public void WritePepXML_xl(List <CrosslinkSpectralMatch> items, List <Protein> proteinList, string databasePath, List <Modification> variableModifications, List <Modification> fixedModifications, List <string> localizeableModificationTypes, string outputFolder, string fileName, List <string> nestedIds)
{
if (!items.Any())
{
return;
}
XmlSerializer _indexedSerializer = new XmlSerializer(typeof(pepXML.Generated.msms_pipeline_analysis));
var _pepxml = new pepXML.Generated.msms_pipeline_analysis();
_pepxml.date = DateTime.Now;
_pepxml.summary_xml = items[0].FullFilePath + ".pep.XML";
string proteaseC = ""; string proteaseNC = "";
foreach (var x in CommonParameters.DigestionParams.Protease.DigestionMotifs.Select(m => m.InducingCleavage))
{
proteaseC += x;
}
foreach (var x in CommonParameters.DigestionParams.Protease.DigestionMotifs.Select(m => m.PreventingCleavage))
{
proteaseNC += x;
}
Crosslinker crosslinker = XlSearchParameters.Crosslinker;
string fileNameNoExtension = Path.GetFileNameWithoutExtension(items[0].FullFilePath);
string filePathNoExtension = Path.ChangeExtension(items[0].FullFilePath, null);
string modSites = crosslinker.CrosslinkerModSites.ToCharArray().Concat(crosslinker.CrosslinkerModSites2.ToCharArray()).Distinct().ToString();
var para = new List <pepXML.Generated.nameValueType>();
{
para.Add(new pepXML.Generated.nameValueType {
name = "threads", value = CommonParameters.MaxThreadsToUsePerFile.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "database", value = databasePath
});
para.Add(new pepXML.Generated.nameValueType {
name = "MS_data_file", value = items[0].FullFilePath
});
para.Add(new pepXML.Generated.nameValueType {
name = "Cross-link precursor Mass Tolerance", value = CommonParameters.PrecursorMassTolerance.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Cross-linker type", value = crosslinker.CrosslinkerName
});
para.Add(new pepXML.Generated.nameValueType {
name = "Cross-linker mass", value = crosslinker.TotalMass.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Cross-linker cleavable", value = crosslinker.Cleavable.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Cross-linker cleavable long mass", value = crosslinker.CleaveMassLong.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Cross-linker cleavable short mass", value = crosslinker.CleaveMassShort.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Cross-linker xl site", value = modSites
});
para.Add(new pepXML.Generated.nameValueType {
name = "Generate decoy proteins", value = XlSearchParameters.DecoyType.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "MaxMissed Cleavages", value = CommonParameters.DigestionParams.MaxMissedCleavages.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Protease", value = CommonParameters.DigestionParams.Protease.Name
});
para.Add(new pepXML.Generated.nameValueType {
name = "Initiator Methionine", value = CommonParameters.DigestionParams.InitiatorMethionineBehavior.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Max Modification Isoforms", value = CommonParameters.DigestionParams.MaxModificationIsoforms.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Min Peptide Len", value = CommonParameters.DigestionParams.MinPeptideLength.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Max Peptide Len", value = CommonParameters.DigestionParams.MaxPeptideLength.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Product Mass Tolerance", value = CommonParameters.ProductMassTolerance.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Ions to search", value = String.Join(", ", DissociationTypeCollection.ProductsFromDissociationType[CommonParameters.DissociationType])
});
foreach (var fixedMod in fixedModifications)
{
para.Add(new pepXML.Generated.nameValueType {
name = "Fixed Modifications: " + fixedMod.IdWithMotif, value = fixedMod.MonoisotopicMass.ToString()
});
}
foreach (var variableMod in variableModifications)
{
para.Add(new pepXML.Generated.nameValueType {
name = "Variable Modifications: " + variableMod.IdWithMotif, value = variableMod.MonoisotopicMass.ToString()
});
}
para.Add(new pepXML.Generated.nameValueType {
name = "Localize All Modifications", value = "true"
});
}
_pepxml.msms_run_summary = new pepXML.Generated.msms_pipeline_analysisMsms_run_summary[1]
{
new pepXML.Generated.msms_pipeline_analysisMsms_run_summary
{
base_name = filePathNoExtension,
raw_data_type = "raw",
raw_data = ".mzML",
sample_enzyme = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySample_enzyme()
{
name = CommonParameters.DigestionParams.Protease.Name,
specificity = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySample_enzymeSpecificity[1]
{
new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySample_enzymeSpecificity
{
cut = proteaseC,
no_cut = proteaseNC,
}
}
},
search_summary = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySearch_summary[1]
{
new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySearch_summary
{
base_name = filePathNoExtension,
