public List <IPeptide> PeptidesFilter(ISpectrum spectrum)
{
List <IPeptide> peptides = new List <IPeptide>();
List <double> massList = new List <double>();
int parentCharge = (spectrum as ISpectrumMSn).GetParentCharge();
for (int i = 1; i <= parentCharge; i++)
{
foreach (IPeak peak in spectrum.GetPeaks())
{
massList.Add(calcualtor.CalcChargeMass(peak.GetMZ(), i, option));
}
}
if (massList.Count > 0)
{
massList.Sort();
}
foreach (IPeptide peptide in peptideDB)
{
double mass = calcualtor.CalcPeptideMass(peptide, option) + UtilMass.HexNAc;
if (MassBinarySearch.FindPPM(mass, massList, matcher.GetTolerance()))
{
peptides.Add(peptide);
}
}
return(peptides);
}
public PrecursorMatcherByBinSearchOnPeptidesTemplate(List <IPeptide> peptides, List <IGlycan> glycans, double tol)
{
matcher = new BinarySearch();
parameter = new PrecursorParameter(tol);
peptidePoints = new List <Point>();
calculator = UtilMass.Instance;
option = UtilMassOption.Instance;
this.glycans = glycans;
// build points on peptides
Dictionary <double, PrecursorPoint <IPeptide> > seen = new Dictionary <double, PrecursorPoint <IPeptide> >();
foreach (IPeptide peptide in peptides)
{
double mass = calculator.CalcPeptideMass(peptide, option);
if (!seen.ContainsKey(mass))
{
PrecursorPoint <IPeptide> pt = new PrecursorPoint <IPeptide>(mass);
seen[mass] = pt;
peptidePoints.Add(pt);
}
seen[mass].Add(peptide);
}
matcher.SetPoints(peptidePoints);
}
public NGlycoPeptideNode(ITableNGlycan nGlycan, IPeptide peptide, IScore score)
{
glycan = nGlycan.TableClone();
this.peptide = peptide.Clone();
this.score = score.Clone();
calculator = UtilMass.Instance;
option = UtilMassOption.Instance;
mass = calculator.CalcGlycanMass(glycan, option) + calculator.CalcPeptideMass(peptide, option);
}
public void Run()
{
//AccumulatedStructBruteForceNGlycanCreator creator = new AccumulatedStructBruteForceNGlycanCreator();
//creator.Generate();
////http://db.systemsbiology.net:8080/proteomicsToolkit/FragIonServlet.html
IPeptide peptide = new GeneralPeptide("test", "VVLHPNYSQVD");
//IPeptide peptide = new GeneralPeptide("test", "SRNLTK");
//IPeptide peptide = new GeneralPeptide("test", "LCPDCPLLAPLNDSR");
ICalcMass calculator = UtilMass.Instance;
ICalcMassOption option = UtilMassOption.Instance;
//double mass = calculator.CalcPeptideMass(peptide, option); //1154.63213937
//
//double mass = calculator.CalcPeptideMass(peptide, option);
//double mass = calculator.CalcPeptideIonMass("CHS", IonType.xIon, option);
//Console.WriteLine(mass);
//double mass = calculator.CalcPeptideIonMass("VVLHPNYSQV", IonType.cIon, option);
//Console.WriteLine(mass);
//mass = calculator.CalcPeptideIonMass("CHS", IonType.zIon, option);
//Console.WriteLine(mass);
//IGlycan glycan = new GeneralGlycan(6, 7, 2, 3, 0);
IGlycan glycan = new GeneralGlycan(1, 0, 0, 0, 0);
//option.SetPermethylation(true);
double mass = calculator.CalcPeptideMass(peptide, option);
mass += calculator.CalcGlycanMass(glycan, option);
//mass = calculator.CalcGlycanYIonMass(glycan, option);
//peptide = new GeneralPeptide("1", "EPTIDE");
//mass = calculator.CalcPeptideIonMass(peptide, IonType.xIon, option);
//Console.WriteLine((mass+Hydrogen)/1);
//peptide = new GeneralPeptide("1", "TIDE");
//mass = calculator.CalcPeptideIonMass(peptide, IonType.xIon, option);
//Console.WriteLine((mass+Hydrogen)/1);
//2322.82285937
Console.WriteLine(mass);
Console.WriteLine(mass / 1.0 + Hydrogen);
//Console.WriteLine(calculator.CalcPPM(mass, 329.09256));
Console.Read();
}
public void SetPeptides(List <IPeptide> peptides)
{
// build points on peptides
