public PhosphoRSConfig()
{
fragmentMassTolerance = 0.5;
scoreNLToo = "true";
phosphorylationSymbol = 1;
maxIsoformCount = 2000;
maxPTMCount = 20;
maxPackageSize = 3000;
scoredAA = new phosphoRS.AminoAcidModification(phosphorylationSymbol.ToString()[0], "Phosphorylation", "Pho", "H3PO4", 79.966331, 97.976896, phosphoRS.AminoAcidSequence.ParseAASequence("STY"));
pwizMod = new proteome.Modification("H1P1O3");
}
private phosphoRS.PeptideSpectrumMatch getPhosphoRS_PSM(PhosphoRSConfig config, PhosphoPeptideAttestationRow variant)
{
// Get the phosphorylated peptide and add all modifications to the base sequence.
proteome.Peptide phosphoPeptide = new proteome.Peptide(variant.UnphosphorylatedSequence, proteome.ModificationParsing.ModificationParsing_Auto, proteome.ModificationDelimiter.ModificationDelimiter_Brackets);
proteome.ModificationMap variantPeptideMods = phosphoPeptide.modifications();
variant.OriginalPhosphoSites.Keys.ToList().ForEach(location => { variantPeptideMods[location].Add(config.pwizMod); });
// This modification ID is used to tell phosphoRS how to modify the sequence.
int modificationID = config.phosphorylationSymbol + 1;
// Build a string representation of all modificaitons in a peptide for phospoRS
// "0.00011000000000.0" : 1 is the ID of the modification. All phosphos in a data
// set need to have one ID. This ID is used by the PhosphoRS to figure out which
// mods need to be scored.
var ptmRepresentation = new StringBuilder();
// Store all modifications in phosphoRS modification objects
var modifications = new List<phosphoRS.AminoAcidModification>();
// Get the n-terminal modifications.
if (variantPeptideMods.ContainsKey(proteome.ModificationMap.NTerminus()))
{
phosphoRS.AminoAcidModification otherMod = new phosphoRS.AminoAcidModification('2', "unknown", "unk", "none", variantPeptideMods[proteome.ModificationMap.NTerminus()].monoisotopicDeltaMass(), 0.0, null);
modifications.Add(otherMod);
ptmRepresentation.Append(modificationID.ToString() + ".");
//++modificationID;
}
else
{
ptmRepresentation.Append("0.");
}
// Process all other modifications.
for (int aaIndex = 0; aaIndex < phosphoPeptide.sequence.Length; ++aaIndex)
{
// If phosphorylation, use the existing scoredAA variable.
if (variantPeptideMods.ContainsKey(aaIndex))
{
if (variant.OriginalPhosphoSites.Keys.Contains(aaIndex))
{
modifications.Add(config.scoredAA);
ptmRepresentation.Append(config.phosphorylationSymbol.ToString()[0]);
}
else
{
// Otherwise, make an "unknown" modification with a separate modification ID.
var otherMod = new phosphoRS.AminoAcidModification(modificationID.ToString()[0], "unknown", "unk", "none", variantPeptideMods[aaIndex].monoisotopicDeltaMass(), 0.0, phosphoRS.AminoAcidSequence.ParseAASequence("" + phosphoPeptide.sequence[aaIndex]));
modifications.Add(otherMod);
ptmRepresentation.Append(modificationID.ToString());
//++modificationID;
}
}
else
{
ptmRepresentation.Append("0");
}
}
// Process any c-terminal modifications.
if (variantPeptideMods.ContainsKey(proteome.ModificationMap.CTerminus()))
{
var otherMod = new phosphoRS.AminoAcidModification(modificationID.ToString()[0], "unknown", "unk", "none", variantPeptideMods[proteome.ModificationMap.CTerminus()].monoisotopicDeltaMass(), 0.0, null);
modifications.Add(otherMod);
ptmRepresentation.Append("." + modificationID.ToString());
}
else
{
ptmRepresentation.Append(".0");
}
// Get the phosphoRS peptide sequence.
// Assign spectrum ID, amino acid sequence, list of all modifications, a so-called 'modification position string' (here every digit represents an amino acid within the peptide sequence
// '0' indicates not modified, values != '0' indicate the unique identifier of the amino acid's modification the first digit represents the n-terminus the last digit represents the c-terminus)
var AAS = phosphoRS.AminoAcidSequence.Create((int)variant.SpectrumId, phosphoPeptide.sequence, modifications, ptmRepresentation.ToString());
// Make a phosphoRS peptide-spectrum match.
