public void CalculateO18()
{
EmassProfileBuilder builder = new EmassProfileBuilder(@"../../../data/ISOTOPE.DAT");
AtomComposition light = new AtomComposition("C45H73N13O13");
var res = builder.GetProfile(light, 2, 5);
Console.WriteLine("nature");
foreach (var r in res)
{
Console.WriteLine("{0:0.0000}\t{1:0.000000}", r.Mz, r.Intensity);
}
AtomComposition O181 = new AtomComposition("(O18)1C45H73N13O12");
var resH = builder.GetProfile(O181, 2, 5);
Console.WriteLine("O181");
foreach (var r in resH)
{
Console.WriteLine("{0:0.0000}\t{1:0.000000}", r.Mz, r.Intensity);
}
AtomComposition O182 = new AtomComposition("(O18)2C45H73N13O11");
var resH2 = builder.GetProfile(O182, 2, 5);
Console.WriteLine("O182");
foreach (var r in resH2)
{
Console.WriteLine("{0:0.0000}\t{1:0.000000}", r.Mz, r.Intensity);
}
Console.WriteLine(string.Format("O18 - O16 = {0:0.0000}", Atom.O18.MonoMass - Atom.O.MonoMass));
Console.WriteLine(string.Format("2 * (C13 - C12) = {0:0.0000}", 2 * (Atom.C13.MonoMass - Atom.C.MonoMass)));
Console.WriteLine(string.Format("O18 - O181, ppm = {0:0.00}ppm", PrecursorUtils.mz2ppm(res[0].Mz, resH[0].Mz - res[2].Mz)));
Console.WriteLine(string.Format("O18 - O182, ppm = {0:0.00}ppm", PrecursorUtils.mz2ppm(res[0].Mz, resH2[0].Mz - res[4].Mz)));
Console.WriteLine(string.Format("O181- O182, ppm = {0:0.00}ppm", PrecursorUtils.mz2ppm(resH[0].Mz, resH2[0].Mz - resH[2].Mz)));
}
public void CalculateO18_charge1()
{
EmassProfileBuilder builder = new EmassProfileBuilder(@"../../../data/ISOTOPE.DAT");
AtomComposition light = new AtomComposition("C45H73N13O13");
var res = builder.GetProfile(light, 1, 5);
var max = res.Max(m => m.Intensity);
Console.WriteLine("nature");
foreach (var r in res)
{
Console.WriteLine("{0:0.0000}\t{1:0.000000}", r.Mz - Atom.H.MonoMass, r.Intensity * 100 / max);
}
}
public void Calculate()
{
var calc = new EmassCalculator(@"../../../data/ISOTOPE.DAT");
EmassProfileBuilder builder = new EmassProfileBuilder();
AtomComposition light = new AtomComposition("C45H73N13O13");
var res = builder.GetProfile(light, 2, 4);
Console.WriteLine("light");
foreach (var r in res)
{
Console.WriteLine("{0:0.0000}\t{1:0.000000}", r.Mz, r.Intensity);
}
AtomComposition heavy = new AtomComposition("(C13)6(N15)4C39H73N9O13");
var resH = builder.GetProfile(heavy, 2, 4);
Console.WriteLine("heavy");
foreach (var r in resH)
{
Console.WriteLine("{0:0.0000}\t{1:0.000000}", r.Mz, r.Intensity);
}
}
public SilacQuantificationSummaryItem ReadFromFile(string filename)
{
XElement root = XElement.Load(filename);
var result = new SilacQuantificationSummaryItem(root.GetChildValue("SampleIsLight", true));
result.RawFilename = root.GetChildValue("RawFilename", "");
result.SoftwareVersion = root.GetChildValue("SoftwareVersion", "");
result.PeptideSequence = root.GetChildValue("PeptideSequence");
result.Charge = root.GetChildValue("Charge", 2);
result.SampleAtomComposition = root.GetChildValue("SampleAtomComposition");
result.ReferenceAtomComposition = root.GetChildValue("ReferenceAtomComposition");
result.Ratio = root.GetChildValue("Ratio", 0.0);
result.RegressionCorrelation = root.GetChildValue("Correlation", 0.0);
result.SampleAbundance = root.GetChildValue("SampleAbundance", 0.0);
result.ReferenceAbundance = root.GetChildValue("ReferenceAbundance", 0.0);
result.SampleProfile = new List <Peak>();
ReadProfile(root, "SampleProfile", result.SampleProfile);
result.ReferenceProfile = new List <Peak>();
ReadProfile(root, "ReferenceProfile", result.ReferenceProfile);
var observed = root.Element("ObservedEnvelopes");
result.ObservedEnvelopes = new SilacEnvelopes();
foreach (var pkl in observed.Elements())
{
var peakList = new SilacPeakListPair();
int scan = Convert.ToInt32(pkl.Attribute("Scan").Value);
double retentiontime = MyConvert.ToDouble(pkl.Attribute("Retentiontime").Value);
peakList.Enabled = Convert.ToBoolean(pkl.Attribute("Enabled").Value);
peakList.IsIdentified = Convert.ToBoolean(pkl.Attribute("Identified").Value);
var extended = pkl.Attribute("ExtendedIdentification");
if (extended != null)
{
peakList.IsExtendedIdentification = Convert.ToBoolean(pkl.Attribute("ExtendedIdentification").Value);
}
else
{
peakList.IsExtendedIdentification = false;
}
peakList.LightIntensity = MyConvert.ToDouble(pkl.Attribute("LightIntensity").Value);
peakList.HeavyIntensity = MyConvert.ToDouble(pkl.Attribute("HeavyIntensity").Value);
peakList.Light = new PeakList <Peak>();
peakList.Light.ScanTimes.Add(new ScanTime(scan, retentiontime));
peakList.Heavy = new PeakList <Peak>();
peakList.Heavy.ScanTimes.Add(new ScanTime(scan, retentiontime));
ReadPeakList(pkl, "LightPeakList", peakList.Light);
ReadPeakList(pkl, "HeavyPeakList", peakList.Heavy);
result.ObservedEnvelopes.Add(peakList);
}
if (result.LightProfile[0].Mz == 0.0)
{
EmassProfileBuilder builder = new EmassProfileBuilder();
double minPercentage = 0.0001;
AtomComposition acSample = new AtomComposition(result.SampleAtomComposition);
result.SampleProfile = builder.GetProfile(acSample, result.Charge, minPercentage);
AtomComposition acRef = new AtomComposition(result.ReferenceAtomComposition);
result.ReferenceProfile = builder.GetProfile(acRef, result.Charge, minPercentage);
}
result.CalculateCorrelation();
return(result);
}
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);
}
