public static Target FromSerializableString(string val)
{
if (!val.StartsWith(@"#"))
{
return(new Target(val));
}
return(new Target(CustomMolecule.FromSerializableString(val)));
}
public new static CustomIon FromTSV(string val)
{
var lastTab = val.LastIndexOf(TextUtil.SEPARATOR_TSV_STR, StringComparison.Ordinal);
var adduct = Adduct.FromStringAssumeChargeOnly(val.Substring(lastTab + 1));
var mol = CustomMolecule.FromTSV(val.Substring(0, lastTab));
if (adduct.IsEmpty && mol.IsEmpty)
{
return(EMPTY);
}
return(new CustomIon(mol, adduct));
}
public static bool Equivalent(Transition t, Transition obj)
{
if (ReferenceEquals(t, obj))
{
return(true);
}
return(Equals(obj.IonType, t.IonType) &&
obj.CleavageOffset == t.CleavageOffset &&
obj.Charge == t.Charge &&
obj.MassIndex == t.MassIndex &&
CustomMolecule.Equivalent(obj.CustomIon, t.CustomIon) && // Looks at unlabeled formula or name only
(obj.DecoyMassShift.Equals(t.DecoyMassShift) ||
// Deal with strange case of mProphet golden standard data set - only a concern for peptides, not small molecules
(obj.DecoyMassShift.HasValue && t.DecoyMassShift.HasValue &&
(obj.Group.LabelType.IsLight && obj.DecoyMassShift == 0 && !t.Group.LabelType.IsLight && t.DecoyMassShift != 0) ||
(!obj.Group.LabelType.IsLight && obj.DecoyMassShift != 0 && t.Group.LabelType.IsLight && t.DecoyMassShift == 0))));
}
private void Validate()
{
if (IsCustomMolecule)
{
Assume.IsNull(_fastaSequence);
Assume.IsNull(Sequence);
CustomMolecule.Validate();
}
else if (_fastaSequence == null)
{
if (Begin.HasValue || End.HasValue)
{
throw new InvalidDataException(Resources.Peptide_Validate_Peptides_without_a_protein_sequence_do_not_support_the_start_and_end_properties);
}
// No FastaSequence checked the sequence, so check it here.
FastaSequence.ValidateSequence(Target.Sequence);
}
else
{
// Otherwise, validate the peptide sequence against the group sequence
if (!Begin.HasValue || !End.HasValue)
{
throw new InvalidDataException(Resources.Peptide_Validate_Peptides_from_protein_sequences_must_have_start_and_end_values);
}
if (0 > Begin.Value || End.Value > _fastaSequence.Sequence.Length)
{
throw new InvalidDataException(Resources.Peptide_Validate_Peptide_sequence_exceeds_the_bounds_of_the_protein_sequence);
}
var j = 0;
for (var i = Begin.Value; i < End.Value;)
{
if (!Equals(Target.Sequence[j++], _fastaSequence.Sequence[i++]))
{
string sequenceCheck = _fastaSequence.Sequence.Substring(Begin.Value, End.Value - Begin.Value);
throw new InvalidDataException(
string.Format(Resources.Peptide_Validate_The_peptide_sequence__0__does_not_agree_with_the_protein_sequence__1__at__2__3__,
Target, sequenceCheck, Begin.Value, End.Value));
}
}
}
// CONSIDER: Validate missed cleavages some day?