search_engine_version = GlobalVariables.MetaMorpheusVersion,
precursor_mass_type = pepXML.Generated.massType.monoisotopic,
fragment_mass_type = pepXML.Generated.massType.monoisotopic,
search_id = 1,
search_database = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySearch_summarySearch_database
{
local_path = databasePath,
type = pepXML.Generated.msms_pipeline_analysisMsms_run_summarySearch_summarySearch_databaseType.AA,
},
enzymatic_search_constraint = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySearch_summaryEnzymatic_search_constraint
{
enzyme = CommonParameters.DigestionParams.Protease.Name,
max_num_internal_cleavages = CommonParameters.DigestionParams.MaxMissedCleavages.ToString(),
//min_number_termini = "2"
},
parameter = para.ToArray()
}
},
}
};
_pepxml.msms_run_summary[0].spectrum_query = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_query[items.Count];
var searchHits = new List <pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hit>();
for (int i = 0; i < items.Count; i++)
{
var mods = new List <pepXML.Generated.modInfoDataTypeMod_aminoacid_mass>();
var alphaPeptide = items[i].BestMatchingPeptides.First().Peptide;
foreach (var modification in alphaPeptide.AllModsOneIsNterminus)
{
var mod = new pepXML.Generated.modInfoDataTypeMod_aminoacid_mass
{
mass = modification.Value.MonoisotopicMass.Value,
// convert from one-based to zero-based (N-term is zero in the pepXML output)
position = (modification.Key - 1).ToString()
};
mods.Add(mod);
}
if (items[i].CrossType == PsmCrossType.Single)
{
var searchHit = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hit
{
hit_rank = 1,
peptide = alphaPeptide.BaseSequence,
peptide_prev_aa = alphaPeptide.PreviousAminoAcid.ToString(),
peptide_next_aa = alphaPeptide.NextAminoAcid.ToString(),
protein = alphaPeptide.Protein.Accession,
num_tot_proteins = 1,
calc_neutral_pep_mass = (float)items[i].ScanPrecursorMass,
massdiff = (items[i].ScanPrecursorMass - items[i].PeptideMonisotopicMass.Value).ToString(),
xlink_typeSpecified = true,
xlink_type = pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlink_type.na,
modification_info = new pepXML.Generated.modInfoDataType {
mod_aminoacid_mass = mods.ToArray()
},
search_score = new pepXML.Generated.nameValueType[]
{
new pepXML.Generated.nameValueType {
name = "xlTotalScore", value = items[i].XLTotalScore.ToString()
},
new pepXML.Generated.nameValueType {
name = "Qvalue", value = items[i].FdrInfo.QValue.ToString()
}
},
};
searchHits.Add(searchHit);
}
else if (items[i].CrossType == PsmCrossType.DeadEnd || items[i].CrossType == PsmCrossType.DeadEndH2O || items[i].CrossType == PsmCrossType.DeadEndNH2 || items[i].CrossType == PsmCrossType.DeadEndTris)
{
double crosslinkerDeadEndMass = 0;
switch (items[i].CrossType)
{
case PsmCrossType.DeadEndNH2:
crosslinkerDeadEndMass = crosslinker.DeadendMassNH2;
break;
case PsmCrossType.DeadEndTris:
crosslinkerDeadEndMass = crosslinker.DeadendMassTris;
break;
default:
crosslinkerDeadEndMass = crosslinker.DeadendMassH2O;
break;
}
var mod = new pepXML.Generated.modInfoDataTypeMod_aminoacid_mass {
mass = crosslinkerDeadEndMass, position = items[i].LinkPositions.First().ToString()
};
mods.Add(mod);
var searchHit = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hit
{
hit_rank = 1,
peptide = alphaPeptide.BaseSequence,
peptide_prev_aa = alphaPeptide.PreviousAminoAcid.ToString(),
peptide_next_aa = alphaPeptide.NextAminoAcid.ToString(),
protein = alphaPeptide.Protein.Accession,
num_tot_proteins = 1,
calc_neutral_pep_mass = (float)items[i].ScanPrecursorMass,
massdiff = (items[i].ScanPrecursorMass - items[i].PeptideMonisotopicMass.Value - crosslinkerDeadEndMass).ToString(),
xlink_typeSpecified = true,
xlink_type = pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlink_type.na,
modification_info = new pepXML.Generated.modInfoDataType {
mod_aminoacid_mass = mods.ToArray()
},
search_score = new pepXML.Generated.nameValueType[]
{
new pepXML.Generated.nameValueType {
name = "xlTotalScore", value = items[i].XLTotalScore.ToString()
},
new pepXML.Generated.nameValueType {
name = "Qvalue", value = items[i].FdrInfo.QValue.ToString()
}
},
};
searchHits.Add(searchHit);
}
else if (items[i].CrossType == PsmCrossType.Inter || items[i].CrossType == PsmCrossType.Intra || items[i].CrossType == PsmCrossType.Cross)
{
var betaPeptide = items[i].BetaPeptide.BestMatchingPeptides.First().Peptide;
var modsBeta = new List <pepXML.Generated.modInfoDataTypeMod_aminoacid_mass>();
foreach (var mod in betaPeptide.AllModsOneIsNterminus)
{
var modBeta = new pepXML.Generated.modInfoDataTypeMod_aminoacid_mass
{
mass = mod.Value.MonoisotopicMass.Value,
// convert from one-based to zero-based (N-term is zero in the pepXML output)
position = (mod.Key - 1).ToString()
};
modsBeta.Add(modBeta);
}
var alpha = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlinkLinked_peptide
{
peptide = alphaPeptide.BaseSequence,
peptide_prev_aa = alphaPeptide.PreviousAminoAcid.ToString(),
peptide_next_aa = alphaPeptide.NextAminoAcid.ToString(),
