public void TestUnimodNameMapping()
{
var termGroup = CV.TermAccessionLookup["UNIMOD"].Where(x => x.Value != CV.CVID.UNIMOD_unimod_root_node);
foreach (var term in termGroup)
{
var info = CV.TermData[term.Value];
var mod = new ModificationObj(CV.CVID.CVID_Unknown, info.Name, 5, 42);
if (mod.CVParams.Count == 1)
{
Assert.AreEqual(term.Value, mod.CVParams[0].Cvid, "Enums do not match!");
}
else
{
var foundMatch = false;
foreach (var cvParam in mod.CVParams)
{
if (cvParam.Cvid.Equals(term.Value))
{
foundMatch = true;
break;
}
}
if (!foundMatch)
{
Assert.Fail("No matching enum found! {0}", term.Value);
}
}
}
}
public void WriteResultsToMzid(IEnumerable <DatabaseSearchResultData> matches, string outputFilePath)
{
var datasetName = Path.GetFileNameWithoutExtension(outputFilePath);
var creator = new IdentDataCreator("MSPathFinder_" + datasetName, "MSPathFinder_" + datasetName);
var soft = creator.AddAnalysisSoftware("Software_1", "MSPathFinder", System.Reflection.Assembly.GetCallingAssembly().GetName().Version.ToString(), CV.CVID.MS_MSPathFinder, "MSPathFinder");
var settings = creator.AddAnalysisSettings(soft, "Settings_1", CV.CVID.MS_ms_ms_search);
var searchDb = creator.AddSearchDatabase(database.GetFastaFilePath(), database.GetNumEntries(), Path.GetFileNameWithoutExtension(database.GetFastaFilePath()), CV.CVID.CVID_Unknown,
CV.CVID.MS_FASTA_format);
if (options.TargetDecoySearchMode.HasFlag(DatabaseSearchMode.Decoy))
{
searchDb.CVParams.AddRange(new CVParamObj[]
{
new CVParamObj()
{
Cvid = CV.CVID.MS_DB_composition_target_decoy,
},
new CVParamObj()
{
Cvid = CV.CVID.MS_decoy_DB_accession_regexp, Value = "^XXX",
},
//new CVParamObj() { Cvid = CV.CVID.MS_decoy_DB_type_reverse, },
new CVParamObj()
{
Cvid = CV.CVID.MS_decoy_DB_type_randomized,
},
});
}
// store the settings...
CreateMzidSettings(settings);
var path = options.SpecFilePath;
var run = lcmsRun as PbfLcMsRun;
if (run != null)
{
var rawPath = run.RawFilePath;
if (!string.IsNullOrWhiteSpace(rawPath))
{
path = rawPath;
}
}
// TODO: fix this to match correctly to the original file - May need to modify the PBF format to add an input format specifier
// TODO: Should probably? request a CV Term for the PBF format?
var nativeIdFormat = lcmsRun.NativeIdFormat;
if (nativeIdFormat == CV.CVID.CVID_Unknown)
{
nativeIdFormat = CV.CVID.MS_scan_number_only_nativeID_format;
}
var specData = creator.AddSpectraData(path, datasetName, nativeIdFormat, lcmsRun.NativeFormat);
// Get the search modifications as they were passed into the AminoAcidSet constructor, so we can retrieve masses from them
var modDict = new Dictionary <string, Modification>();
foreach (var mod in options.AminoAcidSet.SearchModifications)
{
if (!modDict.ContainsKey(mod.Modification.Name))
{
modDict.Add(mod.Modification.Name, mod.Modification);
}
else if (!modDict[mod.Modification.Name].Composition.Equals(mod.Modification.Composition))
{
throw new System.Exception(
"ERROR: Cannot have modifications with the same name and different composition/mass! Fix input modifications! Duplicated modification name: " +
mod.Modification.Name);
}
}
foreach (var match in matches)
{
var scanNum = match.ScanNum;
var spec = lcmsRun.GetSpectrum(scanNum, false);
var matchIon = new Ion(Composition.Parse(match.Composition), match.Charge);
var nativeId = spec.NativeId;
