//If XlSites is of same types
private PsmCross XlSitesSame(Ms2ScanWithSpecificMass theScan, PsmCross psmCrossAlpha, PsmCross psmCrossBeta,
CrosslinkerTypeClass crosslinker, int ind, int inx)
{
PsmCross psmCross = null;
var xlPosAlpha = PsmCross.XlPosCal(psmCrossAlpha.compactPeptide, crosslinker.CrosslinkerModSites);
var xlPosBeta = PsmCross.XlPosCal(psmCrossBeta.compactPeptide, crosslinker.CrosslinkerModSites);
if (xlPosAlpha.Count() >= 1 && xlPosBeta.Count() >= 1)
{
PsmCross.XlLocalization(theScan, psmCrossAlpha, psmCrossBeta.compactPeptide.MonoisotopicMassIncludingFixedMods + crosslinker.TotalMass, crosslinker, ProductTypes, commonParameters.ProductMassTolerance, Charge_2_3, Charge_2_3_PrimeFragment, xlPosAlpha);
PsmCross.XlLocalization(theScan, psmCrossBeta, psmCrossAlpha.compactPeptide.MonoisotopicMassIncludingFixedMods + crosslinker.TotalMass, crosslinker, ProductTypes, commonParameters.ProductMassTolerance, Charge_2_3, Charge_2_3_PrimeFragment, xlPosBeta);
if (psmCrossAlpha.XLBestScore < psmCrossBeta.XLBestScore)
{
var swap = psmCrossAlpha;
psmCrossAlpha = psmCrossBeta;
psmCrossBeta = swap;
}
psmCrossAlpha.XlRank = new int[] { ind, inx };
psmCrossAlpha.XLTotalScore = psmCrossAlpha.XLBestScore + psmCrossBeta.XLBestScore;
psmCrossAlpha.XLQvalueTotalScore = Math.Sqrt(psmCrossAlpha.XLBestScore) * psmCrossBeta.XLBestScore;
psmCrossAlpha.BetaPsmCross = psmCrossBeta;
if (crosslinker.Cleavable)
{
psmCrossAlpha.ParentIonMaxIntensityRanks.AddRange(psmCrossBeta.ParentIonMaxIntensityRanks);
psmCrossAlpha.ParentIonExistNum += psmCrossBeta.ParentIonExistNum;
}
psmCrossAlpha.CrossType = PsmCrossType.Cross;
psmCross = psmCrossAlpha;
}
return(psmCross);
}
public TwoPassCrosslinkSearchEngine(List <PsmCross> globalPsmsCross, Ms2ScanWithSpecificMass[] listOfSortedms2Scans, List <CompactPeptide> peptideIndex, List <int>[] fragmentIndex, List <ProductType> lp, int currentPartition, CommonParameters commonParameters, bool addCompIons, Tolerance XLPrecusorMsTl, CrosslinkerTypeClass crosslinker, bool CrosslinkSearchTop, int CrosslinkSearchTopNum, bool quench_H2O, bool quench_NH2, bool quench_Tris, bool charge_2_3, bool charge_2_3_PrimeFragment, List <string> nestedIds) : base(commonParameters, nestedIds)
{
this.GlobalPsmsCross = globalPsmsCross;
this.ListOfSortedms2Scans = listOfSortedms2Scans;
this.PeptideIndex = peptideIndex;
this.FragmentIndex = fragmentIndex;
this.ProductTypes = lp;
this.CurrentPartition = currentPartition + 1;
this.AddComplementaryIons = addCompIons;
//Here use LowTheoreticalDiffAcceptor in practice doesn't work in 12/2/2017
this.MassDiffAcceptor = new OpenSearchMode();
this.DissociationTypes = DetermineDissociationType(lp);
this.XLPrecusorMsTl = XLPrecusorMsTl;
XLPrecusorSearchMode = new SinglePpmAroundZeroSearchMode(XLPrecusorMsTl.Value);
//if (XLBetaPrecusorMsTl.ToString().Contains("Absolute"))