protein = alphaPeptide.Protein.Accession,
num_tot_proteins = 1,
calc_neutral_pep_mass = (float)items[i].PeptideMonisotopicMass.Value,
complement_mass = (float)(items[i].ScanPrecursorMass - alphaPeptide.MonoisotopicMass),
designation = "alpha",
modification_info = new pepXML.Generated.modInfoDataType {
mod_aminoacid_mass = mods.ToArray()
},
xlink_score = new pepXML.Generated.nameValueType[]
{
new pepXML.Generated.nameValueType {
name = "xlscore", value = items[i].XLTotalScore.ToString()
},
new pepXML.Generated.nameValueType {
name = "link", value = items[i].LinkPositions.First().ToString()
},
}
};
var beta = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlinkLinked_peptide
{
peptide = betaPeptide.BaseSequence,
peptide_prev_aa = betaPeptide.PreviousAminoAcid.ToString(),
peptide_next_aa = betaPeptide.NextAminoAcid.ToString(),
protein = betaPeptide.Protein.Accession,
num_tot_proteins = 1,
calc_neutral_pep_mass = (float)betaPeptide.MonoisotopicMass,
complement_mass = (float)(items[i].ScanPrecursorMass - betaPeptide.MonoisotopicMass),
designation = "beta",
modification_info = new pepXML.Generated.modInfoDataType {
mod_aminoacid_mass = modsBeta.ToArray()
},
xlink_score = new pepXML.Generated.nameValueType[]
{
new pepXML.Generated.nameValueType {
name = "xlscore", value = items[i].BetaPeptide.Score.ToString()
},
new pepXML.Generated.nameValueType {
name = "link", value = items[i].BetaPeptide.LinkPositions.First().ToString()
},
}
};
var cross = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlinkLinked_peptide[2] {
alpha, beta
};
var searchHit = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hit
{
hit_rank = 1,
peptide = "-",
peptide_prev_aa = "-",
peptide_next_aa = "-",
protein = "-",
num_tot_proteins = 1,
calc_neutral_pep_mass = (float)items[i].ScanPrecursorMass,
massdiff = (items[i].ScanPrecursorMass - betaPeptide.MonoisotopicMass - alphaPeptide.MonoisotopicMass - crosslinker.TotalMass).ToString(),
xlink_typeSpecified = true,
xlink_type = pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlink_type.xl,
xlink = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlink
{
identifier = crosslinker.CrosslinkerName,
mass = (float)crosslinker.TotalMass,
linked_peptide = cross
},
search_score = new pepXML.Generated.nameValueType[]
{
new pepXML.Generated.nameValueType {
name = "xlTotalScore", value = items[i].XLTotalScore.ToString()
},
new pepXML.Generated.nameValueType {
name = "Qvalue", value = items[i].FdrInfo.QValue.ToString()
}
}
};
searchHits.Add(searchHit);
}
else if (items[i].CrossType == PsmCrossType.Loop)
{
var thePeptide = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlinkLinked_peptide
{
xlink_score = new pepXML.Generated.nameValueType[]
{
new pepXML.Generated.nameValueType {
name = "link", value = items[i].LinkPositions.First().ToString()
},
new pepXML.Generated.nameValueType {
name = "link", value = items[i].LinkPositions[1].ToString()
}
}
};
var cross = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlinkLinked_peptide[1] {
thePeptide
};
var searchHit = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hit
{
hit_rank = 1,
peptide = alphaPeptide.BaseSequence,
peptide_prev_aa = alphaPeptide.PreviousAminoAcid.ToString(),
peptide_next_aa = alphaPeptide.NextAminoAcid.ToString(),
protein = alphaPeptide.Protein.Accession,
num_tot_proteins = 1,
calc_neutral_pep_mass = (float)items[i].ScanPrecursorMass,
massdiff = (items[i].ScanPrecursorMass - alphaPeptide.MonoisotopicMass - crosslinker.LoopMass).ToString(),
xlink_typeSpecified = true,
xlink_type = pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlink_type.loop,
modification_info = new pepXML.Generated.modInfoDataType {
mod_aminoacid_mass = mods.ToArray()
},
xlink = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlink
{
identifier = crosslinker.CrosslinkerName,
mass = (float)crosslinker.TotalMass,
linked_peptide = cross
},
search_score = new pepXML.Generated.nameValueType[]
{
new pepXML.Generated.nameValueType {
name = "xlTotalScore", value = items[i].XLTotalScore.ToString()
},
new pepXML.Generated.nameValueType {
name = "Qvalue", value = items[i].FdrInfo.QValue.ToString()
}
}
};
searchHits.Add(searchHit);
}
}
for (int i = 0; i < items.Count; i++)
{
_pepxml.msms_run_summary[0].spectrum_query[i] = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_query()
{
spectrum = fileNameNoExtension + "." + items[i].ScanNumber.ToString(),
start_scan = Convert.ToUInt32(items[i].ScanNumber),
end_scan = Convert.ToUInt32(items[i].ScanNumber),
precursor_neutral_mass = (float)items[i].ScanPrecursorMass,
assumed_charge = items[i].ScanPrecursorCharge.ToString(),
index = Convert.ToUInt32(i + 1),
retention_time_sec = (float)(items[i].ScanRetentionTime * 60),
search_result = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_result[1]
{
new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_result
{
search_hit = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hit[1]
{
searchHits[i]
}
}
}
};
}
TextWriter writer = new StreamWriter(Path.Combine(outputFolder, fileName + ".pep.XML"));
