//method was originally written recursively, but large peptides result in stackoverflow exceptions
public void MassMatch(string B, string Y, PSM psm, int BIndex, int YIndex, out string error_message) //this is the workhorse of SpliceFragments
{
error_message = "";
test = psm.getScan().ToString();
double ExperimentalMass = psm.getExpMass();
string BFrag = IonCrop(B, ExperimentalMass, BIndex, IonType.b, false, out string e4); //returns a B ion sequence that has a mass smaller than the experimental mass by cleaving C term AA
//BIndex = B.Length - BFrag.Length; //added 11/8/16 Useful first pass to record how many AA have been cleaved from C term
string YFrag = IonCrop(Y, ExperimentalMass, YIndex, IonType.y, false, out string e3); //returns a Y ion sequence that has a mass smaller than the experimental mass by cleaving N term AA
//YIndex = Y.Length - YFrag.Length; //added 11/8/16 Useful first pass to record how many AA have been cleaved from N term
double TheoreticalMass = MassCalculator.MonoIsoptopicMass(BFrag, out string e) + MassCalculator.MonoIsoptopicMass(YFrag, out string e2) - Constants.WATER_MONOISOTOPIC_MASS + fixedModMass; //water added once in b and once in y
error_message += e3 + e4 + e + e2;
//add PTM masses
foreach (PTM ptm in psm.getNInfo().getPTMs())
{
if (ptm.index < BFrag.Length)
{
TheoreticalMass += ptm.mass;
}
}
foreach (PTM ptm in psm.getCInfo().getPTMs())
{
if (Y.Length - ptm.index < YFrag.Length)
{
TheoreticalMass += ptm.mass;
}
}
if (YFrag.Length < ionsUsedMassVer) //If the number of AA from the C-term peptide is less than desired amount, end recursion.
{
//we're done
}
else if (BFrag.Length < ionsUsedMassVer) //If the number of AA from the N-term peptide is less than desired amount, start over loop and remove a single aa from the C-term
{
// MassMatch(B, Y, psm, 0, YIndex+1);
}
//if match
//bool elif = true; //"else if" where not a match==true
else if (FalsePositives.generateDecoys)
{
//else if (((TheoreticalMass - Constants.PEPTIDE_N_TERMINAL_MONOISOTOPIC_MASS * 7) > (ExperimentalMass - 1 * Constants.PEPTIDE_N_TERMINAL_MONOISOTOPIC_MASS) && (TheoreticalMass - Constants.PEPTIDE_N_TERMINAL_MONOISOTOPIC_MASS * 7) < (ExperimentalMass + 1 * Constants.PEPTIDE_N_TERMINAL_MONOISOTOPIC_MASS)) | ((TheoreticalMass + Constants.PEPTIDE_N_TERMINAL_MONOISOTOPIC_MASS * 7) > (ExperimentalMass - 1 * Constants.PEPTIDE_N_TERMINAL_MONOISOTOPIC_MASS) && (TheoreticalMass + Constants.PEPTIDE_N_TERMINAL_MONOISOTOPIC_MASS * 7) < (ExperimentalMass + 1 * Constants.PEPTIDE_N_TERMINAL_MONOISOTOPIC_MASS)))//if match //if ((TheoreticalMass) > (ExperimentalMass+ i -PrecursorMassToleranceDa) && (TheoreticalMass) < (ExperimentalMass+i +PrecursorMassToleranceDa)) //if match
if (((TheoreticalMass) > (ExperimentalMass - 9.5) && (TheoreticalMass) < (ExperimentalMass - 4.5)) | ((TheoreticalMass) > (ExperimentalMass + 5.5) && (TheoreticalMass) < (ExperimentalMass + 7.5)))//if match //if ((TheoreticalMass) > (ExperimentalMass+ i -PrecursorMassToleranceDa) && (TheoreticalMass) < (ExperimentalMass+i +PrecursorMassToleranceDa)) //if match //else if(Math.Abs(ExperimentalMass - TheoreticalMass)<40 && (ExperimentalMass - TheoreticalMass)-Math.Floor(ExperimentalMass-TheoreticalMass)>0.3 && (ExperimentalMass - TheoreticalMass) - Math.Floor(ExperimentalMass - TheoreticalMass) < 0.8)
{
// elif = false;
bool previouslyFound = false;
foreach (FusionCandidate oldCandidate in psm.getFusionCandidates())
{
if ((BFrag + YFrag).Equals(oldCandidate.seq)) //see if that sequence was already recorded
{
previouslyFound = true;
}
}
if (!previouslyFound) //if fusion sequence was not previously assigned to this psm
{
FusionCandidate candidate = new FusionCandidate(BFrag + YFrag);
psm.addFusionCandidate(candidate);
// MassMatch(B, Y, psm, BIndex + 1, YIndex);
}
}
}
else
{
if ((TheoreticalMass) > (ExperimentalMass * (1 - FalsePositives.precursorMassTolerancePpm / 1000000)) && (TheoreticalMass) < (ExperimentalMass * (1 + FalsePositives.precursorMassTolerancePpm / 1000000))) //if match //if ((TheoreticalMass) > (ExperimentalMass+ i -PrecursorMassToleranceDa) && (TheoreticalMass) < (ExperimentalMass+i +PrecursorMassToleranceDa)) //if match
