public static void TestMzIdentMlWriterWithUniprotPsiMod()
{
Protein protein = new Protein("PEPTIDE", "", databaseFilePath: "temp");
ModificationMotif.TryGetMotif("T", out var motif);
Modification fakeMod = new Modification(_originalId: "FAKE", _accession: "FAKE_MOD_ACCESSION", _modificationType: "fake",
_target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 0,
_databaseReference: new Dictionary <string, IList <string> > {
{ "PSI-MOD", new List <string> {
"FAKE_MOD_ACCESSION"
} }
});
string resIdAccession = fakeMod.DatabaseReference["PSI-MOD"].First();
var peptide = protein.Digest(new DigestionParams(), new List <Modification> {
fakeMod
}, new List <Modification>()).First();
MsDataScan dfb = new MsDataScan(new MzSpectrum(new double[] { 1 }, new double[] { 1 }, false), 0, 1, true, Polarity.Positive, double.NaN, null,
null, MZAnalyzerType.Orbitrap, double.NaN, null, null, "scan=1", double.NaN, null, null, double.NaN, null, DissociationType.AnyActivationType, 0, null);
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(dfb, 2, 0, "File", new CommonParameters());
var psm = new PeptideSpectralMatch(peptide, 0, 1, 0, scan, new DigestionParams(), new List <MatchedFragmentIon>());
psm.ResolveAllAmbiguities();
psm.SetFdrValues(0, 0, 0, 0, 0, 0, 0, 0);
string path = Path.Combine(TestContext.CurrentContext.TestDirectory, "ResIdOutput.mzID");
MzIdentMLWriter.WriteMzIdentMl(new List <PeptideSpectralMatch> {
psm
}, new List <ProteinGroup>(), new List <Modification>(),
new List <Modification>(), new List <SilacLabel>(), new List <Protease>(), 0, new PpmTolerance(20), new PpmTolerance(20),
0, path);
var file = File.ReadAllLines(path);
bool found = false;
foreach (var line in file)
{
if (line.Contains("FAKE on T") && line.Contains("PSI-MOD:" + resIdAccession))
{
found = true;
}
}
Assert.That(found);
File.Delete(path);
}
public static void TestMzIdentMlWriterWithUniprotResId()
{
Protein protein = new Protein("PEPTIDE", "", databaseFilePath: "temp");
Modification uniProtMod = GlobalVariables.AllModsKnown.First(p =>
p.IdWithMotif == "FMN phosphoryl threonine on T" &&
p.ModificationType == "UniProt" &&
p.Target.ToString() == "T" &&
p.DatabaseReference.ContainsKey("RESID") &&
p.LocationRestriction == "Anywhere.");
string resIdAccession = uniProtMod.DatabaseReference["RESID"].First();
var peptide = protein.Digest(new DigestionParams(), new List <Modification> {
uniProtMod
}, new List <Modification>()).First();
MsDataScan dfb = new MsDataScan(new MzSpectrum(new double[] { 1 }, new double[] { 1 }, false), 0, 1, true, Polarity.Positive, double.NaN, null,
null, MZAnalyzerType.Orbitrap, double.NaN, null, null, "scan=1", double.NaN, null, null, double.NaN, null, DissociationType.AnyActivationType, 0, null);
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(dfb, 2, 0, "File", new CommonParameters());
var psm = new PeptideSpectralMatch(peptide, 0, 1, 0, scan, new DigestionParams(), new List <MatchedFragmentIon>());
psm.ResolveAllAmbiguities();
psm.SetFdrValues(0, 0, 0, 0, 0, 0, 0, 0);
string path = Path.Combine(TestContext.CurrentContext.TestDirectory, "ResIdOutput.mzID");
MzIdentMLWriter.WriteMzIdentMl(new List <PeptideSpectralMatch> {
psm
}, new List <ProteinGroup>(), new List <Modification>(),
new List <Modification>(), new List <SilacLabel>(), new List <Protease>(), 0, new PpmTolerance(20), new PpmTolerance(20),
0, path);
var file = File.ReadAllLines(path);
bool found = false;
foreach (var line in file)
{
if (line.Contains("FMN phosphoryl threonine on T") && line.Contains("RESID:" + resIdAccession))
{
found = true;
}
}
Assert.That(found);
File.Delete(path);
}
