public void TestModificationItem()
{
var strings = new string[] {
"delta1=42.010559,Acetyl (Protein N-term)",
"NeutralLoss1=0.000000",
"delta2=8.014206,Lysine-13C615N2 (K-full) (K)",
"NeutralLoss2=0.000000",
"delta3=15.994919,Oxidation (M)",
"NeutralLoss3=63.998285",
"NeutralLoss3_master=0.000000",
"delta4=79.966324,Phospho (STY)",
"NeutralLoss4=0.000000",
"NeutralLoss4_master=97.976898",
"FixedMod1=57.021465,Carbamidomethyl (C)",
"FixedModResidues1=C"
};
var dic = strings.ToDictionary(m => m.Substring(0, m.IndexOf('=')), m => m.Substring(m.IndexOf('=') + 1));
var mm = new MascotModification();
mm.Parse(dic);
Assert.AreEqual(4, mm.DynamicModification.Count);
Assert.AreEqual("42.010559 Acetyl (Protein N-term)", mm.DynamicModification[0].ToString());
Assert.AreEqual("8.014206 Lysine-13C615N2 (K-full) (K)", mm.DynamicModification[1].ToString());
Assert.AreEqual("15.994919 Oxidation (M)", mm.DynamicModification[2].ToString());
Assert.AreEqual("79.966324 Phospho (STY)", mm.DynamicModification[3].ToString());
Assert.AreEqual(1, mm.StaticModification.Count);
Assert.AreEqual("57.021465 Carbamidomethyl (C)", mm.StaticModification[0].ToString());
}
//-102.091507,Acetyl (K)
protected MascotModification ParseModification(Dictionary <string, string> parameters)
{
var result = new MascotModification();
result.Parse(parameters);
return(result);
}
public void TestModification()
{
using (var sr = new StreamReader(@TestContext.CurrentContext.TestDirectory + "/../../../data//F001264.dat"))
{
Dictionary <string, string> parameters = base.ParseSection(sr, "masses");
MascotModification mm = base.ParseModification(parameters);
Assert.AreEqual(4, mm.DynamicModification.Count);
Assert.AreEqual("42.010559 Acetyl (Protein N-term)", mm.DynamicModification[0].ToString());
Assert.AreEqual("8.014206 Lysine-13C615N2 (K-full) (K)", mm.DynamicModification[1].ToString());
Assert.AreEqual("15.994919 Oxidation (M)", mm.DynamicModification[2].ToString());
Assert.AreEqual("79.966324 Phospho (STY)", mm.DynamicModification[3].ToString());
Assert.AreEqual(3, mm.StaticModification.Count);
Assert.AreEqual("127.063332 SMA (K)", mm.StaticModification[0].ToString());
Assert.AreEqual("128.071154 SMA (N-term)", mm.StaticModification[1].ToString());
Assert.AreEqual("15.994920 Oxidation (M)", mm.StaticModification[2].ToString());
}
}
protected void AssignModification(IIdentifiedSpectrum mph, string modification, MascotModification mm)
{
foreach (char c in modification)
{
if (c != '0')
{
int ci = int.Parse(c.ToString()) - 1;
string mod = mm.DynamicModification[ci].ToString();
if (mph.Modifications == null || mph.Modifications.Length == 0)
{
mph.Modifications = mod;
}
else if (!mph.Modifications.Contains(mod))
{
mph.Modifications += "; " + mod;
}
}
}
}
