//Returns an empirical formula string with or without PTMs.
//Accounts for the PTMs using the Averagine formula.
//Parses out the PTMs and calculates the empirical formula for the known unmodified sequence.
//Adds or subtracts the PTM formula from the sequence formula based on the overall mass of the PTMs
public string GetEmpiricalFormulaFromSequence(string code, bool cysteinesAreModified = false)
{
var ptmFormula = "";
var sequenceFormula = "";
var empiricalFormula = "";
var ptmMass = PtmMassFromCode(code);
ptmFormula = IsotopicDistributionCalculator.Instance.GetAveragineFormulaAsString(Math.Abs(ptmMass), false);
sequenceFormula = SequenceToEmpiricalFormula(code, cysteinesAreModified);
if (ptmMass < 0)
{
empiricalFormula = EmpiricalFormulaUtilities.SubtractFormula(sequenceFormula, ptmFormula);
}
else
{
empiricalFormula = EmpiricalFormulaUtilities.AddFormula(sequenceFormula, ptmFormula);
}
//TEMPORARY HANDLING OF BAD TARGETS WITH PTM > SEQUENCE
//CHECK THE UPDATEMISSINGTARGETINFO IN IQTARGETUTILITES WHEN CHANGING
if (String.IsNullOrEmpty(empiricalFormula))
{
empiricalFormula = "C0H0N0O0S0";
}
return(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 PyroglutamateTest1()
{
const string testPeptide = "SAMPLER";
var peptideUtils = new PeptideUtils();
var formula = peptideUtils.GetEmpiricalFormulaForPeptideSequence(testPeptide);
const string pyroglutamateMod = "H3N1";
var empiricalFormula = EmpiricalFormulaUtilities.SubtractFormula(formula, pyroglutamateMod);
var massUnmodified = EmpiricalFormulaUtilities.GetMonoisotopicMassFromEmpiricalFormula(formula);
var massModified = EmpiricalFormulaUtilities.GetMonoisotopicMassFromEmpiricalFormula(empiricalFormula);
var diff = Math.Round(massModified - massUnmodified, 1, MidpointRounding.AwayFromZero);
Console.WriteLine(formula + "\t" + massUnmodified);
Console.WriteLine(empiricalFormula + "\t" + massModified);
Console.WriteLine("diff= " + diff);
Assert.AreEqual(-17.0, diff);
}
//Returns an empirical formula string with or without PTMs.
//Accounts for the PTMs using the Averagine formula.
//Parses out the PTMs and calculates the empirical formula for the known unmodified sequence.
//Adds or subtracts the PTM formula from the sequence formula based on the overall mass of the PTMs
public string GetEmpiricalFormulaFromSequence(string code)
{
string PTM_Formula = "";
string SequenceFormula = "";
string EmpiricalFormula = "";
double ptm_mass = PTMMassFromCode(code);
PTM_Formula = IsotopicDistributionCalculator.Instance.GetAveragineFormulaAsString(Math.Abs(ptm_mass), false);
SequenceFormula = SequenceToEmpiricalFormula(code);
if (ptm_mass < 0)
{
EmpiricalFormula = EmpiricalFormulaUtilities.SubtractFormula(SequenceFormula, PTM_Formula);
}
else
{
EmpiricalFormula = EmpiricalFormulaUtilities.AddFormula(SequenceFormula, PTM_Formula);
}
return(EmpiricalFormula);
}
public string GetEmpiricalFormulaForSequenceWithMods(string code)
{
// Check for pyroglutamate modification
var containsPyroglutamateMod = false;
if (_modPyroglutamate.IsMatch(code))
{
containsPyroglutamateMod = true;
// Remove the modification from the string
var pieces = _modPyroglutamate.Match(code).Groups;
code = pieces["prefix"].Value + pieces["modified"].Value + pieces["suffix"].Value;
}
// Check for acetylation modification
var containsAcetylationMod = false;
if (_modAcetylation.IsMatch(code))
{
containsAcetylationMod = true;
// Remove the modification from the string
var pieces = _modAcetylation.Match(code).Groups;
code = pieces["prefix"].Value + pieces["modified"].Value + pieces["suffix"].Value;
}
// Check for phosphorylation modification
// TODO: this function does not account for the fact that phosphorylation could occur multiple times
var containsPhosphorylationMod = false;
if (_modPhosphorylation.IsMatch(code))
{
containsPhosphorylationMod = true;
// Remove the modification from the string
var pieces = _modPhosphorylation.Match(code).Groups;
code = pieces["prefix"].Value + pieces["modified"].Value + pieces["suffix"].Value;
}
// If the peptide sequence still has modifications, we can't get the empirical formula
if (code.Contains("("))
{
return(String.Empty);
}
// Get the empirical formula as if the peptide sequence was unmodified
var empiricalFormula = _peptideUtils.GetEmpiricalFormulaForPeptideSequence(code);
// Apply modifications to empirical formula
if (containsPyroglutamateMod)
{
empiricalFormula = EmpiricalFormulaUtilities.SubtractFormula(empiricalFormula, "H3N1");
}
if (containsAcetylationMod)
{
empiricalFormula = EmpiricalFormulaUtilities.AddFormula(empiricalFormula, "C2H2O");
}
if (containsPhosphorylationMod)
{
empiricalFormula = EmpiricalFormulaUtilities.AddFormula(empiricalFormula, "HPO3");
}
return(empiricalFormula);
}