/// <summary>
/// Sequences are passed to Prosit as an array of indices mapping into an array
/// of amino acids (with modifications). Actually throwing exceptions in this method
/// slows down constructing inputs (for larger data sets with unknown mods (and aa's)significantly,
/// which is why PrositExceptions (only) are set as an output parameter and null is returned.
/// </summary>
public static int[] EncodeSequence(SrmSettings settings, ISequenceContainer peptide, IsotopeLabelType label, out PrositException exception)
{
if (!peptide.Target.IsProteomic)
{
throw new PrositSmallMoleculeException(peptide.ModifiedTarget);
}
var sequence = peptide.Target.Sequence;
if (sequence.Length > PrositConstants.PEPTIDE_SEQ_LEN)
{
exception = new PrositPeptideTooLongException(peptide.ModifiedTarget);
return(null);
}
var modifiedSequence = ModifiedSequence.GetModifiedSequence(settings, peptide, label);
var result = new int[PrositConstants.PEPTIDE_SEQ_LEN];
for (var i = 0; i < sequence.Length; ++i)
{
if (!PrositConstants.AMINO_ACIDS.TryGetValue(sequence[i], out var prositAA))
{
exception = new PrositUnsupportedAminoAcidException(peptide.ModifiedTarget, i);
return(null);
}
var mods = modifiedSequence.ExplicitMods.Where(m => m.IndexAA == i).ToArray();
foreach (var mod in mods)
{
if (mod.MonoisotopicMass == 0.0)
{
continue;
}
var staticMod = UniMod.FindMatchingStaticMod(mod.StaticMod, true) ?? mod.StaticMod;
if (!PrositConstants.MODIFICATIONS.TryGetValue(staticMod.Name, out var prositAAMod))
{
exception = new PrositUnsupportedModificationException(peptide.ModifiedTarget,
mod.StaticMod,
mod.IndexAA);
return(null);
}
result[i] = prositAAMod.PrositIndex;
break;
}
if (result[i] == 0)
{
// Not modified
result[i] = prositAA.PrositIndex;
}
}
exception = null;
return(result);
}
public FragmentedMolecule GetSimplePrecursorMolecule()
{
if (_precursorMolecule == null)
{
var modifiedSequence = ModifiedSequence.GetModifiedSequence(Settings, Peptide.Sequence, ExplicitMods, LabelType)
.SeverCrosslinks();
_precursorMolecule = FragmentedMolecule.EMPTY.ChangeModifiedSequence(modifiedSequence);
}
return(_precursorMolecule);
}
public static PeptideFormatter MakePeptideFormatter(SrmSettings srmSettings, Peptide peptide,
ExplicitMods explicitMods, ICollection <IsotopeLabelType> heavyLabelTypes,
ModFontHolder modFontHolder)
{
var lightModifiedSequence =
ModifiedSequence.GetModifiedSequence(srmSettings, peptide.Sequence, explicitMods, IsotopeLabelType.light);
var heavyModifiedSequences = new List <KeyValuePair <IsotopeLabelType, ModifiedSequence> >();
foreach (var labelType in srmSettings.PeptideSettings.Modifications.GetHeavyModificationTypes())
{
if (!heavyLabelTypes.Contains(labelType))
{
continue;
}
heavyModifiedSequences.Add(new KeyValuePair <IsotopeLabelType, ModifiedSequence>(labelType,
ModifiedSequence.GetModifiedSequence(srmSettings, peptide.Sequence, explicitMods, labelType)));
}
var peptideFormatter = new PeptideFormatter(srmSettings, lightModifiedSequence, heavyModifiedSequences, modFontHolder);
if (explicitMods != null && explicitMods.HasCrosslinks)
{
var linkedPeptides = new List <KeyValuePair <ModificationSite, PeptideFormatter> >();
foreach (var entry in explicitMods.Crosslinks)
{
if (entry.Value.Peptide == null)
{
continue;
}