return new phosphoRS.PeptideSpectrumMatch((int)variant.PSMId, variant.SpectrumType, variant.Charge, variant.PrecursorMZ, variant.Peaks, AAS);
}
public PhosphoRSConfig()
{
fragmentMassTolerance = 0.5;
scoreNLToo = "true";
phosphorylationSymbol = 1;
maxIsoformCount = 2000;
maxPTMCount = 20;
maxPackageSize = 3000;
scoredAA = new phosphoRS.AminoAcidModification(phosphorylationSymbol.ToString()[0], "Phosphorylation", "Pho", "H3PO4", 79.966331, 97.976896, phosphoRS.AminoAcidSequence.ParseAASequence("STY"));
pwizMod = new proteome.Modification("H1P1O3");
}
private phosphoRS.PeptideSpectrumMatch getPhosphoRS_PSM(PhosphoRSConfig config, PhosphoPeptideAttestationRow variant)
{
// Get the phosphorylated peptide and add all modifications to the base sequence.
proteome.Peptide phosphoPeptide = new proteome.Peptide(variant.UnphosphorylatedSequence, proteome.ModificationParsing.ModificationParsing_Auto, proteome.ModificationDelimiter.ModificationDelimiter_Brackets);
proteome.ModificationMap variantPeptideMods = phosphoPeptide.modifications();
variant.OriginalPhosphoSites.Keys.ToList().ForEach(location => { variantPeptideMods[location].Add(config.pwizMod); });
// This modification ID is used to tell phosphoRS how to modify the sequence.
int modificationID = config.phosphorylationSymbol + 1;
// Build a string representation of all modificaitons in a peptide for phospoRS
// "0.00011000000000.0" : 1 is the ID of the modification. All phosphos in a data
// set need to have one ID. This ID is used by the PhosphoRS to figure out which
// mods need to be scored.
var ptmRepresentation = new StringBuilder();
// Store all modifications in phosphoRS modification objects
var modifications = new List <phosphoRS.AminoAcidModification>();
// Get the n-terminal modifications.
if (variantPeptideMods.ContainsKey(proteome.ModificationMap.NTerminus()))
{
phosphoRS.AminoAcidModification otherMod = new phosphoRS.AminoAcidModification('2', "unknown", "unk", "none", variantPeptideMods[proteome.ModificationMap.NTerminus()].monoisotopicDeltaMass(), 0.0, null);
modifications.Add(otherMod);
ptmRepresentation.Append(modificationID.ToString() + ".");
//++modificationID;
}
else
{
ptmRepresentation.Append("0.");
}
// Process all other modifications.
for (int aaIndex = 0; aaIndex < phosphoPeptide.sequence.Length; ++aaIndex)
{
// If phosphorylation, use the existing scoredAA variable.
if (variantPeptideMods.ContainsKey(aaIndex))
{
if (variant.OriginalPhosphoSites.Keys.Contains(aaIndex))
{
modifications.Add(config.scoredAA);
ptmRepresentation.Append(config.phosphorylationSymbol.ToString()[0]);
}
else
{
// Otherwise, make an "unknown" modification with a separate modification ID.
var otherMod = new phosphoRS.AminoAcidModification(modificationID.ToString()[0], "unknown", "unk", "none", variantPeptideMods[aaIndex].monoisotopicDeltaMass(), 0.0, phosphoRS.AminoAcidSequence.ParseAASequence("" + phosphoPeptide.sequence[aaIndex]));
modifications.Add(otherMod);
ptmRepresentation.Append(modificationID.ToString());
//++modificationID;
}
}
else
{
ptmRepresentation.Append("0");
}
}
// Process any c-terminal modifications.
if (variantPeptideMods.ContainsKey(proteome.ModificationMap.CTerminus()))
{
var otherMod = new phosphoRS.AminoAcidModification(modificationID.ToString()[0], "unknown", "unk", "none", variantPeptideMods[proteome.ModificationMap.CTerminus()].monoisotopicDeltaMass(), 0.0, null);
modifications.Add(otherMod);
ptmRepresentation.Append("." + modificationID.ToString());
}
else
{
ptmRepresentation.Append(".0");
}
// Get the phosphoRS peptide sequence.
// Assign spectrum ID, amino acid sequence, list of all modifications, a so-called 'modification position string' (here every digit represents an amino acid within the peptide sequence
// '0' indicates not modified, values != '0' indicate the unique identifier of the amino acid's modification the first digit represents the n-terminus the last digit represents the c-terminus)
var AAS = phosphoRS.AminoAcidSequence.Create((int)variant.SpectrumId, phosphoPeptide.sequence, modifications, ptmRepresentation.ToString());
// Make a phosphoRS peptide-spectrum match.
return(new phosphoRS.PeptideSpectrumMatch((int)variant.PSMId, variant.SpectrumType, variant.Charge, variant.PrecursorMZ, variant.Peaks, AAS));
}