_indexedSerializer.Serialize(writer, _pepxml);
writer.Close();
FinishedWritingFile(Path.Combine(outputFolder, fileName + ".pep.XML"), nestedIds);
}
public static void WritePepXml(List <PeptideSpectralMatch> psms, List <DbForTask> database, List <ModificationWithMass> variableModifications, List <ModificationWithMass> fixedModifications, CommonParameters CommonParameters, string outputPath, double qValueFilter)
{
// TODO: needs a unit test
psms = psms.Where(p => p.FdrInfo.QValue <= qValueFilter && p.FdrInfo.QValueNotch < qValueFilter).ToList();
if (!psms.Any())
{
return;
}
XmlSerializer _indexedSerializer = new XmlSerializer(typeof(pepXML.Generated.msms_pipeline_analysis));
var _pepxml = new pepXML.Generated.msms_pipeline_analysis();
_pepxml.date = DateTime.Now;
_pepxml.summary_xml = psms[0].FullFilePath + ".pep.XML";
string proteaseNC = string.Join(string.Empty, CommonParameters.DigestionParams.Protease.SequencesPreventingCleavage);
string proteaseC = string.Join(string.Empty, CommonParameters.DigestionParams.Protease.SequencesInducingCleavage);
string fileNameNoExtension = Path.GetFileNameWithoutExtension(psms[0].FullFilePath);
string filePathNoExtension = Path.ChangeExtension(psms[0].FullFilePath, null);
var para = new List <pepXML.Generated.nameValueType>();
{
para.Add(new pepXML.Generated.nameValueType {
name = "threads", value = CommonParameters.MaxThreadsToUsePerFile.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "database", value = database.First().FilePath
});
para.Add(new pepXML.Generated.nameValueType {
name = "MS_data_file", value = psms[0].FullFilePath
});
para.Add(new pepXML.Generated.nameValueType {
name = "MaxMissed Cleavages", value = CommonParameters.DigestionParams.MaxMissedCleavages.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Protease", value = CommonParameters.DigestionParams.Protease.Name
});
para.Add(new pepXML.Generated.nameValueType {
name = "Initiator Methionine", value = CommonParameters.DigestionParams.InitiatorMethionineBehavior.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Max Modification Isoforms", value = CommonParameters.DigestionParams.MaxModificationIsoforms.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Min Peptide Len", value = CommonParameters.DigestionParams.MinPeptideLength.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Max Peptide Len", value = CommonParameters.DigestionParams.MaxPeptideLength.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Product Mass Tolerance", value = CommonParameters.ProductMassTolerance.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Ions to search", value = "B " + CommonParameters.BIons.ToString() + " Y " + CommonParameters.YIons.ToString() + " C " + CommonParameters.CIons.ToString() + " Z " + CommonParameters.ZdotIons.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Q-value Filter", value = CommonParameters.QValueOutputFilter.ToString()
});
foreach (var item in fixedModifications)
{
para.Add(new pepXML.Generated.nameValueType {
name = "Fixed Modifications: " + item.id, value = item.monoisotopicMass.ToString()
});
}
foreach (var item in variableModifications)
{
para.Add(new pepXML.Generated.nameValueType {
name = "Variable Modifications: " + item.id, value = item.monoisotopicMass.ToString()
});
}
para.Add(new pepXML.Generated.nameValueType {
name = "Localize All Modifications", value = "true"
});
}
_pepxml.msms_run_summary = new pepXML.Generated.msms_pipeline_analysisMsms_run_summary[1]
{
new pepXML.Generated.msms_pipeline_analysisMsms_run_summary
{
base_name = filePathNoExtension,
raw_data_type = "raw",
raw_data = ".mzML", //TODO: use file format of spectra file used
sample_enzyme = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySample_enzyme()
{
name = CommonParameters.DigestionParams.Protease.Name,
specificity = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySample_enzymeSpecificity[1]
{
new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySample_enzymeSpecificity
{
cut = proteaseC,
no_cut = proteaseNC,
}
}
},
search_summary = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySearch_summary[1]
{
new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySearch_summary
{
base_name = filePathNoExtension,
// TODO: get MetaMorpheus recognized as a search engine type
//search_engine = pepXML.Generated.engineType.MetaMorpheus
search_engine_version = GlobalVariables.MetaMorpheusVersion,
precursor_mass_type = pepXML.Generated.massType.monoisotopic,
fragment_mass_type = pepXML.Generated.massType.monoisotopic,
search_id = 1,
//generate database information
//TODO: multiple databases
search_database = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySearch_summarySearch_database
{
local_path = database.First().FilePath,
type = pepXML.Generated.msms_pipeline_analysisMsms_run_summarySearch_summarySearch_databaseType.AA,
},
enzymatic_search_constraint = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySearch_summaryEnzymatic_search_constraint
{
