public Metadata CreateMetadataDefault(IMatrixData parameters, IMatrixData experiment, IMatrixData search)
{
Metadata mtd = new Metadata(new MZTabDescription(MzTabMode.Complete, MzTabType.Quantification));
List<MsRunImpl> runs = null;
List<StudyVariable> studyvariables = null;
List<Assay> assays = null;
List<Sample> samples = null;
List<Instrument> instruments = null;
GetExperminetValues(null, null, experiment, search, ref runs, ref studyvariables, ref assays, ref samples,
ref instruments);
foreach (var msRun in runs){
mtd.MsRunMap.Add(msRun.Id, msRun);
}
foreach (var studyvariable in studyvariables){
mtd.StudyVariableMap.Add(studyvariable.Id, studyvariable);
}
foreach (var sample in samples){
mtd.SampleMap.Add(sample.Id, sample);
}
foreach (var assay in assays){
mtd.AssayMap.Add(assay.Id, assay);
}
foreach (var instrument in instruments){
mtd.InstrumentMap.Add(instrument.Id, instrument);
}
SplitList<Lib.Model.Param> sampleProcessing = new SplitList<Lib.Model.Param>{
cv.GetParam("enzyme digestion", "SEP"),
cv.GetParam("reversed-phase chromatography", "SEP")
};
//sampleProcessing.Add(_cv.GetParam("ion-exchange chromatography", "SEP"));
mtd.SampleProcessingMap.Add(1, sampleProcessing);
var paramDict = MzTabMatrixUtils.ConvertToParamDict(parameters);
string key = Constants.GetKeywordName(Utils.parameters.fixedMod, paramDict.Keys.ToArray());
if (key != null){
string[] values = paramDict[key].Split(';');
foreach (var mod in values.Select(x => BaseLib.Mol.Tables.Modifications[x])){
int id = mtd.FixedModMap.Count + 1;
mtd.AddFixedModParam(id, cv.GetModificationParam(mod));
mtd.AddFixedModPosition(id, mod.Position.ToString());
mtd.AddFixedModSite(id, StringUtils.Concat(", ", mod.GetSiteArray()));
}
}
key = Constants.GetKeywordName(Utils.parameters.variableMod, paramDict.Keys.ToArray());
if (key != null){
string[] values = paramDict[key].Split(';');
foreach (var mod in values.Select(x => BaseLib.Mol.Tables.Modifications[x])){
int id = mtd.VariableModMap.Count + 1;
mtd.AddVariableModParam(id, cv.GetModificationParam(mod));
mtd.AddVariableModPosition(id, mod.Position.ToString());
mtd.AddVariableModSite(id, StringUtils.Concat(", ", mod.GetSiteArray()));
}
}
string version = Constants.GetKeywordName(Utils.parameters.version, paramDict.Keys.ToArray());
Software software = new Software(1){
Param = cv.GetParam("MaxQuant", "MS", GetParameterString(parameters, version, null))
};
mtd.SoftwareMap.Add(software.Id, software);
software = new Software(2){
Param = cv.GetParam("Andromeda", "MS", GetParameterString(parameters, version, null))
};
mtd.SoftwareMap.Add(software.Id, software);
if (assays.Count > 0){
var tmp = ArrayUtils.UniqueValues(assays.Select(x => x.QuantificationReagent.Name).ToArray());
if (tmp.Length == 1 && tmp.First().Equals("Unlabeled sample")){
mtd.QuantificationMethod = cv.GetParam("label-free proteingroup level quantitation", "MS");
}
else if (tmp.Any(x => x.Contains("SILAC"))){
mtd.QuantificationMethod = cv.GetParam("SILAC quantitation analysis", "MS");
}
}
return mtd;
}
public static void main(string[] args)
{
MZTabDescription tabDescription = new MZTabDescription(MzTabMode.Summary, MzTabType.Identification){
Id = "PRIDE_1234"
};
Metadata mtd = new Metadata(tabDescription);
mtd.Title = "My first test experiment";
mtd.Description = "An experiment investigating the effects of Il-6.";
