public void TestLooplinkCrosslinkLibraryKey()
{
var crosslinkLibraryKey = new CrosslinkLibraryKey(new [] { new PeptideLibraryKey("AKIQDKEGIPPDQQR", 0) }, new[] { new CrosslinkLibraryKey.Crosslink("+138.0681", new[] { new [] { 2, 6 } }) }, 3);
var srmSettings = SrmSettingsList.GetDefault();
srmSettings = srmSettings.ChangePeptideSettings(
srmSettings.PeptideSettings.ChangeModifications(srmSettings.PeptideSettings.Modifications
.ChangeStaticModifications(
srmSettings.PeptideSettings.Modifications.StaticModifications
.Append(new StaticMod("DSS", "K", null, "C8H10O2").ChangeCrosslinkerSettings(
CrosslinkerSettings.EMPTY)).ToList()
)));
var libKeyModificationMatcher = new LibKeyModificationMatcher();
libKeyModificationMatcher.CreateMatches(srmSettings, new[] { new LibKey(crosslinkLibraryKey) },
new MappedList <string, StaticMod>(), new MappedList <string, StaticMod>());
var peptideDocNode = libKeyModificationMatcher.CreateDocNodeFromSettings(new LibKey(crosslinkLibraryKey),
new Peptide("AKIQDKEGIPPDQQR"), SrmSettingsDiff.ALL, out _);
Assert.IsNotNull(peptideDocNode);
Assert.IsNotNull(peptideDocNode.ExplicitMods);
Assert.AreEqual(1, peptideDocNode.ExplicitMods.Crosslinks.Count);
Assert.AreEqual(null, peptideDocNode.ExplicitMods.Crosslinks[0].Value.Peptide);
}
public void TestCrosslinkWithModifications()
{
CrosslinkLibraryKey libKey = CrosslinkSequenceParser.ParseCrosslinkLibraryKey(
"C[+57.02146]C[+57.02146]TKPESER-EKVLTSSAR-[+138.0681@4,2]", 1);
Assert.AreEqual(2, libKey.PeptideLibraryKeys.Count);
Assert.AreEqual("C[+57.02146]C[+57.02146]TKPESER", libKey.PeptideLibraryKeys[0].ModifiedSequence);
Assert.AreEqual("EKVLTSSAR", libKey.PeptideLibraryKeys[1].ModifiedSequence);
Assert.AreEqual("+138.0681", libKey.Crosslinks[0].Name);
Assert.AreEqual(2, libKey.Crosslinks[0].Positions.Count);
Assert.AreEqual(ImmutableList.Singleton(4), libKey.Crosslinks[0].Positions[0]);
Assert.AreEqual(ImmutableList.Singleton(2), libKey.Crosslinks[0].Positions[1]);
}
public void TestCrosslinkSequenceParser()
{
CrosslinkLibraryKey libKey =
CrosslinkSequenceParser.ParseCrosslinkLibraryKey("VTIAQGGVLPNIQAVLLPKK-TESHHKACGK-[+138.0681@19,6]", 1);
Assert.AreEqual(2, libKey.PeptideLibraryKeys.Count);
Assert.AreEqual("VTIAQGGVLPNIQAVLLPKK", libKey.PeptideLibraryKeys[0].ModifiedSequence);
Assert.AreEqual("TESHHKACGK", libKey.PeptideLibraryKeys[1].ModifiedSequence);
Assert.AreEqual(1, libKey.Crosslinks.Count);
Assert.AreEqual("+138.0681", libKey.Crosslinks[0].Name);
Assert.AreEqual(2, libKey.Crosslinks[0].Positions.Count);
Assert.AreEqual(ImmutableList.Singleton(19), libKey.Crosslinks[0].Positions[0]);
Assert.AreEqual(ImmutableList.Singleton(6), libKey.Crosslinks[0].Positions[1]);
}
public override IEnumerable <AAModInfo> GetCurrentSequenceInfos()
{
if (_sequences.Current != null)
{
CrosslinkLibraryKey crosslinkLibraryKey =
CrosslinkSequenceParser.TryParseCrosslinkLibraryKey(_sequences.Current, 0);
if (crosslinkLibraryKey != null)
{
return(crosslinkLibraryKey.PeptideLibraryKeys.SelectMany(peptideLibraryKey =>
EnumerateAaModInfos(peptideLibraryKey.ModifiedSequence)));
}
}
return(EnumerateAaModInfos(_sequences.Current ?? string.Empty));
}
/// <summary>
/// Transforms an ordinary peptide sequence into a crosslinked peptide composed of three parts attached together
/// with the Hydrolysis crosslinker.
/// The crosslinked peptide ends up being the middle peptide sequence which has attachments to the left and right parts of
/// the peptide sequence.
///
/// For example, AVVQDPALKPLALVYGEATSR becomes:
/// LKPLALV-AVVQDPA-YGEATSR-[Hydrolysis@1,7,*][Hydrolysis@7,*,1]
/// </summary>
private string MakeCrosslinkedSequence(string flatPeptideSequence)
{
var aaMods = TokenizeModifiedSequence(flatPeptideSequence).ToList();
int leftLength = aaMods.Count / 3;
int middleLength = (2 * aaMods.Count) / 3 - leftLength;
var left = new PeptideLibraryKey(string.Join(string.Empty, aaMods.Take(leftLength)), 0);
var middle = new PeptideLibraryKey(string.Join(string.Empty, aaMods.Skip(leftLength).Take(middleLength)), 0);
var right = new PeptideLibraryKey(string.Join(string.Empty, aaMods.Skip(leftLength + middleLength)), 0);
var crosslinkLibraryKey = new CrosslinkLibraryKey(new [] { middle, left, right }, new []
{
new CrosslinkLibraryKey.Crosslink(crosslinkerName, new [] { new[] { 1 }, new [] { leftLength }, Enumerable.Empty <int>() }),
new CrosslinkLibraryKey.Crosslink(crosslinkerName, new[] { new[] { middleLength }, Enumerable.Empty <int>(), new [] { 1 } })
}, 0);
return(crosslinkLibraryKey.ToString());
}