Dictionary <double, PrecursorPoint <IPeptide> > seen = new Dictionary <double, PrecursorPoint <IPeptide> >();
foreach (IPeptide peptide in peptides)
{
double mass = calculator.CalcPeptideMass(peptide, option);
if (!seen.ContainsKey(mass))
{
PrecursorPoint <IPeptide> pt = new PrecursorPoint <IPeptide>(mass);
seen[mass] = pt;
peptidePoints.Add(pt);
}
seen[mass].Add(peptide);
}
matcher.SetPoints(peptidePoints);
}
protected void MatchPrecursorMass(double precusorMass, List <T> glycoPeptides)
{
HashSet <string> seen = new HashSet <string>();
List <Point> matches = new List <Point>();
foreach (IPeptide peptide in peptides)
{
//search on glycans for a peptide
double target = precusorMass - calculator.CalcPeptideMass(peptide, option);
if (target <= 0)
{
continue;
}
PrecursorPoint <IGlycan> p = new PrecursorPoint <IGlycan>(target);
matches.AddRange(matcher.GetSearchResult(p, parameter));
//build glycopeptide
foreach (Point pt in matches)
{
foreach (IGlycan glycan in (pt as PrecursorPoint <IGlycan>).GetObjects())
{
//check redundant
string s = glycan.GetName();
if (!seen.Contains(s))
{
//Console.WriteLine(glycan.GetName());
//Console.WriteLine(peptide.GetSequence());
glycoPeptides.AddRange(GenerateNewGlycoPeptide(peptide, glycan));
seen.Add(s);
}
}
}
matches.Clear();
seen.Clear();
}
}
public GeneralAccumulatedGlycoPeptideMassProxy(
SpecialGlycoPeptide <IAccumulatedGlycanMassProxy> glycoPeptide)
{
calculator = UtilMass.Instance;
option = UtilMassOption.Instance;
mass = new HashSet <double>();
this.glycoPeptide = glycoPeptide;
foreach (double glycanMass in (glycoPeptide.GetGlycan()
as IAccumulatedGlycanMassProxy).GetMass())
{
foreach (double peptideMass in CalcPTMPeptideMass.GetNGlycanPeptideMass(
GetPeptide().GetSequence(), GetPosition()))
{
mass.Add(glycanMass + peptideMass);
}
mass.Add(glycanMass + calculator.CalcPeptideMass(glycoPeptide.GetPeptide(), option));
}
mass.UnionWith(CalcPTMPeptideMass.GetNonGlycanPeptideMass(GetPeptide().GetSequence(), GetPosition()));
massList = mass.ToList();
massList.Sort();
}
protected void InitMatcher(IGlycoPeptide glycoPeptide)
{
List <Point> points = new List <Point>();
List <ITableNGlycan> glycans = glycansTable[
glycoPeptide.GetGlycan().GetName()];
IPeptide peptide = glycoPeptide.GetPeptide();
string seq = peptide.GetSequence();
int pos = glycoPeptide.GetPosition();
Dictionary <double, BinSearchAnnotatedPoint> seen =
new Dictionary <double, BinSearchAnnotatedPoint>();
//glycanfrag
foreach (ITableNGlycan g in glycans)
{
double glycanMass = calculator.CalcGlycanMass(g, option);
double mass = calculator.CalcPeptideMass(seq, option) + glycanMass;
if (!seen.ContainsKey(mass))
{
BinSearchAnnotatedPoint p = new BinSearchAnnotatedPoint(mass);
seen[mass] = p;
points.Add(p);
}
seen[mass].AddGlycoPeptide(
new GeneralPeptide(peptide.GetID(), seq), g, pos);
//n-peptidefrag
for (int i = 0; i < pos; i++)
{
mass = calculator.CalcPeptideIonMass(
seq.Substring(0, i + 1), IonType.cIon, option) + glycanMass;
if (!seen.ContainsKey(mass))
{
BinSearchAnnotatedPoint p = new BinSearchAnnotatedPoint(mass);
seen[mass] = p;
points.Add(p);
}
seen[mass].AddGlycoPeptide(
new GeneralPeptide(peptide.GetID(), seq.Substring(0, i + 1)),
g, pos);
}
//c-peptidefrag
for (int i = pos + 1; i < seq.Length; i++)
{
mass = calculator.CalcPeptideIonMass(
seq.Substring(i, seq.Length - i), IonType.zIon, option) + glycanMass;
if (!seen.ContainsKey(mass))
{
BinSearchAnnotatedPoint p = new BinSearchAnnotatedPoint(mass);
seen[mass] = p;
points.Add(p);
}
seen[mass].AddGlycoPeptide(
new GeneralPeptide(peptide.GetID(), seq.Substring(i, seq.Length - i)),
g, pos);
}
}
points.Sort();
matcher.SetPoints(points);
}