enzyme = CommonParameters.DigestionParams.Protease.Name,
max_num_internal_cleavages = CommonParameters.DigestionParams.MaxMissedCleavages.ToString(),
},
parameter = para.ToArray()
}
},
}
};
_pepxml.msms_run_summary[0].spectrum_query = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_query[psms.Count];
var searchHits = new List <pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hit>();
foreach (var psm in psms)
{
PeptideWithSetModifications peptide = psm.CompactPeptides.First().Value.Item2.First();
var mods = new List <pepXML.Generated.modInfoDataTypeMod_aminoacid_mass>();
foreach (var mod in peptide.AllModsOneIsNterminus)
{
var pepXmlMod = new pepXML.Generated.modInfoDataTypeMod_aminoacid_mass
{
mass = mod.Value.monoisotopicMass,
position = (mod.Key - 1).ToString()
};
mods.Add(pepXmlMod);
}
var proteinAccessions = psm.CompactPeptides.SelectMany(b => b.Value.Item2).Select(b => b.Protein.Accession).Distinct();
var searchHit = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hit
{
// TODO: handle PSM ambiguity if pepXML supports it (base sequence, mod localization, protein)
// TODO: add target/decoy/contaminant designation for each PSM
// TODO: add amino acid substitution
hit_rank = 1,
peptide = ((psm.BaseSequence != null) ? psm.BaseSequence : "Ambiguous"),
peptide_prev_aa = peptide.PreviousAminoAcid.ToString(),
peptide_next_aa = peptide.NextAminoAcid.ToString(),
protein = ((peptide.Protein.Accession != null) ? peptide.Protein.Accession : string.Join("|", proteinAccessions)),
num_tot_proteins = (uint)proteinAccessions.Count(),
calc_neutral_pep_mass = (float)((psm.PeptideMonisotopicMass != null) ? psm.PeptideMonisotopicMass : float.NaN),
massdiff = ((psm.PeptideMonisotopicMass != null) ? (psm.ScanPrecursorMass - psm.PeptideMonisotopicMass.Value).ToString() : "Ambiguous"),
modification_info = (mods.Count == 0 ? new pepXML.Generated.modInfoDataType {
mod_aminoacid_mass = mods.ToArray()
} : null),
search_score = new pepXML.Generated.nameValueType[]
{
new pepXML.Generated.nameValueType {
name = "Score", value = psm.Score.ToString()
},
new pepXML.Generated.nameValueType {
name = "Qvalue", value = psm.FdrInfo.QValue.ToString()
}
},
};
searchHits.Add(searchHit);
}
for (int i = 0; i < psms.Count; i++)
{
_pepxml.msms_run_summary[0].spectrum_query[i] = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_query()
{
spectrum = fileNameNoExtension + "." + psms[i].ScanNumber.ToString(),
start_scan = Convert.ToUInt32(psms[i].ScanNumber),
end_scan = Convert.ToUInt32(psms[i].ScanNumber),
precursor_neutral_mass = (float)psms[i].ScanPrecursorMass,
assumed_charge = psms[i].ScanPrecursorCharge.ToString(),
index = Convert.ToUInt32(i + 1),
retention_time_sec = (float)(psms[i].ScanRetentionTime * 60),
search_result = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_result[1]
{
new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_result
{
search_hit = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hit[1]
{
searchHits[i]
}
}
}
};
}
TextWriter writer = new StreamWriter(Path.Combine(outputPath));
_indexedSerializer.Serialize(writer, _pepxml);
writer.Close();
}
private void WritePepXML_xl(List <PsmCross> items, List <DbForTask> dbFilenameList, List <ModificationWithMass> variableModifications, List <ModificationWithMass> fixedModifications, List <string> localizeableModificationTypes, string outputFolder, string fileName, List <string> nestedIds)
{
XmlSerializer _indexedSerializer = new XmlSerializer(typeof(pepXML.Generated.msms_pipeline_analysis));
var _pepxml = new pepXML.Generated.msms_pipeline_analysis();
#region Add element to pepXML
_pepxml.date = DateTime.Now;
_pepxml.summary_xml = items[0].FullFilePath + ".pep.xml";
string proteaseC = ""; string proteaseNC = "";
foreach (var x in CommonParameters.DigestionParams.Protease.SequencesInducingCleavage)
{
proteaseC += x;
}
foreach (var x in CommonParameters.DigestionParams.Protease.SequencesPreventingCleavage)
{
proteaseNC += x;
}
CrosslinkerTypeClass crosslinker = new CrosslinkerTypeClass().SelectCrosslinker(XlSearchParameters.CrosslinkerType);
var proteinList = dbFilenameList.SelectMany(b => LoadProteinDb(b.FilePath, true, XlSearchParameters.DecoyType, localizeableModificationTypes, b.IsContaminant, out Dictionary <string, Modification> unknownModifications)).ToList();
uint proteinTot = Convert.ToUInt32(proteinList.Count);
string fileNameNoExtension = Path.GetFileNameWithoutExtension(items[0].FullFilePath);
string filePathNoExtension = Path.ChangeExtension(items[0].FullFilePath, null);
var para = new List <pepXML.Generated.nameValueType>();
{
para.Add(new pepXML.Generated.nameValueType {
name = "threads", value = ""
});
para.Add(new pepXML.Generated.nameValueType {
name = "database", value = dbFilenameList[0].FilePath
});
para.Add(new pepXML.Generated.nameValueType {
name = "MS_data_file", value = items[0].FullFilePath
});
para.Add(new pepXML.Generated.nameValueType {
