public SearchModificationAndSymbol(SearchModificationObj mod, char symbol)
{
Mod = mod;
Symbol = symbol;
IsNTerm = GetIsNTerm(mod);
IsCTerm = GetIsCTerm(mod);
Residues = mod.Residues;
}
private void CreateMzidSettings(SpectrumIdentificationProtocolObj settings)
{
settings.AdditionalSearchParams.Items.AddRange(new ParamBaseObj[]
{
new CVParamObj(CV.CVID.MS_parent_mass_type_mono),
new CVParamObj(CV.CVID.MS_fragment_mass_type_mono),
new UserParamObj()
{
Name = "TargetDecoyApproach", Value = (options.TargetDecoySearchMode == DatabaseSearchMode.Both).ToString()
},
new UserParamObj()
{
Name = "MinSequenceLength", Value = options.MinSequenceLength.ToString()
},
new UserParamObj()
{
Name = "MaxSequenceLength", Value = options.MaxSequenceLength.ToString()
},
new UserParamObj()
{
Name = "MaxNumNTermCleavages", Value = options.MaxNumNTermCleavages.ToString()
},
new UserParamObj()
{
Name = "MaxNumCTermCleavages", Value = options.MaxNumCTermCleavages.ToString()
},
new UserParamObj()
{
Name = "MinPrecursorIonCharge", Value = options.MinPrecursorIonCharge.ToString()
},
new UserParamObj()
{
Name = "MaxPrecursorIonCharge", Value = options.MaxPrecursorIonCharge.ToString()
},
new UserParamObj()
{
Name = "MinProductIonCharge", Value = options.MinProductIonCharge.ToString()
},
new UserParamObj()
{
Name = "MaxProductIonCharge", Value = options.MaxProductIonCharge.ToString()
},
new UserParamObj()
{
Name = "MinSequenceMass", Value = options.MinSequenceMass.ToString(CultureInfo.InvariantCulture)
},
new UserParamObj()
{
Name = "MaxSequenceMass", Value = options.MaxSequenceMass.ToString(CultureInfo.InvariantCulture)
},
new UserParamObj()
{
Name = "PrecursorIonTolerance", Value = options.PrecursorIonTolerance.ToString()
},
new UserParamObj()
{
Name = "ProductIonTolerance", Value = options.ProductIonTolerance.ToString()
},
new UserParamObj()
{
Name = "SearchMode", Value = options.InternalCleavageMode.ToString()
},
new UserParamObj()
{
Name = "NumMatchesPerSpectrum", Value = options.NumMatchesPerSpectrum.ToString()
},
new UserParamObj()
{
Name = "TagBasedSearch", Value = options.TagBasedSearch.ToString()
},
});
var activationMethod = options.ActivationMethod.ToString();
if (options.ActivationMethod == ActivationMethod.Unknown)
{
activationMethod = $"Determined By Spectrum ({options.ActivationMethod})";
}
settings.AdditionalSearchParams.Items.Add(new UserParamObj()
{
Name = "SpecifiedActivationMethod", Value = activationMethod
});
// Add search type, if not a target-deacoy search
if (options.TargetDecoySearchMode != DatabaseSearchMode.Both)
{
settings.AdditionalSearchParams.Items.Add(new UserParamObj()
{
Name = "SearchType", Value = options.TargetDecoySearchMode.ToString()
});
}
// Get the search modifications as they were passed into the AminoAcidSet constructor...
foreach (var mod in options.AminoAcidSet.SearchModifications)
{
var modObj = new SearchModificationObj()
{
FixedMod = mod.IsFixedModification,
MassDelta = (float)mod.Modification.Mass,
Residues = mod.TargetResidue.ToString(),
};
// "*" is used for wildcard residue N-Term or C-Term modifications. mzIdentML standard says that "." should be used instead.
if (modObj.Residues.Contains("*"))
{
modObj.Residues = modObj.Residues.Replace("*", ".");
}
// Really only using this for the modification name parsing for CVParams that exists with ModificationObj
var tempMod = new ModificationObj(CV.CVID.MS_unknown_modification, mod.Modification.Name, 0, modObj.MassDelta);
modObj.CVParams.Add(tempMod.CVParams.First());
if (mod.Location != SequenceLocation.Everywhere)
{
// specificity rules should be added
var rule = new SpecificityRulesListObj();
switch (mod.Location)
{
case SequenceLocation.PeptideNTerm:
rule.CVParams.Add(new CVParamObj(CV.CVID.MS_modification_specificity_peptide_N_term));
break;
case SequenceLocation.PeptideCTerm:
rule.CVParams.Add(new CVParamObj(CV.CVID.MS_modification_specificity_peptide_C_term));
break;
case SequenceLocation.ProteinNTerm:
rule.CVParams.Add(new CVParamObj(CV.CVID.MS_modification_specificity_protein_N_term));
break;
case SequenceLocation.ProteinCTerm:
rule.CVParams.Add(new CVParamObj(CV.CVID.MS_modification_specificity_protein_C_term));
break;
case SequenceLocation.Everywhere:
// not needed, the enclosing if should prevent ever hitting this
break;
default:
// Limited by enum...
break;
}
modObj.SpecificityRules.Add(rule);
}
settings.ModificationParams.Add(modObj);
}
// No enzyme for top-down search
//settings.Enzymes.Enzymes.Add(new EnzymeObj());
settings.ParentTolerances.AddRange(new CVParamObj[]
{
new CVParamObj(CV.CVID.MS_search_tolerance_plus_value, options.PrecursorIonTolerancePpm.ToString(CultureInfo.InvariantCulture))
{
UnitCvid = CV.CVID.UO_parts_per_million
},
new CVParamObj(CV.CVID.MS_search_tolerance_minus_value, options.PrecursorIonTolerancePpm.ToString(CultureInfo.InvariantCulture))
{
UnitCvid = CV.CVID.UO_parts_per_million
},
});
settings.FragmentTolerances.AddRange(new CVParamObj[]
{
new CVParamObj(CV.CVID.MS_search_tolerance_plus_value, options.ProductIonTolerancePpm.ToString(CultureInfo.InvariantCulture))
{
UnitCvid = CV.CVID.UO_parts_per_million
},
new CVParamObj(CV.CVID.MS_search_tolerance_minus_value, options.ProductIonTolerancePpm.ToString(CultureInfo.InvariantCulture))
{
UnitCvid = CV.CVID.UO_parts_per_million
},
});
settings.Threshold.Items.Add(new CVParamObj(CV.CVID.MS_no_threshold));
}
