public void EmpiricalFormulaCalculatorTest()
{
var parser = new IqCodeParser();
var exampleSequence = @"A.ADLEDNMDILNDNLKVVEKTDSAPELKAALTKMRAAALDAQKATPPKLEDKAPDSPEMKDFRHGFDILVGQIDGALKLANEGNVKEAKAAAEALKTTRNTYHKKYR.";
var empiricalFormula = parser.GetEmpiricalFormulaFromSequence(exampleSequence);
Console.WriteLine(empiricalFormula);
Assert.AreEqual("C507H832N144O163S3", empiricalFormula);
}
public void ProteinSequenceToMassHugePTMTest()
{
var parser = new IqCodeParser();
var proteoform =
"M.V(HLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVC)[-11849.17]VLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH.";
var trueMass = 4008.08; // only one significant decimal really. could be 4008.07 or .08 Can't tell yet
var unmodifiedProteoform =
"M.VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH.";
var ptm = "[-11849.17]";
var proteoformComposition = parser.GetEmpiricalFormulaFromSequence(proteoform);
var unmodifiedProteoformComposition = parser.GetEmpiricalFormulaFromSequence(unmodifiedProteoform);
var ptmComposition = parser.GetEmpiricalFormulaFromSequence(ptm);
var difference = EmpiricalFormulaUtilities.SubtractFormula(unmodifiedProteoformComposition, ptmComposition);
Console.WriteLine(proteoformComposition);
Console.WriteLine(difference);
Assert.AreEqual(proteoformComposition, difference);
var differenceMass = EmpiricalFormulaUtilities.GetMonoisotopicMassFromEmpiricalFormula(difference);
var proteformMass = EmpiricalFormulaUtilities.GetMonoisotopicMassFromEmpiricalFormula(proteoformComposition);
var unmodifiedProteoformMass = EmpiricalFormulaUtilities.GetMonoisotopicMassFromEmpiricalFormula(unmodifiedProteoformComposition);
Console.WriteLine(unmodifiedProteoformMass);
var ptmMass = EmpiricalFormulaUtilities.GetMonoisotopicMassFromEmpiricalFormula(ptmComposition);
Console.WriteLine(ptmMass);
var conversionFirst = unmodifiedProteoformMass - ptmMass;
Console.WriteLine(conversionFirst);
Assert.AreEqual(trueMass, conversionFirst, 0.1);
Assert.AreEqual(trueMass, differenceMass, .1);
Assert.AreEqual(trueMass, proteformMass, .1);
}
public void MsAlignCodeParserTest()
{
var parser = new IqCodeParser();
var examplemod =
"A.AENVVHHKLDGMPISEAVEINAGNNLVF(LSGKVPTKKSADAPEGELASYGNTE)[713.72]EQTINVLEQIKTNLNNLGLDMKDVVKMQVFLVGGEENNGTMDFKGFMNGYSKFYDASKTNQLPARSAFQVA(K)[1.02]LANPAWRVEIEVIAVRPAK.";
var checkmass = "[714.74]";
var examplenomod = "A.AENVVHHKLDGMPISEAVEINAGNNLVLSGKVPTKKSADAPEGELASYGNTEFEQTINVLEQIKTNLNNLGLDMKDVVKMQVFLVGGEENNGTMDFKGFMNGYSKFYDASKTNQLPARSAFQVAKLANPAWRVEIEVIAVRPAK.";
var examplemodresult = parser.GetEmpiricalFormulaFromSequence(examplemod);
var checkmassresult = parser.GetEmpiricalFormulaFromSequence(checkmass);
var examplenomodresult = parser.GetEmpiricalFormulaFromSequence(examplenomod);
Console.WriteLine(examplemodresult);
Console.WriteLine(checkmassresult);
Console.WriteLine(examplenomodresult);
var difference = EmpiricalFormulaUtilities.SubtractFormula(examplemodresult, checkmassresult);
Assert.AreEqual(examplenomodresult, difference);
}
public void MsgfCodeParserTest()
{
var parser = new IqCodeParser();
var examplemod =
"+144.102PRYRK+144.102RTPVSLY+79.966QK+144.102T+79.966PNGEK+144.102PYEC+57.021GEC+57.021GK+144.102-202";
var checkmass = "+792.484";
var examplenomod = "PRYRKRTPVSLYQKTPNGEKPYECGECGK";
var examplemodresult = parser.GetEmpiricalFormulaFromSequence(examplemod);
var checkmassresult = parser.GetEmpiricalFormulaFromSequence(checkmass);
var examplenomodresult = parser.GetEmpiricalFormulaFromSequence(examplenomod);
Console.WriteLine(examplemodresult);
Console.WriteLine(checkmassresult);
Console.WriteLine(examplenomodresult);
var difference = EmpiricalFormulaUtilities.SubtractFormula(examplemodresult, checkmassresult);
Assert.AreEqual(examplenomodresult, difference);
}
public void EmpiricalFormulaCalculatorRoundingTest()
{
var parser = new IqCodeParser();
var testSequence = @".MITGIQITKA(AN)[1.02]DDLLNSFWLLDSEKGEARCIVAKAGYAEDEVVAVSKLGDIEYREVPVEVKPEVRVEGGQHLNVNVLRRETLEDAVKHPEKYPQLTI(RV)[-.99]S.G";
var empiricalFormula = parser.GetEmpiricalFormulaFromSequence(testSequence);
Console.WriteLine(empiricalFormula);
Assert.IsTrue(!empiricalFormula.Contains("E"));
}
public void AveragineRoundTripTest()
{
var parser = new IqCodeParser();
var ptmDouble = -11849.17;
var ptmMass = "[" + ptmDouble.ToString() + "]"; // this is done just for formatting of the function call below
var absPtmDouble = Math.Abs(ptmDouble); //this is done because the emperical formula returns a positive amount of atoms (not negative)
//so in the assert comparison we have to use the positive mass value
var empiricalFormula = parser.GetEmpiricalFormulaFromSequence(ptmMass);
Console.WriteLine("This is my emperical formula:" + empiricalFormula + ":");
var returnedMass = EmpiricalFormulaUtilities.GetMonoisotopicMassFromEmpiricalFormula(empiricalFormula);
Console.WriteLine(empiricalFormula);
Console.WriteLine(returnedMass);
Assert.AreEqual(absPtmDouble, returnedMass, .0001);
}
protected TopDownIqTarget CreateParentTarget(List <List <string> > processedGroup)
{
var target = new TopDownIqTarget();
var parser = new IqCodeParser();
target.DatabaseReference = ParseStringField(processedGroup[0], ProteinNameHeader);
target.Code = ParseStringField(processedGroup[0], PeptideHeader);
target.EmpiricalFormula = parser.GetEmpiricalFormulaFromSequence(target.Code);
target.PTMList = parser.GetPTMList(target.Code);
target.MonoMassTheor = ParseDoubleField(processedGroup[0], AdjustedPrecursorMassHeader);
var children = new List <IqTarget>();
foreach (var line in processedGroup)
{
children.Add(ConvertTextToIqTarget(line));
}
target.AddTargetRange(children);
return(target);
}
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;
}
}