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; } } } }