if (string.IsNullOrWhiteSpace(spec.NativeId))
{
nativeId = "scan=" + spec.ScanNum;
}
var specIdent = creator.AddSpectrumIdentification(specData, nativeId, spec.ElutionTime, match.MostAbundantIsotopeMz,
match.Charge, 1, double.NaN);
specIdent.CalculatedMassToCharge = matchIon.GetMonoIsotopicMz();
var pep = new PeptideObj(match.Sequence);
var modText = match.Modifications;
if (!string.IsNullOrWhiteSpace(modText))
{
var mods = modText.Split(',');
foreach (var mod in mods)
{
var tokens = mod.Split(' ');
var modInfo = modDict[tokens[0]];
var modObj = new ModificationObj(CV.CVID.MS_unknown_modification, modInfo.Name, int.Parse(tokens[1]), modInfo.Mass);
pep.Modifications.Add(modObj);
}
}
specIdent.Peptide = pep;
var proteinName = match.ProteinName;
var protLength = match.ProteinLength;
var proteinDescription = match.ProteinDescription;
var dbSeq = new DbSequenceObj(searchDb, protLength, proteinName, proteinDescription);
var start = match.Start;
var end = match.End;
var pepEv = new PeptideEvidenceObj(dbSeq, pep, start, end, match.Pre, match.Post, match.ProteinName.StartsWith("XXX"));
specIdent.AddPeptideEvidence(pepEv);
var probability = match.Probability;
specIdent.CVParams.Add(new CVParamObj()
{
Cvid = CV.CVID.MS_chemical_compound_formula, Value = match.Composition,
});
//specIdent.CVParams.Add(new CVParamObj() { Cvid = CV.CVID.MS_number_of_matched_peaks, Value = match.NumMatchedFragments.ToString(), });
specIdent.CVParams.Add(new CVParamObj()
{
Cvid = CV.CVID.MS_MSPathFinder_RawScore, Value = probability.ToString(CultureInfo.InvariantCulture),
});
specIdent.CVParams.Add(new CVParamObj()
{
Cvid = CV.CVID.MS_MSPathFinder_SpecEValue, Value = match.SpecEValue.ToString(CultureInfo.InvariantCulture),
});
specIdent.CVParams.Add(new CVParamObj()
{
Cvid = CV.CVID.MS_MSPathFinder_EValue, Value = match.EValue.ToString(CultureInfo.InvariantCulture),
});
if (match.HasTdaScores)
{
specIdent.CVParams.Add(new CVParamObj()
{
Cvid = CV.CVID.MS_MSPathFinder_QValue, Value = match.QValue.ToString(CultureInfo.InvariantCulture),
});
specIdent.CVParams.Add(new CVParamObj()
{
Cvid = CV.CVID.MS_MSPathFinder_PepQValue, Value = match.PepQValue.ToString(CultureInfo.InvariantCulture),
});
}
// MS-GF+ similarity: find/add isotope error?
// MS-GF+ similarity: find/add assumed dissociation method?
//specIdent.UserParams.Add(new UserParamObj() {Name = "Assumed Dissociation Method", Value = match.});
}
var identData = creator.GetIdentData();
MzIdentMlReaderWriter.Write(new MzIdentMLType(identData), outputFilePath);
}
private void CreateMzidSettings(SpectrumIdentificationProtocolObj settings)
{
settings.AdditionalSearchParams.Items.AddRange(new ParamBaseObj[]
{
new CVParamObj(CV.CVID.MS_parent_mass_type_mono),
new CVParamObj(CV.CVID.MS_fragment_mass_type_mono),
new UserParamObj()
{
Name = "TargetDecoyApproach", Value = (options.TargetDecoySearchMode == DatabaseSearchMode.Both).ToString()
},
new UserParamObj()
{
Name = "MinSequenceLength", Value = options.MinSequenceLength.ToString()
},
new UserParamObj()
{
Name = "MaxSequenceLength", Value = options.MaxSequenceLength.ToString()
},
new UserParamObj()
{
Name = "MaxNumNTermCleavages", Value = options.MaxNumNTermCleavages.ToString()
},
new UserParamObj()
{
Name = "MaxNumCTermCleavages", Value = options.MaxNumCTermCleavages.ToString()
},
new UserParamObj()
{