}
public Transition(TransitionGroup group, IonType type, int?offset, int?massIndex, Adduct adduct,
int?decoyMassShift, CustomMolecule customMolecule = null)
{
_group = group;
IonType = type;
CleavageOffset = offset ?? 0;
MassIndex = massIndex ?? 0;
Adduct = adduct;
DecoyMassShift = decoyMassShift;
// Small molecule precursor transition should have same custom molecule as parent
if (IsPrecursor(type) && group.IsCustomIon)
{
CustomIon = new CustomIon(group.CustomMolecule, adduct);
}
else if (customMolecule is CustomIon)
{
// As with reporter ions
CustomIon = (CustomIon)customMolecule;
Assume.IsTrue(Equals(adduct.AdductCharge, CustomIon.Adduct.AdductCharge));
Adduct = CustomIon.Adduct; // Ion mass is part of formula, so use charge only adduct
}
else if (customMolecule != null)
{
CustomIon = new CustomIon(customMolecule, adduct);
}
// Derived values
if (!IsCustom(type, group))
{
Peptide peptide = group.Peptide;
Ordinal = OffsetToOrdinal(type, (int)offset, peptide.Length);
AA = (IsNTerminal()
? peptide.Sequence[(int)offset]
: peptide.Sequence[(int)offset + 1]);
}
else
{
// caller may have passed in offset = group.Peptide.Length - 1, which for custom ions gives -1
CleavageOffset = 0;
}
Validate();
}
public SmallMoleculeLibraryAttributes GetSmallMoleculeLibraryAttributes()
{
return(IsCustomMolecule ? CustomMolecule.GetSmallMoleculeLibraryAttributes() : SmallMoleculeLibraryAttributes.EMPTY);
}
public Transition(TransitionGroup group, Adduct charge, int?massIndex, CustomMolecule customMolecule, IonType type = IonType.custom)
: this(group, type, null, massIndex, charge, null, customMolecule)
{
}
/// <summary>
/// Creates a precursor transition
/// </summary>
/// <param name="group">The <see cref="TransitionGroup"/> which the transition represents</param>
/// <param name="massIndex">Isotope mass shift</param>
/// <param name="productAdduct">Adduct on the transition</param>
/// <param name="customMolecule">Non-null if this is a custom transition</param>
public Transition(TransitionGroup group, int massIndex, Adduct productAdduct, CustomMolecule customMolecule = null)
: this(group, IonType.precursor, group.Peptide.Length - 1, massIndex, productAdduct, null, customMolecule)
{
}
public Target(CustomMolecule molecule)
{
Molecule = molecule;
}
public Target(SmallMoleculeLibraryAttributes molecule)
{
Molecule = new CustomMolecule(molecule);
}
private TransitionDocNode CreateTransitionNode(int massIndex, TypedMass precursorMassH, TransitionIsotopeDistInfo isotopeDistInfo,
TransitionLosses losses, IDictionary <double, LibraryRankedSpectrumInfo.RankedMI> transitionRanks, Adduct productAdduct, CustomMolecule customMolecule = null)
{
Transition transition = new Transition(this, massIndex, productAdduct, customMolecule);
var quantInfo = TransitionDocNode.TransitionQuantInfo.GetLibTransitionQuantInfo(transition, losses,
Transition.CalcMass(precursorMassH, losses), transitionRanks).ChangeIsotopeDistInfo(isotopeDistInfo);
var transitionDocNode = new TransitionDocNode(transition, losses, precursorMassH, quantInfo, ExplicitTransitionValues.EMPTY);
if (massIndex < 0)
{
transitionDocNode = transitionDocNode.ChangeQuantitative(false);
}
return(transitionDocNode);
}
public Peptide(CustomMolecule customMolecule)
{
Target = new Target(customMolecule);
Validate();
}
public Target(SmallMoleculeLibraryAttributes molecule)
{
Molecule = CustomMolecule.FromSmallMoleculeLibraryAttributes(molecule);
}
public IEnumerable <TransitionDocNode> GetPrecursorTransitions(SrmSettings settings,
ExplicitMods mods,
IPrecursorMassCalc calcPredictPre,
IFragmentMassCalc calcPredict,
double precursorMz,
IsotopeDistInfo isotopeDist,
IList <IList <ExplicitLoss> > potentialLosses,
IDictionary <double, LibraryRankedSpectrumInfo.RankedMI> transitionRanks,
bool libraryFilter,
bool useFilter)
{
var tranSettings = settings.TransitionSettings;
var fullScan = tranSettings.FullScan;
int minMz = tranSettings.Instrument.GetMinMz(precursorMz);
int maxMz = tranSettings.Instrument.MaxMz;
bool precursorMS1 = fullScan.IsEnabledMs;
MassType massType = tranSettings.Prediction.FragmentMassType;
MassType massTypeIon = precursorMS1 ? tranSettings.Prediction.PrecursorMassType : massType;
var sequence = Peptide.Target;
var ionTypes = IsProteomic ? tranSettings.Filter.PeptideIonTypes : tranSettings.Filter.SmallMoleculeIonTypes;
bool precursorNoProducts = precursorMS1 && !fullScan.IsEnabledMsMs &&
ionTypes.Count == 1 && ionTypes[0] == IonType.precursor;
var precursorMassPredict = precursorMS1
? calcPredictPre.GetPrecursorMass(sequence)
: calcPredict.GetPrecursorFragmentMass(sequence);
foreach (var losses in CalcTransitionLosses(IonType.precursor, 0, massType, potentialLosses))
{
double ionMz = IsProteomic ?