name = "Search with All Possible Beta Peptides", value = XlSearchParameters.CrosslinkSearchWithAllBeta.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Cross-link Precusor Mass Tolence", value = XlSearchParameters.XlPrecusorMsTl.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Cross-linker Type", value = crosslinker.CrosslinkerName
});
para.Add(new pepXML.Generated.nameValueType {
name = "Cross-linker mass", value = crosslinker.TotalMass.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Cross-linker cleavable", value = crosslinker.Cleavable.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Cross-linker cleavable long mass", value = crosslinker.CleaveMassLong.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Cross-linker cleavable short mass", value = crosslinker.CleaveMassShort.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Cross-linker xl site", value = crosslinker.CrosslinkerModSite.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Generate decoy proteins", value = XlSearchParameters.DecoyType.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "MaxMissed Cleavages", value = CommonParameters.DigestionParams.MaxMissedCleavages.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Protease", value = CommonParameters.DigestionParams.Protease.Name
});
para.Add(new pepXML.Generated.nameValueType {
name = "Initiator Methionine", value = CommonParameters.DigestionParams.InitiatorMethionineBehavior.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Max Modification Isoforms", value = CommonParameters.DigestionParams.MaxModificationIsoforms.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Min Peptide Len", value = CommonParameters.DigestionParams.MinPeptideLength.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Max Peptide Len", value = CommonParameters.DigestionParams.MaxPeptideLength.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Product Mass Tolerance", value = CommonParameters.ProductMassTolerance.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Ions to search", value = "B " + CommonParameters.BIons.ToString() + " Y " + CommonParameters.YIons.ToString() + " C " + CommonParameters.CIons.ToString() + " Z " + CommonParameters.ZdotIons.ToString()
});
para.Add(new pepXML.Generated.nameValueType {
name = "Allowed Beta Precusor Mass Difference", value = XlSearchParameters.XlBetaPrecusorMsTl.ToString()
});
foreach (var item in fixedModifications)
{
para.Add(new pepXML.Generated.nameValueType {
name = "Fixed Modifications: " + item.id, value = item.monoisotopicMass.ToString()
});
}
foreach (var item in variableModifications)
{
para.Add(new pepXML.Generated.nameValueType {
name = "Variable Modifications: " + item.id, value = item.monoisotopicMass.ToString()
});
}
para.Add(new pepXML.Generated.nameValueType {
name = "Localize All Modifications", value = CommonParameters.LocalizeAll.ToString()
});
}
_pepxml.msms_run_summary = new pepXML.Generated.msms_pipeline_analysisMsms_run_summary[1]
{
new pepXML.Generated.msms_pipeline_analysisMsms_run_summary
{
base_name = filePathNoExtension,
raw_data_type = "raw",
raw_data = ".mzML",
sample_enzyme = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySample_enzyme()
{
name = CommonParameters.DigestionParams.Protease.Name,
specificity = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySample_enzymeSpecificity[1]
{
new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySample_enzymeSpecificity
{
cut = proteaseC,
no_cut = proteaseNC,
}
}
},
search_summary = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySearch_summary[1]
{
new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySearch_summary
{
base_name = filePathNoExtension,
//search_engine = pepXML.Generated.engineType.Kojak,
search_engine_version = GlobalVariables.MetaMorpheusVersion,
precursor_mass_type = pepXML.Generated.massType.monoisotopic,
fragment_mass_type = pepXML.Generated.massType.monoisotopic,
search_id = 1,
search_database = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySearch_summarySearch_database
{
local_path = dbFilenameList[0].FilePath,
type = pepXML.Generated.msms_pipeline_analysisMsms_run_summarySearch_summarySearch_databaseType.AA,
},
enzymatic_search_constraint = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySearch_summaryEnzymatic_search_constraint
{
enzyme = CommonParameters.DigestionParams.Protease.Name,
max_num_internal_cleavages = CommonParameters.DigestionParams.MaxMissedCleavages.ToString(),
//min_number_termini = "2"
},
parameter = para.ToArray()
}
},
}
};
_pepxml.msms_run_summary[0].spectrum_query = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_query[items.Count];
var searchHits = new List <pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hit>();
for (int i = 0; i < items.Count; i++)
{
int modsFixedNum = items[i].CompactPeptides.First().Value.Item2.First().allModsOneIsNterminus.Count;
var mods = new List <pepXML.Generated.modInfoDataTypeMod_aminoacid_mass> ();
for (int j = 0; j < modsFixedNum; j++)
{
var mod = new pepXML.Generated.modInfoDataTypeMod_aminoacid_mass
{
