public void TestRead()
{
var mods = MaxQuantModificationList.ReadFromFile(TestContext.CurrentContext.TestDirectory + "/../../../data/maxquant_modifications.xml");
Assert.AreEqual(550, mods.Count);
Assert.AreEqual("Acetyl (K)", mods[0].FullName);
Assert.AreEqual("(ac)", mods[0].ShortName);
Assert.AreEqual("C2H2O", mods[0].Composition.ToString());
Assert.AreEqual("Cysteinyl - carbamidomethyl", mods[549].FullName);
Assert.AreEqual("(cy)", mods[549].ShortName);
Assert.AreEqual("CH2OS", mods[549].Composition.ToString());
}
public List <IIdentifiedSpectrum> ExtractPeptides(Dictionary <string, MaxQuantModificationItem> shortModMap, string peptideFile)
{
var mods = MaxQuantModificationList.ReadFromFile(_option.MaxQuantModificationXml);
var sites = new AnnotationFormat().ReadFromFile(_option.MaxQuantSiteFile);
var msmsIds = new HashSet <string>(from s in sites
let msmsids = s.Annotations["MS/MS IDs"] as string
let msmsIdList = msmsids.Split(';')
from msmsId in msmsIdList
select msmsId);
var format = new AnnotationFormat();
var msmsList = format.ReadFromFile(_option.MaxQuantMSMSFile);
msmsList.RemoveAll(l => !msmsIds.Contains(l.Annotations["id"].ToString()));
using (var sw = new StreamWriter(peptideFile))
{
sw.WriteLine("FileScan\tSequence\tMH+\tDiff(MH+)\tCharge\tScore\tReference\tModification\tRetentionTime");
foreach (var msms in msmsList)
{
string modification;
string modifiedSequence;
ParseModification(msms, shortModMap, mods, out modification, out modifiedSequence);
var mh = double.Parse(msms.Annotations["Mass"].ToString()) + Atom.H.MonoMass;
var diffStr = msms.Annotations["Mass Error [ppm]"].ToString();
var diffmh = diffStr.Equals("NaN") ? 0 : PrecursorUtils.ppm2mz(mh, double.Parse(diffStr));
sw.WriteLine("{0},{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}\t{9}",
msms.Annotations["Raw file"],
msms.Annotations["Scan number"],
modifiedSequence,
mh,
diffmh,
msms.Annotations["Charge"],
msms.Annotations["Score"],
msms.Annotations["Proteins"].ToString().Replace(";", "/"),
modification,
msms.Annotations["Retention time"]);
}
}
return(new MascotPeptideTextFormat().ReadFromFile(peptideFile));
}