SequenceMassCalc.GetMZ(Transition.CalcMass(precursorMassPredict, losses), PrecursorAdduct) :
PrecursorAdduct.MzFromNeutralMass(CustomMolecule.GetMass(massTypeIon), massTypeIon);
if (losses == null)
{
if (precursorMS1 && isotopeDist != null)
{
foreach (int i in fullScan.SelectMassIndices(isotopeDist, useFilter))
{
var precursorMS1Mass = isotopeDist.GetMassI(i, DecoyMassShift);
ionMz = SequenceMassCalc.GetMZ(precursorMS1Mass, PrecursorAdduct);
if (minMz > ionMz || ionMz > maxMz)
{
continue;
}
var isotopeDistInfo = new TransitionIsotopeDistInfo(
isotopeDist.GetRankI(i), isotopeDist.GetProportionI(i));
yield return(CreateTransitionNode(i, precursorMS1Mass, isotopeDistInfo, null, transitionRanks));
}
continue;
}
}
// If there was loss, it is possible (though not likely) that the ion m/z value
// will now fall below the minimum measurable value for the instrument
else if (minMz > ionMz)
{
continue;
}
// If filtering precursors from MS1 scans, then ranking in MS/MS does not apply
bool precursorIsProduct = !precursorMS1 || losses != null;
// Skip product ion precursors, if the should not be included
if (useFilter && precursorIsProduct && precursorNoProducts)
{
continue;
}
if (!useFilter || !precursorIsProduct ||
!libraryFilter || IsMatched(transitionRanks, ionMz, IonType.precursor,
PrecursorAdduct, losses))
{
yield return(CreateTransitionNode(0, precursorMassPredict, null, losses,
precursorIsProduct ? transitionRanks : null));
}
}
}
public PeptideDocNode GetModifiedNode(LibKey key, SrmSettings settings, SrmSettingsDiff diff)
{
var smallMoleculeKey = key.LibraryKey as MoleculeLibraryKey;
var peptideKey = key.LibraryKey as PeptideLibraryKey;
Peptide peptide;
if (smallMoleculeKey != null)
{
peptide = new Peptide(CustomMolecule.FromSmallMoleculeLibraryAttributes(smallMoleculeKey.SmallMoleculeLibraryAttributes));
}
else if (peptideKey != null)
{
peptide = new Peptide(null, peptideKey.UnmodifiedSequence, null, null,
settings.PeptideSettings.Enzyme.CountCleavagePoints(peptideKey.UnmodifiedSequence));
}
else
{
return(null);
}
// First try and create the match from the settings created to match the library explorer.
Settings = HasMatches
? settings.ChangePeptideModifications(mods => MatcherPepMods)
: settings;
TransitionGroupDocNode nodeGroup;
var nodePep = CreateDocNodeFromSettings(key, peptide, diff, out nodeGroup);
if (nodePep != null)
{
if (diff == null)
{
nodePep = (PeptideDocNode)nodePep.ChangeAutoManageChildren(false);
}
else
{
// Keep only the matching transition group, so that modifications
// will be highlighted differently for light and heavy forms.