mass = items[i].CompactPeptides.First().Value.Item2.First().allModsOneIsNterminus.Values.Select(p => p.monoisotopicMass).ToList()[j],
position = items[i].CompactPeptides.First().Value.Item2.First().allModsOneIsNterminus.Keys.ToList()[j].ToString()
};
mods.Add(mod);
}
if (items[i].CrossType == PsmCrossType.Singe)
{
var searchHit = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hit
{
hit_rank = 1,
peptide = items[i].BaseSequence,
peptide_prev_aa = items[i].CompactPeptides.First().Value.Item2.First().PreviousAminoAcid.ToString(),
peptide_next_aa = items[i].CompactPeptides.First().Value.Item2.First().NextAminoAcid.ToString(),
protein = items[i].CompactPeptides.First().Value.Item2.First().Protein.Accession,
num_tot_proteins = 1,
calc_neutral_pep_mass = (float)items[i].ScanPrecursorMonoisotopicPeakMz * items[i].ScanPrecursorCharge,
massdiff = (items[i].ScanPrecursorMass - items[i].PeptideMonisotopicMass.Value).ToString(),
xlink_typeSpecified = true,
xlink_type = pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlink_type.na,
modification_info = new pepXML.Generated.modInfoDataType {
mod_aminoacid_mass = mods.ToArray()
},
search_score = new pepXML.Generated.nameValueType[]
{
new pepXML.Generated.nameValueType {
name = "xlTotalScore", value = items[i].XLTotalScore.ToString()
},
new pepXML.Generated.nameValueType {
name = "Qvalue", value = items[i].FdrInfo.QValue.ToString()
}
},
};
searchHits.Add(searchHit);
}
if (items[i].CrossType == PsmCrossType.DeadEnd || items[i].CrossType == PsmCrossType.DeadEndH2O || items[i].CrossType == PsmCrossType.DeadEndNH2 || items[i].CrossType == PsmCrossType.DeadEndTris)
{
double crosslinkerDeadEndMass = 0;
switch (items[i].CrossType)
{
case PsmCrossType.DeadEndNH2:
crosslinkerDeadEndMass = crosslinker.DeadendMassNH2;
break;
case PsmCrossType.DeadEndTris:
crosslinkerDeadEndMass = crosslinker.DeadendMassTris;
break;
default:
crosslinkerDeadEndMass = crosslinker.DeadendMassH2O;
break;
}
var mod = new pepXML.Generated.modInfoDataTypeMod_aminoacid_mass {
mass = crosslinkerDeadEndMass, position = items[i].XlPos.ToString()
};
mods.Add(mod);
var searchHit = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hit
{
hit_rank = 1,
peptide = items[i].BaseSequence,
peptide_prev_aa = items[i].CompactPeptides.First().Value.Item2.First().PreviousAminoAcid.ToString(),
peptide_next_aa = items[i].CompactPeptides.First().Value.Item2.First().NextAminoAcid.ToString(),
protein = items[i].CompactPeptides.First().Value.Item2.First().Protein.Accession,
num_tot_proteins = 1,
calc_neutral_pep_mass = (float)items[i].ScanPrecursorMonoisotopicPeakMz * items[i].ScanPrecursorCharge,
massdiff = (items[i].ScanPrecursorMass - items[i].PeptideMonisotopicMass.Value - crosslinkerDeadEndMass).ToString(),
xlink_typeSpecified = true,
xlink_type = pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlink_type.na,
modification_info = new pepXML.Generated.modInfoDataType {
mod_aminoacid_mass = mods.ToArray()
},
search_score = new pepXML.Generated.nameValueType[]
{
new pepXML.Generated.nameValueType {
name = "xlTotalScore", value = items[i].XLTotalScore.ToString()
},
new pepXML.Generated.nameValueType {
name = "Qvalue", value = items[i].FdrInfo.QValue.ToString()
}
},
};
searchHits.Add(searchHit);
}
if (items[i].CrossType == PsmCrossType.Inter || items[i].CrossType == PsmCrossType.Intra || items[i].CrossType == PsmCrossType.Cross)
{
int modsFixedNumBeta = items[i].BetaPsmCross.CompactPeptides.First().Value.Item2.First().allModsOneIsNterminus.Count;
var modsBeta = new List <pepXML.Generated.modInfoDataTypeMod_aminoacid_mass>();
for (int j = 0; j < modsFixedNumBeta; j++)
{
var modBeta = new pepXML.Generated.modInfoDataTypeMod_aminoacid_mass
{
mass = items[i].BetaPsmCross.CompactPeptides.First().Value.Item2.First().allModsOneIsNterminus.Values.Select(p => p.monoisotopicMass).ToList()[j],
position = items[i].BetaPsmCross.CompactPeptides.First().Value.Item2.First().allModsOneIsNterminus.Keys.ToList()[j].ToString()
};
modsBeta.Add(modBeta);
}
var alpha = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlinkLinked_peptide
{
peptide = items[i].BaseSequence,
peptide_prev_aa = items[i].CompactPeptides.First().Value.Item2.First().PreviousAminoAcid.ToString(),
peptide_next_aa = items[i].CompactPeptides.First().Value.Item2.First().NextAminoAcid.ToString(),
protein = items[i].CompactPeptides.First().Value.Item2.First().Protein.Accession,
num_tot_proteins = 1,
calc_neutral_pep_mass = (float)items[i].PeptideMonisotopicMass.Value,
complement_mass = (float)(items[i].ScanPrecursorMass - items[i].PeptideMonisotopicMass.Value),
designation = "alpha",
modification_info = new pepXML.Generated.modInfoDataType {
mod_aminoacid_mass = mods.ToArray()
},
xlink_score = new pepXML.Generated.nameValueType[]
{
new pepXML.Generated.nameValueType {
name = "xlscore", value = items[i].XLBestScore.ToString()
},
new pepXML.Generated.nameValueType {
name = "link", value = items[i].XlPos.ToString()
},
}
};
var beta = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlinkLinked_peptide
{
peptide = items[i].BetaPsmCross.BaseSequence,