//{
// XLPrecusorSearchMode = new SingleAbsoluteAroundZeroSearchMode(XLPrecusorMsTl.Value);
//}
this.Crosslinker = crosslinker;
this.CrosslinkSearchTop = CrosslinkSearchTop;
this.CrosslinkSearchTopNum = CrosslinkSearchTopNum;
this.QuenchH2O = quench_H2O;
this.QuenchNH2 = quench_NH2;
this.QuenchTris = quench_Tris;
this.Charge_2_3 = charge_2_3;
this.Charge_2_3_PrimeFragment = charge_2_3_PrimeFragment;
}
//Calculate if crosslink amino acid exist and return its position based on compactPeptide
public static List <int> XlPosCal(CompactPeptide compactPeptide, CrosslinkerTypeClass crosslinker)
{
Tolerance tolerance = new PpmTolerance(1);
List <int> xlpos = new List <int>();
if (tolerance.Within(compactPeptide.NTerminalMasses[0], Residue.GetResidue(crosslinker.CrosslinkerModSite).MonoisotopicMass))
{
xlpos.Add(0);
}
for (int i = 1; i < compactPeptide.NTerminalMasses.Length; i++)
{
if (tolerance.Within(compactPeptide.NTerminalMasses[i] - compactPeptide.NTerminalMasses[i - 1], Residue.GetResidue(crosslinker.CrosslinkerModSite).MonoisotopicMass))
{
xlpos.Add(i);
}
}
if (tolerance.Within(compactPeptide.CTerminalMasses[0], Residue.GetResidue(crosslinker.CrosslinkerModSite).MonoisotopicMass))
{
xlpos.Add(compactPeptide.NTerminalMasses.Length);
}
return(xlpos);
}
//Calculate score based on All possible Products Masses for inter- or intra- crosslinks and deadend.
public static void XlLocalizationForLoopCrosslink(Ms2ScanWithSpecificMass theScan, PsmCross psmCross, double modMass, CrosslinkerTypeClass crosslinker, List <ProductType> lp, Tolerance fragmentTolerance, List <int> linkPos)
{
var pmmhList = PsmCross.XlCalculateTotalProductMassesForLoopCrosslink(psmCross, modMass, crosslinker, lp, linkPos);
List <double> scoreList = new List <double>();
List <MatchedIonInfo> miil = new List <MatchedIonInfo>();
foreach (var pmm in pmmhList)
{
var matchedIonMassesListPositiveIsMatch = new MatchedIonInfo(pmm.ProductMz.Length);
double pmmScore = PsmCross.XlMatchIons(theScan.TheScan, fragmentTolerance, pmm.ProductMz, pmm.ProductName, matchedIonMassesListPositiveIsMatch);
miil.Add(matchedIonMassesListPositiveIsMatch);
scoreList.Add(pmmScore);
}
psmCross.XLBestScore = scoreList.Max();
psmCross.MatchedIonInfo = miil[scoreList.IndexOf(scoreList.Max())];
psmCross.XlPos = pmmhList[scoreList.IndexOf(scoreList.Max())].XlPos + 1;
psmCross.XlPos2 = pmmhList[scoreList.IndexOf(scoreList.Max())].XlPos2 + 1;
}
//Calculate All possible Products Masses based on ModMass and linkPos
public static List <ProductMassesMightHave> XlCalculateTotalProductMassesForLoopCrosslink(PsmCross psmCross, double modMass, CrosslinkerTypeClass crosslinker, List <ProductType> lp, List <int> linkPos)
{
int length = psmCross.compactPeptide.NTerminalMasses.Length;
var pmmh = psmCross.ProductMassesMightHaveDuplicatesAndNaNs(lp);