Name = "MinPrecursorIonCharge", Value = options.MinPrecursorIonCharge.ToString()
},
new UserParamObj()
{
Name = "MaxPrecursorIonCharge", Value = options.MaxPrecursorIonCharge.ToString()
},
new UserParamObj()
{
Name = "MinProductIonCharge", Value = options.MinProductIonCharge.ToString()
},
new UserParamObj()
{
Name = "MaxProductIonCharge", Value = options.MaxProductIonCharge.ToString()
},
new UserParamObj()
{
Name = "MinSequenceMass", Value = options.MinSequenceMass.ToString(CultureInfo.InvariantCulture)
},
new UserParamObj()
{
Name = "MaxSequenceMass", Value = options.MaxSequenceMass.ToString(CultureInfo.InvariantCulture)
},
new UserParamObj()
{
Name = "PrecursorIonTolerance", Value = options.PrecursorIonTolerance.ToString()
},
new UserParamObj()
{
Name = "ProductIonTolerance", Value = options.ProductIonTolerance.ToString()
},
new UserParamObj()
{
Name = "SearchMode", Value = options.InternalCleavageMode.ToString()
},
new UserParamObj()
{
Name = "NumMatchesPerSpectrum", Value = options.NumMatchesPerSpectrum.ToString()
},
new UserParamObj()
{
Name = "TagBasedSearch", Value = options.TagBasedSearch.ToString()
},
});
var activationMethod = options.ActivationMethod.ToString();
if (options.ActivationMethod == ActivationMethod.Unknown)
{
activationMethod = $"Determined By Spectrum ({options.ActivationMethod})";
}
settings.AdditionalSearchParams.Items.Add(new UserParamObj()
{
Name = "SpecifiedActivationMethod", Value = activationMethod
});
// Add search type, if not a target-deacoy search
if (options.TargetDecoySearchMode != DatabaseSearchMode.Both)
{
settings.AdditionalSearchParams.Items.Add(new UserParamObj()
{
Name = "SearchType", Value = options.TargetDecoySearchMode.ToString()
});
}
// Get the search modifications as they were passed into the AminoAcidSet constructor...
foreach (var mod in options.AminoAcidSet.SearchModifications)
{
var modObj = new SearchModificationObj()
{
FixedMod = mod.IsFixedModification,
MassDelta = (float)mod.Modification.Mass,
Residues = mod.TargetResidue.ToString(),
};
// "*" is used for wildcard residue N-Term or C-Term modifications. mzIdentML standard says that "." should be used instead.
if (modObj.Residues.Contains("*"))
{
modObj.Residues = modObj.Residues.Replace("*", ".");
}
// Really only using this for the modification name parsing for CVParams that exists with ModificationObj
var tempMod = new ModificationObj(CV.CVID.MS_unknown_modification, mod.Modification.Name, 0, modObj.MassDelta);
modObj.CVParams.Add(tempMod.CVParams.First());
if (mod.Location != SequenceLocation.Everywhere)
{
// specificity rules should be added
var rule = new SpecificityRulesListObj();
switch (mod.Location)
{
case SequenceLocation.PeptideNTerm:
rule.CVParams.Add(new CVParamObj(CV.CVID.MS_modification_specificity_peptide_N_term));
break;
case SequenceLocation.PeptideCTerm:
rule.CVParams.Add(new CVParamObj(CV.CVID.MS_modification_specificity_peptide_C_term));
break;
case SequenceLocation.ProteinNTerm:
rule.CVParams.Add(new CVParamObj(CV.CVID.MS_modification_specificity_protein_N_term));
break;
case SequenceLocation.ProteinCTerm:
rule.CVParams.Add(new CVParamObj(CV.CVID.MS_modification_specificity_protein_C_term));
break;
case SequenceLocation.Everywhere:
// not needed, the enclosing if should prevent ever hitting this
break;
default:
// Limited by enum...