mtd.AddSampleProcessingParam(1, new CVParam("SEP", "SEP:00173", "SDS PAGE", null));
mtd.AddSampleProcessingParam(2, new CVParam("SEP", "SEP:00142", "enzyme digestion", null));
mtd.AddSampleProcessingParam(2, new CVParam("MS", "MS:1001251", "Trypsin", null));
mtd.AddInstrumentName(1, new CVParam("MS", "MS:100049", "LTQ Orbitrap", null));
mtd.AddInstrumentName(2,
new CVParam("MS", "MS:1000031", "Instrument model",
"name of the instrument not included in the CV"));
mtd.AddInstrumentSource(1, new CVParam("MS", "MS:1000073", "ESI", null));
mtd.AddInstrumentSource(2, new CVParam("MS", "MS:1000598", "ETD", null));
mtd.AddInstrumentAnalyzer(1, new CVParam("MS", "MS:1000291", "linear ion trap", null));
mtd.AddInstrumentAnalyzer(2, new CVParam("MS", "MS:1000484", "orbitrap", null));
mtd.AddInstrumentDetector(1, new CVParam("MS", "MS:1000253", "electron multiplier", null));
mtd.AddInstrumentDetector(2, new CVParam("MS", "MS:1000348", "focal plane collector", null));
mtd.AddSoftwareParam(1, new CVParam("MS", "MS:1001207", "Mascot", "2.3"));
mtd.AddSoftwareParam(2, new CVParam("MS", "MS:1001561", "Scaffold", "1.0"));
mtd.AddSoftwareSetting(1, "Fragment tolerance = 0.1Da");
mtd.AddSoftwareSetting(1, "Parent tolerance = 0.5Da");
mtd.AddFalseDiscoveryRateParam(new CVParam("MS", "MS:1001364", "pep:global FDR", "0.01"));
mtd.AddFalseDiscoveryRateParam(new CVParam("MS", "MS:1001214", "pep:global FDR", "0.08"));
mtd.AddPublicationItem(1, PublicationType.PUBMED, "21063943");
mtd.AddPublicationItem(1, PublicationType.DOI, "10.1007/978-1-60761-987-1_6");
mtd.AddPublicationItem(2, PublicationType.PUBMED, "20615486");
mtd.AddPublicationItem(2, PublicationType.DOI, "10.1016/j.jprot.2010.06.008");
mtd.AddContactName(1, "James D. Watson");
mtd.AddContactName(2, "Francis Crick");
mtd.AddContactAffiliation(1, "Cambridge University, UK");
mtd.AddContactAffiliation(2, "Cambridge University, UK");
mtd.AddContactEmail(1, "*****@*****.**");
mtd.AddContactEmail(2, "*****@*****.**");
mtd.AddUri(new Uri("http://www.ebi.ac.uk/pride/url/to/experiment"));
mtd.AddUri(new Uri("http://proteomecentral.proteomexchange.org/cgi/GetDataset"));
mtd.AddFixedModParam(1, new CVParam("UNIMOD", "UNIMOD:4", "Carbamidomethyl", null));
mtd.AddFixedModSite(1, "M");
mtd.AddFixedModParam(2, new CVParam("UNIMOD", "UNIMOD:35", "Oxidation", null));
mtd.AddFixedModSite(2, "N-term");
mtd.AddFixedModParam(3, new CVParam("UNIMOD", "UNIMOD:1", "Acetyl", null));
mtd.AddFixedModPosition(3, "Protein C-term");
mtd.AddVariableModParam(1, new CVParam("UNIMOD", "UNIMOD:21", "Phospho", null));
mtd.AddVariableModSite(1, "M");
mtd.AddVariableModParam(2, new CVParam("UNIMOD", "UNIMOD:35", "Oxidation", null));
mtd.AddVariableModSite(2, "N-term");
mtd.AddVariableModParam(3, new CVParam("UNIMOD", "UNIMOD:1", "Acetyl", null));
mtd.AddVariableModPosition(3, "Protein C-term");
mtd.QuantificationMethod = new CVParam("MS", "MS:1001837", "iTRAQ quantitation analysis", null);
mtd.ProteinQuantificationUnit = new CVParam("PRIDE", "PRIDE:0000395", "Ratio", null);
mtd.PeptideQuantificationUnit = new CVParam("PRIDE", "PRIDE:0000395", "Ratio", null);
mtd.SmallMoleculeQuantificationUnit = new CVParam("PRIDE", "PRIDE:0000395", "Ratio", null);
mtd.AddMsRunFormat(1, new CVParam("MS", "MS:1000584", "mzML file", null));
mtd.AddMsRunFormat(2, new CVParam("MS", "MS:1001062", "Mascot MGF file", null));