ProductMassesMightHave pmmhTop = new ProductMassesMightHave();
List <ProductMassesMightHave> pmmhList = new List <ProductMassesMightHave>();
if (linkPos.Count() >= 2)
{
for (int ipos = 0; ipos < linkPos.Count() - 1; ipos++)
{
for (int jpos = ipos + 1; jpos < linkPos.Count(); jpos++)
{
var pmmhCurr = new ProductMassesMightHave();
pmmhCurr.XlPos = linkPos[ipos];
pmmhCurr.XlPos2 = linkPos[jpos];
List <double> x = new List <double>();
List <string> y = new List <string>();
for (int i = 0; i < pmmh.ProductMz.Length; i++)
{
var cr = pmmh.ProductName[i][0];
//get the position of amino acid
var nm = Int32.Parse(System.Text.RegularExpressions.Regex.Match(pmmh.ProductName[i], @"\d+").Value);
if ((cr == 'b' || cr == 'c') && nm < linkPos[ipos] + 1)
{
x.Add(pmmh.ProductMz[i]);
y.Add(pmmh.ProductName[i]);
}
if ((cr == 'y' || cr == 'z') && nm < length - linkPos[jpos] + 1)
{
x.Add(pmmh.ProductMz[i]);
y.Add(pmmh.ProductName[i]);
}
if (cr == 'b' && nm >= linkPos[jpos] + 1)
{
x.Add(pmmh.ProductMz[i] + modMass);
y.Add("t1b" + nm.ToString());
}
if (cr == 'c' && nm >= linkPos[jpos] + 1)
{
x.Add(pmmh.ProductMz[i] + modMass);
y.Add("t1c" + nm.ToString());
}
if (cr == 'y' && (nm >= length - linkPos[ipos] + 1))
{
x.Add(pmmh.ProductMz[i] + modMass);
y.Add("t1y" + nm.ToString());
}
if (cr == 'z' && (nm >= length - linkPos[ipos] + 1))
{
x.Add(pmmh.ProductMz[i] + modMass);
y.Add("t1z" + nm.ToString());
}
}
pmmhCurr.ProductMz = x.ToArray();
pmmhCurr.ProductName = y.ToArray();
Array.Sort(pmmhCurr.ProductMz, pmmhCurr.ProductName);
pmmhList.Add(pmmhCurr);
}
}
}
return(pmmhList);
}
//Calculate score based on All possible Products Masses for inter- or intra- crosslinks and deadend.
public static void XlLocalization(Ms2ScanWithSpecificMass theScan, PsmCross psmCross, double modMass,
CrosslinkerTypeClass crosslinker, List <ProductType> lp, Tolerance fragmentTolerance, bool Charge_2_3, bool Charge_2_3_PrimeFragment, List <int> linkPos)
{
var pmmhList = PsmCross.XlCalculateTotalProductMasses(psmCross, modMass, crosslinker, lp, Charge_2_3, Charge_2_3_PrimeFragment, linkPos);
List <double> scoreList = new List <double>();
List <MatchedIonInfo> miil = new List <MatchedIonInfo>();
foreach (var pmm in pmmhList)
{
var matchedIonMassesListPositiveIsMatch = new MatchedIonInfo(pmm.ProductMz.Length);
double pmmScore = PsmCross.XlMatchIons(theScan.TheScan, fragmentTolerance, pmm.ProductMz, pmm.ProductName, matchedIonMassesListPositiveIsMatch);
miil.Add(matchedIonMassesListPositiveIsMatch);
scoreList.Add(pmmScore);
}
psmCross.XLBestScore = scoreList.Max();
psmCross.MatchedIonInfo = miil[scoreList.IndexOf(scoreList.Max())];
psmCross.XlPos = pmmhList[scoreList.IndexOf(scoreList.Max())].XlPos + 1;
if (crosslinker.Cleavable)
{
psmCross.ParentIonMaxIntensityRanks = new List <int>();
if (psmCross.MatchedIonInfo.MatchedIonName.Any(p => p != null && p.Contains("PepS")))
{