// Only performed when getting peptides for display in the explorer.
nodePep = (PeptideDocNode)nodePep.ChangeChildrenChecked(
new DocNode[] { nodeGroup });
}
return(nodePep);
}
else if (Matches == null)
{
return(null);
}
bool hasHeavy;
// Create explicit mods from the found matches.
nodePep = CreateDocNodeFromMatches(new PeptideDocNode(peptide),
EnumerateSequenceInfos(key.LibraryKey as PeptideLibraryKey, true), false, out hasHeavy);
if (nodePep == null)
{
return(null);
}
// Call change settings with the matched modification settings to enumerate the children.
nodePep = nodePep.ChangeSettings(settings.ChangePeptideModifications(mods =>
!HasMatches ? settings.PeptideSettings.Modifications : MatcherPepMods), diff ?? SrmSettingsDiff.ALL);
if (nodePep.Children.Count == 0)
{
return(null);
}
// Select the correct child, only for use with the library explorer.
if (diff != null && nodePep.Children.Count > 1)
{
nodePep =
(PeptideDocNode)
nodePep.ChangeChildrenChecked(new List <DocNode> {
nodePep.Children[hasHeavy ? 1 : 0]
});
}
if (diff == null)
{
nodePep = (PeptideDocNode)nodePep.ChangeAutoManageChildren(false);
}
return(nodePep);
}
private TransitionDocNode CreateTransitionNode(IonType type, int cleavageOffset, Adduct charge, TypedMass massH,
TransitionLosses losses, IDictionary <double, LibraryRankedSpectrumInfo.RankedMI> transitionRanks, CustomMolecule customMolecule = null)
{
Transition transition = new Transition(this, type, cleavageOffset, 0, charge, null, customMolecule);
var info = TransitionDocNode.TransitionQuantInfo.GetLibTransitionQuantInfo(transition, losses, Transition.CalcMass(massH, losses), transitionRanks);
return(new TransitionDocNode(transition, losses, massH, info));
}
private TransitionDocNode CreateTransitionNode(int massIndex, TypedMass precursorMassH, TransitionIsotopeDistInfo isotopeDistInfo,
TransitionLosses losses, IDictionary <double, LibraryRankedSpectrumInfo.RankedMI> transitionRanks, CustomMolecule customMolecule = null)
{
Transition transition = new Transition(this, massIndex, customMolecule);
var quantInfo = TransitionDocNode.TransitionQuantInfo.GetLibTransitionQuantInfo(transition, losses,
Transition.CalcMass(precursorMassH, losses), transitionRanks).ChangeIsotopeDistInfo(isotopeDistInfo);
return(new TransitionDocNode(transition, losses, precursorMassH, quantInfo));
}
public CustomIon(CustomMolecule mol, Adduct adduct)
: this(mol.Formula, adduct, mol.MonoisotopicMass, mol.AverageMass, mol.Name)
{
}
public static TransitionDocNode FromTransitionProto(AnnotationScrubber scrubber, SrmSettings settings,
TransitionGroup group, ExplicitMods mods, IsotopeDistInfo isotopeDist, ExplicitTransitionValues pre422ExplicitTransitionValues,
SkylineDocumentProto.Types.Transition transitionProto)
{
var stringPool = scrubber.StringPool;
IonType ionType = DataValues.FromIonType(transitionProto.FragmentType);
MeasuredIon measuredIon = null;
if (transitionProto.MeasuredIonName != null)
{
measuredIon = settings.TransitionSettings.Filter.MeasuredIons.SingleOrDefault(
i => i.Name.Equals(transitionProto.MeasuredIonName.Value));
if (measuredIon == null)
{
throw new InvalidDataException(string.Format(Resources.TransitionInfo_ReadXmlAttributes_The_reporter_ion__0__was_not_found_in_the_transition_filter_settings_, transitionProto.MeasuredIonName));
}
ionType = IonType.custom;
}
bool isCustom = Transition.IsCustom(ionType, group);
