptide);
success = searchResult.SearchResultAddModification(
modificationDefinition, character, residueLocInPeptide,
residueTerminusState, updateModOccurrenceCounts);
if (!success)
{
// Error adding this static mod
SetErrorCode(PHRPErrorCode.UnspecifiedError);
mErrorMessage = "Error calling searchResult.SearchResultAddModification for peptide '" + sequenceWithMods + "': " + searchResult.ErrorMessage;
break;
}
}
}
}
}
else if (StringUtilities.IsLetterAtoZ(mostRecentLetter))
{
success = searchResult.SearchResultAddDynamicModification(character, mostRecentLetter, residueLocInPeptide, searchResult.DetermineResidueTerminusState(residueLocInPeptide), updateModOccurrenceCounts);
if (!success)
{
// Error adding this dynamic mod
SetErrorCode(PHRPErrorCode.UnspecifiedError);
mErrorMessage = "Error calling searchResult.SearchResultAddDynamicModification for peptide '" + sequenceWithMods + "': " + searchResult.ErrorMessage;
break;
}
}
else
{
// We found a modification symbol but mostRecentLetter is not a letter
// Therefore, this modification symbol is at the beginning of the string; ignore the symbol
}
}
return(success);
}
