public void Parse(XmlDocument data) { #region Parameter Initialization foreach (XmlNode mod in data.SelectNodes(".//parameters/const_mod")) { MSDigestModification constMod = MSDigestModification.FromURI(mod.InnerText); Parameters.ConstantModifications.Add(constMod); } foreach (XmlNode mod in data.SelectNodes(".//parameters/mod_AA")) { Parameters.VariableModifications.Add(MSDigestModification.FromURI(mod.InnerText)); } Parameters.Enzyme = data.SelectSingleNode(".//parameters/enzyme").InnerText; Parameters.MissedCleavages = Convert.ToInt32(data.SelectSingleNode(".//parameters/missed_cleavages").InnerText); Parameters.UserProteinSequence = data.SelectSingleNode(".//parameters/user_protein_sequence").InnerText; #endregion //No Database extractions for now #region Peptide Extraction foreach (XmlNode peptideNode in data.SelectNodes(".//peptide")) { //Console.WriteLine("------------------------------"); MSDigestPeptide peptideObj = new MSDigestPeptide(); peptideObj.PeptideIndex = Convert.ToInt32(peptideNode.SelectSingleNode(".//protein_index").InnerText); peptideObj.Charge = Convert.ToInt32(peptideNode.SelectSingleNode(".//charge").InnerText); peptideObj.Mass = Convert.ToDouble(peptideNode.SelectSingleNode(".//mi_m_over_z").InnerText); String modStr = ""; foreach (XmlNode mod in peptideNode.SelectNodes(".//modification")) { //Console.WriteLine(mod.InnerText); modStr += mod.InnerText + " "; } peptideObj.Modifications = modStr; peptideObj.StartAA = Convert.ToInt32(peptideNode.SelectSingleNode(".//start_aa").InnerText); peptideObj.EndAA = Convert.ToInt32(peptideNode.SelectSingleNode(".//end_aa").InnerText); peptideObj.NextAA = (peptideNode.SelectSingleNode(".//next_aa").InnerText); peptideObj.PreviousAA = (peptideNode.SelectSingleNode(".//previous_aa").InnerText); peptideObj.MissedCleavages = Convert.ToInt32(peptideNode.SelectSingleNode(".//missed_cleavages").InnerText); peptideObj.Sequence = (peptideNode.SelectSingleNode(".//database_sequence").InnerText); peptideObj.ProteinID = Parameters.UserProteinSequence; peptideObj.NumGlycosylations = PeptideUtilities.CountNGlycanSequons(peptideObj); //Console.WriteLine(peptideObj); Peptides.Add(peptideObj); } #endregion }
public MSDigestPeptide ConvertToMSDigestPeptide() { MSDigestPeptide peptide = new MSDigestPeptide(); peptide.Charge = Charge; peptide.Selected = Selected; peptide.PeptideIndex = PeptideIndex; peptide.Mass = Mass; peptide.Modifications = Modifications; peptide.StartAA = StartAA; peptide.EndAA = EndAA; peptide.MissedCleavages = MissedCleavages; peptide.PreviousAA = PreviousAA; peptide.StartAA = StartAA; peptide.NextAA = NextAA; peptide.NumGlycosylations = NumGlycosylations; peptide.Sequence = Sequence; peptide.ProteinID = ProteinID; return peptide; }
public Peptide(MSDigestPeptide other) : base() { this.Selected = other.Selected; this.PeptideIndex = other.PeptideIndex; this.Mass = other.Mass; this.Charge = other.Charge; this.Modifications = other.Modifications; this.StartAA = other.StartAA; this.EndAA = other.EndAA; this.MissedCleavages = other.MissedCleavages; this.PreviousAA = other.PreviousAA; this.Sequence = other.Sequence; this.NextAA = other.NextAA; this.NumGlycosylations = other.NumGlycosylations; this.ProteinID = other.ProteinID; }
public static int CountNGlycanSequons(MSDigestPeptide sequence) { return CountNGlycanSequons(sequence.Sequence); }
/// <summary> /// Combination Cosntructor /// </summary> /// <param name="glycanComposition"></param> /// <param name="peptide"></param> public GlycopeptideComposition(GlycanComposition glycanComposition, MSDigestPeptide peptide) : base(glycanComposition) { this.PeptideSequence = peptide.Sequence; this.PeptideModification = peptide.Modifications; this.StartAA = peptide.StartAA; this.EndAA = peptide.EndAA; this.GlycosylationCount = peptide.NumGlycosylations; this.MassWeight += peptide.Mass - WaterMass - glycanComposition.AdductMass; MolecularComposition["Water"] -= 1; if (ElementalComposition.ContainsKey("O")) { ElementalComposition["O"] -= 1; ElementalComposition["H"] -= 2; } this.ProteinID = peptide.ProteinID; AdductAmount = 0; AdductReplaces = ""; }
/// <summary> /// Peptide-Only Constructor /// </summary> /// <param name="peptide"></param> public GlycopeptideComposition(MSDigestPeptide peptide) : base() { this.PeptideSequence = peptide.Sequence; this.PeptideModification = peptide.Modifications; this.StartAA = peptide.StartAA; this.EndAA = peptide.EndAA; this.GlycosylationCount = peptide.NumGlycosylations; this.MassWeight += peptide.Mass; this.ProteinID = peptide.ProteinID; }