bool isPrecursor = Transition.IsPrecursor(ionType);
CustomMolecule customIon = null;
if (isCustom)
{
if (measuredIon != null)
{
customIon = measuredIon.SettingsCustomIon;
}
else if (isPrecursor)
{
customIon = group.CustomMolecule;
}
else
{
var formula = DataValues.FromOptional(transitionProto.Formula);
var moleculeID = MoleculeAccessionNumbers.FromString(DataValues.FromOptional(transitionProto.MoleculeId)); // Tab separated list of InChiKey, CAS etc
var monoMassH = DataValues.FromOptional(transitionProto.MonoMassH);
var averageMassH = DataValues.FromOptional(transitionProto.AverageMassH);
var monoMass = DataValues.FromOptional(transitionProto.MonoMass) ?? monoMassH;
var averageMass = DataValues.FromOptional(transitionProto.AverageMass) ?? averageMassH;
customIon = new CustomMolecule(formula,
new TypedMass(monoMass.Value, monoMassH.HasValue ? MassType.MonoisotopicMassH : MassType.Monoisotopic),
new TypedMass(averageMass.Value, averageMassH.HasValue ? MassType.AverageMassH : MassType.Average),
DataValues.FromOptional(transitionProto.CustomIonName), moleculeID);
}
}
Transition transition;
var adductString = DataValues.FromOptional(transitionProto.Adduct);
var adduct = string.IsNullOrEmpty(adductString)
? Adduct.FromChargeProtonated(transitionProto.Charge)
: Adduct.FromStringAssumeChargeOnly(adductString);
if (isCustom)
{
transition = new Transition(group, isPrecursor ? group.PrecursorAdduct :adduct, transitionProto.MassIndex, customIon, ionType);
}
else if (isPrecursor)
{
transition = new Transition(group, ionType, group.Peptide.Length - 1, transitionProto.MassIndex,
group.PrecursorAdduct, DataValues.FromOptional(transitionProto.DecoyMassShift));
}
else
{
int offset = Transition.OrdinalToOffset(ionType, transitionProto.FragmentOrdinal,
group.Peptide.Length);
transition = new Transition(group, ionType, offset, transitionProto.MassIndex, adduct, DataValues.FromOptional(transitionProto.DecoyMassShift));
}
var losses = TransitionLosses.FromLossProtos(settings, transitionProto.Losses);
var mass = settings.GetFragmentMass(group, mods, transition, isotopeDist);
var isotopeDistInfo = GetIsotopeDistInfo(transition, losses, isotopeDist);
if (group.DecoyMassShift.HasValue && transitionProto.DecoyMassShift == null)
{
throw new InvalidDataException(Resources.SrmDocument_ReadTransitionXml_All_transitions_of_decoy_precursors_must_have_a_decoy_mass_shift);
}
TransitionLibInfo libInfo = null;
if (transitionProto.LibInfo != null)
{
libInfo = new TransitionLibInfo(transitionProto.LibInfo.Rank, transitionProto.LibInfo.Intensity);
}
var annotations = scrubber.ScrubAnnotations(Annotations.FromProtoAnnotations(transitionProto.Annotations), AnnotationDef.AnnotationTarget.transition);
var results = TransitionChromInfo.FromProtoTransitionResults(scrubber, settings, transitionProto.Results);
var explicitTransitionValues = pre422ExplicitTransitionValues ?? ExplicitTransitionValues.Create(
DataValues.FromOptional(transitionProto.ExplicitCollisionEnergy),
DataValues.FromOptional(transitionProto.ExplicitIonMobilityHighEnergyOffset),
DataValues.FromOptional(transitionProto.ExplicitSLens),
DataValues.FromOptional(transitionProto.ExplicitConeVoltage),
DataValues.FromOptional(transitionProto.ExplicitDeclusteringPotential));
return(new TransitionDocNode(transition, annotations, losses, mass, new TransitionQuantInfo(isotopeDistInfo, libInfo, !transitionProto.NotQuantitative), explicitTransitionValues, results));
}
