public void InitializeIsotopicIons(double ppmTolerance, double minimumPercentage = 0.05, int maxProfileLength = int.MaxValue)
{
var atomComposition = aas.GetPeptideAtomComposition(this.Sequence);
var profiles = profileBuilder.GetProfile(atomComposition, this.Charge, minimumPercentage).Take(maxProfileLength);
this.IsotopicIons = (from peak in profiles
select new IsotopicIon()
{
Mz = peak.Mz,
Intensity = peak.Intensity,
}).ToArray();
var diff = this.TheoreticalMz - this.IsotopicIons[0].Mz;
//Replace the ion m/z to real ion m/z but keep the distance between ions in case of the peptide contains modification
foreach (var ion in this.IsotopicIons)
{
ion.Mz += diff;
var mzdiff = PrecursorUtils.ppm2mz(ion.Mz, ppmTolerance);
ion.MinimumMzWithinTolerance = ion.Mz - mzdiff;
ion.MaximumMzWithinTolerance = ion.Mz + mzdiff;
}
this.IsotopicIntensities = (from ion in this.IsotopicIons
select ion.Intensity).ToArray();
}
//[Test]
public void TestWuyinPeptide()
{
List<String> lines = FileUtils.ReadFile(@"C:\Documents and Settings\sheng\Desktop\sequences.txt");
var aas = new Aminoacids();
foreach (String line in lines)
{
AtomComposition ac = aas.GetPeptideAtomComposition(line);
ac.Add(new AtomComposition("H2O"));
List<double> profile = this.ip.GetProfile(ac, 10);
Console.WriteLine(line);
Console.WriteLine(ac);
foreach (double d in profile)
{
Console.WriteLine(d);
}
Console.WriteLine();
}
}
//[Test]
public void TestWuyinPeptide()
{
List <String> lines = FileUtils.ReadFile(@"C:\Documents and Settings\sheng\Desktop\sequences.txt");
var aas = new Aminoacids();
foreach (String line in lines)
{
AtomComposition ac = aas.GetPeptideAtomComposition(line);
ac.Add(new AtomComposition("H2O"));
List <double> profile = this.ip.GetProfile(ac, 10);
Console.WriteLine(line);
Console.WriteLine(ac);
foreach (double d in profile)
{
Console.WriteLine(d);
}
Console.WriteLine();
}
}
public O18QuantificationPeptideProcessor(IFileFormat <O18QuantificationSummaryItem> fileFormat,
bool isPostDigestionLabelling, string rawFilename, string peptide,
double purityOfO18Water, List <O18QuanEnvelope> envelopes, double mzTolerance,
string additionalFormula, double scanPercentageStart, double scanPercentageEnd)
{
_fileFormat = fileFormat;
_isPostDigestionLabelling = isPostDigestionLabelling;
_rawFilename = new FileInfo(rawFilename).FullName;
_peptide = peptide;
_additionalFormula = additionalFormula;
_atomComposition = _aas.GetPeptideAtomComposition(peptide);
if (!string.IsNullOrEmpty(additionalFormula))
{
var additionalAtomComposition = new AtomComposition(additionalFormula);
_atomComposition.Add(additionalAtomComposition);
}
_profile = _cp.GetProfile(_atomComposition, 0, 10);
_purityOfO18Water = purityOfO18Water;
_envelopes = envelopes;
_scanPercentageStart = scanPercentageStart;
_scanPercentageEnd = scanPercentageEnd;
}
public override IEnumerable <string> Process()
{
var annos = new AnnotationFormat().ReadFromFile(boundaryFile);
var aas = new Aminoacids();
var pbuilder = new EmassProfileBuilder();
var chroFormat = new ChromatographProfileTextWriter();
foreach (var ann in annos)
{
var chroFile = Path.Combine(ann.Annotations["ChroDirectory"] as string, ann.Annotations["ChroFile"] as string) + ".tsv";
var peptide = (ann.Annotations["PeptideId"] as string).StringBefore("_");
var start = double.Parse(ann.Annotations["ChroLeft"] as string);
var end = double.Parse(ann.Annotations["ChroRight"] as string);
var chro = chroFormat.ReadFromFile(chroFile);
var chroFiltered = chro.Profiles.Where(l => l.RetentionTime >= start && l.RetentionTime <= end).ToArray();
//all observed isotopimers, start from 1, transfer to zero-based
var allIsotopics = (from f in chroFiltered
from s in f
select s.Isotopic - 1).Distinct().OrderBy(l => l).ToArray();
//get minimum intensity of each isotopimer
var minIntensities = (from iso in allIsotopics
select(from f in chroFiltered
where f.Count > iso
select f[iso].Intensity).Min()).ToArray();
//how many isotopic should I trust?
var iso0 = (from f in chroFiltered select f.First().Intensity).ToArray();
int maxIso = 1;
for (int i = 2; i < allIsotopics.Length; i++)
{
var isoi = (from f in chroFiltered select f.Count > i ? f[i].Intensity : minIntensities[i]).ToArray();
var corr = MathNet.Numerics.Statistics.Correlation.Pearson(iso0, isoi);
if (corr < minPearsonCorrelation)
{
maxIso = i;
break;
}
}
var maxIsoArray = allIsotopics.Where(l => l <= maxIso).ToArray();
//get observed profile in each scan
var observedIons = (from f in chroFiltered
select(from iso in maxIsoArray select f.Count > iso ? f[iso].Intensity : minIntensities[iso]).ToArray()).ToArray();
var atomComposition = aas.GetPeptideAtomComposition(peptide);
var hatom = (int)(Math.Round(aas.ExchangableHAtom(peptide)));
for (int h2 = 0; h2 < hatom; h2++)
{
}
var profiles = pbuilder.GetProfile(atomComposition, 1, 3);
var isotopicIons = (from peak in profiles
select new IsotopicIon()
{
Mz = peak.Mz,
Intensity = peak.Intensity,
}).ToArray();
}
return(null);
}