peptide_prev_aa = items[i].BetaPsmCross.CompactPeptides.First().Value.Item2.First().PreviousAminoAcid.ToString(),
peptide_next_aa = items[i].BetaPsmCross.CompactPeptides.First().Value.Item2.First().NextAminoAcid.ToString(),
protein = items[i].BetaPsmCross.CompactPeptides.First().Value.Item2.First().Protein.Accession,
num_tot_proteins = 1,
calc_neutral_pep_mass = (float)items[i].BetaPsmCross.PeptideMonisotopicMass.Value,
complement_mass = (float)(items[i].ScanPrecursorMass - items[i].PeptideMonisotopicMass.Value),
designation = "beta",
modification_info = new pepXML.Generated.modInfoDataType {
mod_aminoacid_mass = modsBeta.ToArray()
},
xlink_score = new pepXML.Generated.nameValueType[]
{
new pepXML.Generated.nameValueType {
name = "xlscore", value = items[i].BetaPsmCross.XLBestScore.ToString()
},
new pepXML.Generated.nameValueType {
name = "link", value = items[i].BetaPsmCross.XlPos.ToString()
},
}
};
var cross = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlinkLinked_peptide[2] {
alpha, beta
};
var searchHit = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hit
{
hit_rank = 1,
peptide = "-",
peptide_prev_aa = "-",
peptide_next_aa = "-",
protein = "-",
num_tot_proteins = 1,
calc_neutral_pep_mass = (float)items[i].ScanPrecursorMonoisotopicPeakMz * items[i].ScanPrecursorCharge,
massdiff = (items[i].ScanPrecursorMass - items[i].BetaPsmCross.PeptideMonisotopicMass.Value - items[i].PeptideMonisotopicMass.Value - crosslinker.TotalMass).ToString(),
xlink_typeSpecified = true,
xlink_type = pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlink_type.xl,
xlink = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlink
{
identifier = crosslinker.CrosslinkerName,
mass = (float)crosslinker.TotalMass,
linked_peptide = cross
},
search_score = new pepXML.Generated.nameValueType[]
{
new pepXML.Generated.nameValueType {
name = "xlTotalScore", value = items[i].XLTotalScore.ToString()
},
new pepXML.Generated.nameValueType {
name = "Qvalue", value = items[i].FdrInfo.QValue.ToString()
}
}
};
searchHits.Add(searchHit);
}
if (items[i].CrossType == PsmCrossType.Loop)
{
var thePeptide = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlinkLinked_peptide
{
xlink_score = new pepXML.Generated.nameValueType[]
{
new pepXML.Generated.nameValueType {
name = "link", value = items[i].XlPos.ToString()
},
new pepXML.Generated.nameValueType {
name = "link", value = items[i].XlPos2.ToString()
}
}
};
var cross = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlinkLinked_peptide[1] {
thePeptide
};
var searchHit = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hit
{
hit_rank = 1,
peptide = items[i].BaseSequence,
peptide_prev_aa = items[i].CompactPeptides.First().Value.Item2.First().PreviousAminoAcid.ToString(),
peptide_next_aa = items[i].CompactPeptides.First().Value.Item2.First().NextAminoAcid.ToString(),
protein = items[i].CompactPeptides.First().Value.Item2.First().Protein.Accession,
num_tot_proteins = 1,
calc_neutral_pep_mass = (float)items[i].ScanPrecursorMonoisotopicPeakMz * items[i].ScanPrecursorCharge,
massdiff = (items[i].ScanPrecursorMass - items[i].PeptideMonisotopicMass.Value - crosslinker.LoopMass).ToString(),
xlink_typeSpecified = true,
xlink_type = pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlink_type.loop,
modification_info = new pepXML.Generated.modInfoDataType {
mod_aminoacid_mass = mods.ToArray()
},
xlink = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hitXlink
{
identifier = crosslinker.CrosslinkerName,
mass = (float)crosslinker.TotalMass,
linked_peptide = cross
},
search_score = new pepXML.Generated.nameValueType[]
{
new pepXML.Generated.nameValueType {
name = "xlTotalScore", value = items[i].XLTotalScore.ToString()
},
new pepXML.Generated.nameValueType {
name = "Qvalue", value = items[i].FdrInfo.QValue.ToString()
}
}
};
searchHits.Add(searchHit);
}
}
for (int i = 0; i < items.Count; i++)
{
_pepxml.msms_run_summary[0].spectrum_query[i] = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_query()
{
spectrum = fileNameNoExtension + "." + items[i].ScanNumber.ToString(),
start_scan = Convert.ToUInt32(items[i].ScanNumber),
end_scan = Convert.ToUInt32(items[i].ScanNumber),
precursor_neutral_mass = (float)items[i].ScanPrecursorMonoisotopicPeakMz * items[i].ScanPrecursorCharge,
assumed_charge = items[i].ScanPrecursorCharge.ToString(),
index = Convert.ToUInt32(i + 1),
retention_time_sec = (float)items[i].ScanRetentionTime,
search_result = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_result[1]
{
new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_result
{
search_hit = new pepXML.Generated.msms_pipeline_analysisMsms_run_summarySpectrum_querySearch_resultSearch_hit[1]
{
searchHits[i]
}
}
}
};
}
#endregion Add element to pepXML
TextWriter writer = new StreamWriter(Path.Combine(outputFolder, fileName + ".pep.xml"));
_indexedSerializer.Serialize(writer, _pepxml);
writer.Close();
SucessfullyFinishedWritingFile(Path.Combine(outputFolder, fileName + ".pep.xml"), nestedIds);
}