var childFormatter = MakePeptideFormatter(srmSettings, entry.Value.Peptide,
entry.Value.ExplicitMods, heavyLabelTypes, modFontHolder)
.ChangeCrosslinkedIndexAa(entry.Value.IndexAa);
linkedPeptides.Add(new KeyValuePair <ModificationSite, PeptideFormatter>(entry.Key, childFormatter));
}
peptideFormatter = peptideFormatter
.ChangeLinkedPeptides(ImmutableSortedList.FromValues(linkedPeptides));
}
return(peptideFormatter);
}
public static PeptideFormatter MakePeptideFormatter(SrmSettings srmSettings, PeptideDocNode peptideDocNode,
ModFontHolder modFontHolder)
{
var lightModifiedSequence =
ModifiedSequence.GetModifiedSequence(srmSettings, peptideDocNode, IsotopeLabelType.light);
var heavyModifiedSequences = new List <KeyValuePair <IsotopeLabelType, ModifiedSequence> >();
foreach (var labelType in srmSettings.PeptideSettings.Modifications.GetHeavyModificationTypes())
{
if (!peptideDocNode.HasChildType(labelType))
{
continue;
}
heavyModifiedSequences.Add(new KeyValuePair <IsotopeLabelType, ModifiedSequence>(labelType,
ModifiedSequence.GetModifiedSequence(srmSettings, peptideDocNode, labelType)));
}
return(new PeptideFormatter(srmSettings, lightModifiedSequence, heavyModifiedSequences, modFontHolder));
}
public void TestLooplink()
{
var peptide = new Peptide("PEPTIDE");
var srmSettings = SrmSettingsList.GetDefault();
var transitionFilter = srmSettings.TransitionSettings.Filter;
transitionFilter = transitionFilter
.ChangeFragmentRangeFirstName(TransitionFilter.StartFragmentFinder.ION_1.Name)
.ChangeFragmentRangeLastName(@"last ion")
.ChangePeptideIonTypes(new[] { IonType.precursor, IonType.y, IonType.b });
srmSettings = srmSettings.ChangeTransitionSettings(
srmSettings.TransitionSettings.ChangeFilter(transitionFilter));
var transitionGroup = new TransitionGroup(peptide, Adduct.SINGLY_PROTONATED, IsotopeLabelType.light);
var crosslinkerDef = new StaticMod("dss", null, null, "C8H10O2");
var linkedPeptide = new LinkedPeptide(null, 5, null);
var crosslinkMod = new ExplicitMod(2, crosslinkerDef).ChangeLinkedPeptide(linkedPeptide);
var explicitModsWithCrosslink = new ExplicitMods(peptide, new[] { crosslinkMod }, new TypedExplicitModifications[0]);
var transitionGroupDocNode = new TransitionGroupDocNode(transitionGroup, Annotations.EMPTY, srmSettings,
explicitModsWithCrosslink, null, ExplicitTransitionGroupValues.EMPTY, null, null, false);
var modifiedSequence = ModifiedSequence.GetModifiedSequence(srmSettings, peptide.Sequence,
explicitModsWithCrosslink, IsotopeLabelType.light);
Assert.AreEqual("PEPTIDE-[dss@3-6]", modifiedSequence.FullNames);
var choices = transitionGroupDocNode.GetPrecursorChoices(srmSettings, explicitModsWithCrosslink, true)
.Cast <TransitionDocNode>().ToArray();
var complexFragmentIons = choices.Select(transition => transition.ComplexFragmentIon.GetName()).ToArray();
// Make sure none of the transitions involve a cleavage in between the two ends of the looplink
// PEpTIdE
var yOrdinals = complexFragmentIons.Where(ion => ion.IonType == IonType.y).Select(ion => ion.Ordinal)
.Distinct().ToList();
var bOrdinals = complexFragmentIons.Where(ion => ion.IonType == IonType.b).Select(ion => ion.Ordinal)
.Distinct().ToList();
CollectionAssert.AreEquivalent(new[] { 6, 5, 1 }, yOrdinals);
CollectionAssert.AreEquivalent(new[] { 1, 2, 6 }, bOrdinals);
}