mtd.AddMsRunLocation(1, new Url("file://C:\\path\\to\\my\\file"));
mtd.AddMsRunLocation(2, new Url("ftp://ftp.ebi.ac.uk/path/to/file"));
mtd.AddMsRunIdFormat(1, new CVParam("MS", "MS:1001530", "mzML unique identifier", null));
mtd.AddMsRunFragmentationMethod(1, new CVParam("MS", "MS:1000133", "CID", null));
mtd.AddMsRunFragmentationMethod(2, new CVParam("MS", "MS:1000422", "HCD", null));
mtd.AddCustom(new UserParam("MS operator", "Florian"));
mtd.AddSampleSpecies(1, new CVParam("NEWT", "9606", "H**o sapiens (Human)", null));
mtd.AddSampleSpecies(1, new CVParam("NEWT", "573824", "Human rhinovirus 1", null));
mtd.AddSampleSpecies(2, new CVParam("NEWT", "9606", "H**o sapiens (Human)", null));
mtd.AddSampleSpecies(2, new CVParam("NEWT", "12130", "Human rhinovirus 2", null));
mtd.AddSampleTissue(1, new CVParam("BTO", "BTO:0000759", "liver", null));
mtd.AddSampleCellType(1, new CVParam("CL", "CL:0000182", "hepatocyte", null));
mtd.AddSampleDisease(1, new CVParam("DOID", "DOID:684", "hepatocellular carcinoma", null));
mtd.AddSampleDisease(1, new CVParam("DOID", "DOID:9451", "alcoholic fatty liver", null));
mtd.AddSampleDescription(1, "Hepatocellular carcinoma samples.");
mtd.AddSampleDescription(2, "Healthy control samples.");
mtd.AddSampleCustom(1, new UserParam("Extraction date", "2011-12-21"));
mtd.AddSampleCustom(1, new UserParam("Extraction reason", "liver biopsy"));
Sample sample1 = mtd.SampleMap[1];
Sample sample2 = mtd.SampleMap[2];
mtd.AddAssayQuantificationReagent(1, new CVParam("PRIDE", "PRIDE:0000114", "iTRAQ reagent", "114"));
mtd.AddAssayQuantificationReagent(2, new CVParam("PRIDE", "PRIDE:0000115", "iTRAQ reagent", "115"));
mtd.AddAssayQuantificationReagent(1, new CVParam("PRIDE", "MS:1002038", "unlabeled sample", null));
mtd.AddAssaySample(1, sample1);
mtd.AddAssaySample(2, sample2);
mtd.AddAssayQuantificationModParam(2, 1, new CVParam("UNIMOD", "UNIMOD:188", "Label:13C(6)", null));
mtd.AddAssayQuantificationModParam(2, 2, new CVParam("UNIMOD", "UNIMOD:188", "Label:13C(6)", null));
mtd.AddAssayQuantificationModSite(2, 1, "R");
mtd.AddAssayQuantificationModSite(2, 2, "K");
mtd.AddAssayQuantificationModPosition(2, 1, "Anywhere");
mtd.AddAssayQuantificationModPosition(2, 2, "Anywhere");
MsRun msRun1 = mtd.MsRunMap[1];
mtd.AddAssayMsRun(1, msRun1);
Assay assay1 = mtd.AssayMap[1];
Assay assay2 = mtd.AssayMap[2];
mtd.AddStudyVariableAssay(1, assay1);
mtd.AddStudyVariableAssay(1, assay2);
mtd.AddStudyVariableSample(1, sample1);
mtd.AddStudyVariableDescription(1, "description Group B (spike-in 0.74 fmol/uL)");
mtd.AddCVLabel(1, "MS");
mtd.AddCVFullName(1, "MS");
mtd.AddCVVersion(1, "3.54.0");
mtd.AddCVURL(1,
"http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo");
mtd.AddProteinColUnit(ProteinColumn.RELIABILITY,
new CVParam("MS", "MS:00001231", "PeptideProphet:Score", null));
MZTabColumnFactory peptideFactory = MZTabColumnFactory.GetInstance(Section.Peptide);
PeptideColumn peptideColumn = (PeptideColumn) peptideFactory.FindColumnByHeader("retention_time");
mtd.AddPeptideColUnit(peptideColumn, new CVParam("UO", "UO:0000031", "minute", null));
mtd.AddPSMColUnit(PSMColumn.RETENTION_TIME, new CVParam("UO", "UO:0000031", "minute", null));
mtd.AddSmallMoleculeColUnit(SmallMoleculeColumn.RETENTION_TIME,
new CVParam("UO", "UO:0000031", "minute", null));
Console.WriteLine(mtd);
}