psmCross.ParentIonExist += "PepS";
psmCross.ParentIonExistNum += 1;
}
if (psmCross.MatchedIonInfo.MatchedIonName.Any(p => p != null && p.Contains("PepL")))
{
psmCross.ParentIonExist += "PepL";
psmCross.ParentIonExistNum += 1;
}
//if (psmCross.MatchedIonInfo.MatchedIonName.Any(p => p != null && p.Equals("PepS2")))
//{
// psmCross.ParentIonExist += "PepS2";
// psmCross.ParentIonExistNum += 1;
//}
//if (psmCross.MatchedIonInfo.MatchedIonName.Any(p => p != null && p.Equals("PepL2")))
//{
// psmCross.ParentIonExist += "PepL2";
// psmCross.ParentIonExistNum += 1;
//}
for (int i = 0; i < psmCross.MatchedIonInfo.MatchedIonName.Length; i++)
{
if (psmCross.MatchedIonInfo.MatchedIonName[i] != null)
{
if (psmCross.MatchedIonInfo.MatchedIonName[i].Contains("Pep"))
{
psmCross.ParentIonMaxIntensityRanks.Add(psmCross.MatchedIonInfo.MatchedIonIntensityRank[i]);
}
}
}
}
if (Charge_2_3 || Charge_2_3_PrimeFragment)
{
int Charge2IonExist = 0;
for (int i = 0; i < psmCross.MatchedIonInfo.MatchedIonName.Length; i++)
{
if (psmCross.MatchedIonInfo.MatchedIonName[i] != null && (psmCross.MatchedIonInfo.MatchedIonName[i].Contains("t2") || psmCross.MatchedIonInfo.MatchedIonName[i].Contains("t3")))
{
Charge2IonExist++;
}
}
psmCross.Charge2IonExist = Charge2IonExist;
}
}
//Calculate All possible Products Masses based on ModMass and linkPos
public static List <ProductMassesMightHave> XlCalculateTotalProductMasses(PsmCross psmCross, double modMass,
CrosslinkerTypeClass crosslinker, List <ProductType> lp, bool Charge_2_3, bool Charge_2_3_PrimeFragment, List <int> linkPos)
{
int length = psmCross.compactPeptide.NTerminalMasses.Length;
var pmmh = psmCross.ProductMassesMightHaveDuplicatesAndNaNs(lp);
ProductMassesMightHave pmmhTop = new ProductMassesMightHave();
List <ProductMassesMightHave> pmmhList = new List <ProductMassesMightHave>();
foreach (var ipos in linkPos)
{
var pmmhCurr = new ProductMassesMightHave();
pmmhCurr.XlPos = ipos;
List <double> x = new List <double>();
List <string> y = new List <string>();
if (crosslinker.Cleavable)
{
x.Add((double)psmCross.compactPeptide.MonoisotopicMassIncludingFixedMods + crosslinker.CleaveMassShort);
y.Add("PepS");
x.Add(((double)psmCross.compactPeptide.MonoisotopicMassIncludingFixedMods + crosslinker.CleaveMassShort) / 2);
y.Add("PepS2");
x.Add((double)psmCross.compactPeptide.MonoisotopicMassIncludingFixedMods + crosslinker.CleaveMassLong);
y.Add("PepL");
x.Add(((double)psmCross.compactPeptide.MonoisotopicMassIncludingFixedMods + crosslinker.CleaveMassLong) / 2);
y.Add("PepL2");
}
for (int i = 0; i < pmmh.ProductMz.Length; i++)
{
var cr = pmmh.ProductName[i][0];
//get the position of amino acid
var nm = Int32.Parse(System.Text.RegularExpressions.Regex.Match(pmmh.ProductName[i], @"\d+").Value);
if ((cr == 'b' || cr == 'c') && nm < ipos + 1)
{
x.Add(pmmh.ProductMz[i]);
y.Add(pmmh.ProductName[i]);