break;
}
modObj.SpecificityRules.Add(rule);
}
settings.ModificationParams.Add(modObj);
}
// No enzyme for top-down search
//settings.Enzymes.Enzymes.Add(new EnzymeObj());
settings.ParentTolerances.AddRange(new CVParamObj[]
{
new CVParamObj(CV.CVID.MS_search_tolerance_plus_value, options.PrecursorIonTolerancePpm.ToString(CultureInfo.InvariantCulture))
{
UnitCvid = CV.CVID.UO_parts_per_million
},
new CVParamObj(CV.CVID.MS_search_tolerance_minus_value, options.PrecursorIonTolerancePpm.ToString(CultureInfo.InvariantCulture))
{
UnitCvid = CV.CVID.UO_parts_per_million
},
});
settings.FragmentTolerances.AddRange(new CVParamObj[]
{
new CVParamObj(CV.CVID.MS_search_tolerance_plus_value, options.ProductIonTolerancePpm.ToString(CultureInfo.InvariantCulture))
{
UnitCvid = CV.CVID.UO_parts_per_million
},
new CVParamObj(CV.CVID.MS_search_tolerance_minus_value, options.ProductIonTolerancePpm.ToString(CultureInfo.InvariantCulture))
{
UnitCvid = CV.CVID.UO_parts_per_million
},
});
settings.Threshold.Items.Add(new CVParamObj(CV.CVID.MS_no_threshold));
}
public void CreateMzidFile()
{
var dir = @"F:\MSPathfinder_Tests";
var datasetName = "QC_ShewIntact_16_12AUG16_Bane_16-03-19";
var input = Path.Combine(dir, "QC_ShewIntact_16_12AUG16_Bane_16-03-19_IcTda.tsv");
var dbName = "ID_005435_435B0CDA.fasta";
// Unused: var database = Path.Combine(dir, "ID_005435_435B0CDA.fasta");
var output = Path.Combine(dir, "QC_ShewIntact_16_12AUG16_Bane_16-03-19.mzid");
var creator = new IdentDataCreator("MSPathFinder_" + datasetName, "MSPathFinder_" + datasetName);
// Unused: var soft = creator.AddAnalysisSoftware("Software_1", "MSPathFinder", "1.3", CV.CVID.CVID_Unknown, "MSPathFinder");
// Unused: var settings = creator.AddAnalysisSettings(soft, "Settings_1", CV.CVID.MS_ms_ms_search);
var searchDb = creator.AddSearchDatabase(Path.Combine(dir, dbName), 1000000, dbName, CV.CVID.CVID_Unknown,
CV.CVID.MS_FASTA_format);
var specData = creator.AddSpectraData(Path.Combine(dir, datasetName + ".raw"), datasetName, CV.CVID.MS_Thermo_nativeID_format,
CV.CVID.MS_Thermo_RAW_format);
foreach (var result in ReadMsPathfinderResults(input))
{
var native = "controllerType=0 controllerNumber=1 scan=" + result.Scan;
var spec = creator.AddSpectrumIdentification(specData, native, result.Scan, result.MostAbundantIsotopeMz,
result.Charge, 1, result.MostAbundantIsotopeMz);
var pep = new PeptideObj(result.Sequence);
foreach (var mod in result.Modifications)
{
var modObj = new ModificationObj(CV.CVID.MS_unknown_modification, mod.Item1, mod.Item2);
pep.Modifications.Add(modObj);
}
spec.Peptide = pep;
var dbSeq = new DbSequenceObj(searchDb, result.ProteinLength, result.ProteinName,
result.ProteinDesc);
var pepEv = new PeptideEvidenceObj(dbSeq, pep, result.Start, result.End, result.Pre, result.Post, false);
spec.AddPeptideEvidence(pepEv);
spec.CVParams.Add(new CVParamObj()
{
Cvid = CV.CVID.MS_monoisotopic_mass_OBSOLETE, Value = result.Mass.ToString(CultureInfo.InvariantCulture), UnitCvid = CV.CVID.MS_m_z,
});
spec.CVParams.Add(new CVParamObj()
{
Cvid = CV.CVID.MS_chemical_formula, Value = result.Composition,
});
spec.CVParams.Add(new CVParamObj()
{
Cvid = CV.CVID.MS_number_of_matched_peaks, Value = result.NumMatchedFragments.ToString(),
});
spec.CVParams.Add(new CVParamObj()
{
Cvid = CV.CVID.MS_SEQUEST_probability, Value = result.Probability.ToString(CultureInfo.InvariantCulture),
});
spec.CVParams.Add(new CVParamObj()
{
Cvid = CV.CVID.MS_MS_GF_SpecEValue, Value = result.SpecEValue.ToString(CultureInfo.InvariantCulture),
});
spec.CVParams.Add(new CVParamObj()
{
Cvid = CV.CVID.MS_MS_GF_SpecEValue, Value = result.EValue.ToString(CultureInfo.InvariantCulture),
});
spec.CVParams.Add(new CVParamObj()
{
Cvid = CV.CVID.MS_MS_GF_QValue, Value = result.QValue.ToString(CultureInfo.InvariantCulture),
});
spec.CVParams.Add(new CVParamObj()
{
Cvid = CV.CVID.MS_MS_GF_PepQValue, Value = result.PepQValue.ToString(CultureInfo.InvariantCulture),
});
}
var identData = creator.GetIdentData();
MzIdentMlReaderWriter.Write(new MzIdentMLType(identData), output);
}