public void GetAveragineFormulaForGivenMass()
{
var averagineEmpiricalFormula = isotopicDistributionCalculator.GetAveragineFormulaAsString(1979, true);
Console.WriteLine(averagineEmpiricalFormula);
averagineEmpiricalFormula = isotopicDistributionCalculator.GetAveragineFormulaAsString(1979, false);
Console.WriteLine(averagineEmpiricalFormula);
}
public virtual void UpdateTargetMissingInfo(IqTarget target, bool calcAveragineForMissingEmpiricalFormula = true, bool cysteinesAreModified = false)
{
var isMissingMonoMass = target.MonoMassTheor <= 0;
if (String.IsNullOrEmpty(target.EmpiricalFormula))
{
if (!String.IsNullOrEmpty(target.Code))
{
//Create empirical formula based on code. Assume it is an unmodified peptide
//target.EmpiricalFormula = _peptideUtils.GetEmpiricalFormulaForPeptideSequence(target.Code);
target.EmpiricalFormula = IqCodeParser.GetEmpiricalFormulaFromSequence(target.Code, cysteinesAreModified);
}
else
{
if (isMissingMonoMass)
{
throw new ApplicationException(
"Trying to fill in missing data on target, but Target is missing both the 'Code' and the Monoisotopic Mass. One or the other is needed.");
}
target.Code = "AVERAGINE";
target.EmpiricalFormula =
IsotopicDistributionCalculator.GetAveragineFormulaAsString(target.MonoMassTheor);
}
}
if (isMissingMonoMass)
{
target.MonoMassTheor =
EmpiricalFormulaUtilities.GetMonoisotopicMassFromEmpiricalFormula(target.EmpiricalFormula);
}
if (target.ChargeState != 0)
{
target.MZTheor = target.MonoMassTheor / target.ChargeState + DeconTools.Backend.Globals.PROTON_MASS;
}
}
protected virtual void UpdateTargetMissingInfo()
{
var canUseReferenceMassTags = MassTagsForReference != null && MassTagsForReference.TargetList.Count > 0;
var massTagIDsAvailableForLookup = new List <int>();
if (canUseReferenceMassTags)
{
massTagIDsAvailableForLookup = MassTagsForReference.TargetList.Select(p => p.ID).ToList();
}
foreach (LcmsFeatureTarget target in Targets.TargetList)
{
var isMissingMonoMass = target.MonoIsotopicMass <= 0;
if (String.IsNullOrEmpty(target.EmpiricalFormula))
{
if (canUseReferenceMassTags && massTagIDsAvailableForLookup.Contains(target.FeatureToMassTagID))
{
var mt = MassTagsForReference.TargetList.First(p => p.ID == target.FeatureToMassTagID);
//in DMS, Sequest will put an 'X' when it can't differentiate 'I' and 'L'
// see: \\gigasax\DMS_Parameter_Files\Sequest\sequest_ETD_N14_NE.params
//To create the theoretical isotopic profile, we will change the 'X' to 'L'
if (mt.Code.Contains("X"))
{
mt.Code = mt.Code.Replace('X', 'L');
mt.EmpiricalFormula = mt.GetEmpiricalFormulaFromTargetCode();
}
target.Code = mt.Code;
target.EmpiricalFormula = mt.EmpiricalFormula;
}
else if (!String.IsNullOrEmpty(target.Code))
{
//Create empirical formula based on code. Assume it is an unmodified peptide
if (target.Code.Contains("X"))
{
target.Code = target.Code.Replace('X', 'L');
}
target.EmpiricalFormula = new PeptideUtils().GetEmpiricalFormulaForPeptideSequence(target.Code);
}
else
{
if (isMissingMonoMass)
{
throw new ApplicationException(
"Trying to prepare target list, but Target is missing both the 'Code' and the Monoisotopic Mass. One or the other is needed.");
}
target.Code = "AVERAGINE";
target.EmpiricalFormula =
IsotopicDistributionCalculator.GetAveragineFormulaAsString(target.MonoIsotopicMass, false);
}
}
if (isMissingMonoMass)
{
target.MonoIsotopicMass =
EmpiricalFormulaUtilities.GetMonoisotopicMassFromEmpiricalFormula(target.EmpiricalFormula);
target.MZ = target.MonoIsotopicMass / target.ChargeState + DeconTools.Backend.Globals.PROTON_MASS;
}
}
}