{
// elif = false;
bool previouslyFound = false;
foreach (FusionCandidate oldCandidate in psm.getFusionCandidates())
{
if ((BFrag + YFrag).Equals(oldCandidate.seq)) //see if that sequence was already recorded
{
previouslyFound = true;
}
}
if (!previouslyFound) //if fusion sequence was not previously assigned to this psm
{
FusionCandidate candidate = new FusionCandidate(BFrag + YFrag);
psm.addFusionCandidate(candidate);
// MassMatch(B, Y, psm, BIndex + 1, YIndex);
}
}
}
// if(elif) //not a match
{
/* if (TheoreticalMass < ExperimentalMass && BIndex == 0) //first pass, theo less than exp and can't take away more ions
* {
* //we're done
* }
* else
* {
* if (TheoreticalMass < ExperimentalMass) //if b out of ions, but y not, crop off a y and start again
* {
* BIndex = 0;
* YIndex++;
* MassMatch(B,Y, psm, BIndex, YIndex);
* }
* else
* { //crop off a b ion
* MassMatch(B, Y, psm, BIndex + 1, YIndex);
* }
* }*/
}
}
//use ion hits to know where peaks have been found by morpheus and where there is ambiguity
public static void findIons(FusionCandidate fusionCandidate, PSM psm, out string error_message)
{
error_message = "";
double[] nPeaks = psm.getNInfo().getPeakHits(); //get peaks
double[] cPeaks = psm.getCInfo().getPeakHits();
fusionCandidate.makeFoundIons();
string candSeq = fusionCandidate.seq;
bool[] foundIons = fusionCandidate.getFoundIons();
//find which aa have peaks
for (int i = 0; i < foundIons.Count() - 1; i++)
{
//B IONS//
if (ionsUsed.Contains(IonType.b))
{
double bTheoMass = MassCalculator.MonoIsoptopicMass(candSeq.Substring(0, 1 + i), out string error_message2) - Constants.WATER_MONOISOTOPIC_MASS;
error_message += error_message2;
foreach (PTM ptm in psm.getNInfo().getPTMs())
{
if (ptm.index <= i)
{
bTheoMass += ptm.mass;
}
}
foreach (double expPeak in nPeaks)
{
if (expPeak > bTheoMass - productMassToleranceDa && expPeak < bTheoMass + productMassToleranceDa)
{
foundIons[i] = true;
}
}
}
//Y IONS//
if (ionsUsed.Contains(IonType.y))
{
double yTheoMass = MassCalculator.MonoIsoptopicMass(candSeq.Substring(candSeq.Length - 1 - i, i + 1), out string error_message3);
error_message += error_message3;
foreach (PTM ptm in psm.getCInfo().getPTMs())
{
if (ptm.index >= candSeq.Length - 2 - i)
{
yTheoMass += ptm.mass;
}
}
foreach (double expPeak in cPeaks)
{
if (expPeak > yTheoMass - productMassToleranceDa && expPeak < yTheoMass + productMassToleranceDa)
{
foundIons[foundIons.Count() - 2 - i] = true;
}
}
}
//C IONS//
if (ionsUsed.Contains(IonType.c))
{
double cTheoMass = MassCalculator.MonoIsoptopicMass(candSeq.Substring(0, 1 + i), out string error_message4) - Constants.WATER_MONOISOTOPIC_MASS + Constants.nitrogenMonoisotopicMass + 3 * Constants.hydrogenMonoisotopicMass;
error_message += error_message4;
foreach (PTM ptm in psm.getNInfo().getPTMs())
{
if (ptm.index <= i)
{
cTheoMass += ptm.mass;
}
}
foreach (double expPeak in nPeaks)
{
if (expPeak > cTheoMass - productMassToleranceDa && expPeak < cTheoMass + productMassToleranceDa)
{
foundIons[i] = true;
}
}
}
//ZDOT IONS//
if (ionsUsed.Contains(IonType.zdot))
{
double zdotTheoMass = MassCalculator.MonoIsoptopicMass(candSeq.Substring(candSeq.Length - 1 - i, i + 1), out string error_message5) - Constants.nitrogenMonoisotopicMass - 2 * Constants.hydrogenMonoisotopicMass;
error_message += error_message5;
foreach (PTM ptm in psm.getCInfo().getPTMs())
{
if (ptm.index >= candSeq.Length - 2 - i)
{
zdotTheoMass += ptm.mass;
}
}
foreach (double expPeak in cPeaks)
{
if (expPeak > zdotTheoMass - productMassToleranceDa && expPeak < zdotTheoMass + productMassToleranceDa)
{
foundIons[foundIons.Count() - 2 - i] = true;
}
}
}
}
//foundIons[0] = true; //AspN always starts with a D
foundIons[foundIons.Count() - 1] = true;//A|B|C|D|E|F|K| where the whole peptide peak is always placed arbitrarly at the c term
}