if (Charge_2_3_PrimeFragment && cr == 'b')
{
x.Add(pmmh.ProductMz[i] / 2);
y.Add("t2b" + nm.ToString());
x.Add(pmmh.ProductMz[i] / 3);
y.Add("t3b" + nm.ToString());
}
if (Charge_2_3_PrimeFragment && cr == 'c')
{
x.Add(pmmh.ProductMz[i] / 2);
y.Add("t2c" + nm.ToString());
x.Add(pmmh.ProductMz[i] / 3);
y.Add("t3c" + nm.ToString());
}
}
if ((cr == 'y' || cr == 'z') && nm < length - ipos + 1)
{
x.Add(pmmh.ProductMz[i]);
y.Add(pmmh.ProductName[i]);
if (Charge_2_3_PrimeFragment && cr == 'y')
{
x.Add(pmmh.ProductMz[i] / 2);
y.Add("t2y" + nm.ToString());
x.Add(pmmh.ProductMz[i] / 3);
y.Add("t3y" + nm.ToString());
}
if (Charge_2_3_PrimeFragment && cr == 'z')
{
x.Add(pmmh.ProductMz[i] / 2);
y.Add("t2z" + nm.ToString());
x.Add(pmmh.ProductMz[i] / 3);
y.Add("t3z" + nm.ToString());
}
}
if (cr == 'b' && nm >= ipos + 1)
{
x.Add(pmmh.ProductMz[i] + modMass);
y.Add("t1b" + nm.ToString());
if (Charge_2_3)
{
x.Add((pmmh.ProductMz[i] + modMass) / 2);
y.Add("t2b" + nm.ToString());
x.Add((pmmh.ProductMz[i] + modMass) / 3);
y.Add("t3b" + nm.ToString());
}
if (crosslinker.Cleavable)
{
x.Add(pmmh.ProductMz[i] + crosslinker.CleaveMassShort);
y.Add("sb" + nm.ToString());
x.Add(pmmh.ProductMz[i] + crosslinker.CleaveMassLong);
y.Add("lb" + nm.ToString());
}
}
if (cr == 'c' && nm >= ipos + 1)
{
x.Add(pmmh.ProductMz[i] + modMass);
y.Add("t1c" + nm.ToString());
if (Charge_2_3)
{
x.Add((pmmh.ProductMz[i] + modMass) / 2);
y.Add("t2c" + nm.ToString());
x.Add((pmmh.ProductMz[i] + modMass) / 3);
y.Add("t3c" + nm.ToString());
}
if (crosslinker.Cleavable)
{
x.Add(pmmh.ProductMz[i] + crosslinker.CleaveMassShort);
y.Add("sc" + nm.ToString());
x.Add(pmmh.ProductMz[i] + crosslinker.CleaveMassLong);
y.Add("lc" + nm.ToString());
}
}
if (cr == 'y' && (nm >= length - ipos + 1))
{
x.Add(pmmh.ProductMz[i] + modMass);
y.Add("t1y" + nm.ToString());
if (Charge_2_3)
{
x.Add((pmmh.ProductMz[i] + modMass) / 2);
y.Add("t2y" + nm.ToString());
x.Add((pmmh.ProductMz[i] + modMass) / 3);
y.Add("t3y" + nm.ToString());
}
if (crosslinker.Cleavable)
{
x.Add(pmmh.ProductMz[i] + crosslinker.CleaveMassShort);
y.Add("sy" + nm.ToString());
x.Add(pmmh.ProductMz[i] + crosslinker.CleaveMassLong);
y.Add("ly" + nm.ToString());
}
}
if (cr == 'z' && (nm >= length - ipos + 1))
{
x.Add(pmmh.ProductMz[i] + modMass);
y.Add("t1z" + nm.ToString());
if (Charge_2_3)
{
x.Add((pmmh.ProductMz[i] + modMass) / 2);
y.Add("t2z" + nm.ToString());
x.Add((pmmh.ProductMz[i] + modMass) / 3);
y.Add("t3z" + nm.ToString());
}
if (crosslinker.Cleavable)
{
x.Add(pmmh.ProductMz[i] + crosslinker.CleaveMassShort);
y.Add("sz" + nm.ToString());
x.Add(pmmh.ProductMz[i] + crosslinker.CleaveMassLong);
y.Add("lz" + nm.ToString());
}
}
}
pmmhCurr.ProductMz = x.ToArray();
pmmhCurr.ProductName = y.ToArray();
Array.Sort(pmmhCurr.ProductMz, pmmhCurr.ProductName);
pmmhList.Add(pmmhCurr);
}
return(pmmhList);
}