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));
}
public static MaxQuantModificationList ReadFromFile(string fileName)
{
var result = new MaxQuantModificationList();
var doc = XDocument.Load(fileName);
var items = (from mod in doc.Descendants("modification")
let fullName = mod.Attribute("title").Value
let shortName = "(" + fullName.Substring(0, 2).ToLower() + ")"
select new MaxQuantModificationItem()
{
FullName = fullName,
ShortName = shortName,
Composition = new AtomComposition(mod.Attribute("composition").Value.Replace(" ", "").Replace("(", "").Replace(")", ""))
}).ToList();
result.AddRange(items);
return(result);
}
private void ParseModification(Annotation msms, Dictionary <string, MaxQuantModificationItem> modCharMap, MaxQuantModificationList mods, out string modification, out string modifiedSequence)
{
var seq = msms.Annotations["Modified sequence"].ToString();
seq = ReplaceModificationStringToChar(seq, modCharMap);
seq = seq.Replace("_", "");
Match m = modReg.Match(seq);
if (m.Success)
{
var modMap = (from mo in msms.Annotations["Modifications"].ToString().Split(',')
let mof = Regex.Replace(mo, "^\\d+\\s+", "")
let shortName = "(" + mof.Substring(0, 2).ToLower() + ")"
select new { FullName = mof, ShortName = shortName }).ToDictionary(l => l.ShortName, l => l.FullName);
while (m.Success)
{
string mod = m.Groups[1].Value;
if (!modCharMap.ContainsKey(mod))
{
var fullName = modMap[mod];
modCharMap[mod] = mods.Find(l => l.FullName.Equals(fullName));
modCharMap[mod].Symbol = ModificationConsts.MODIFICATION_CHAR.Substring(modCharMap.Count + 1, 1);
}
m = m.NextMatch();
}
seq = ReplaceModificationStringToChar(seq, modCharMap);
}
modifiedSequence = seq;
modification = msms.Annotations["Modifications"].ToString();
}