public void TestPermuteComplexIons()
{
var mainPeptide = new Peptide("MERCURY");
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(mainPeptide, Adduct.SINGLY_PROTONATED, IsotopeLabelType.light);
var crosslinkerDef = new StaticMod("disulfide", "C", null, "-H2");
var linkedPeptide = new LinkedPeptide(new Peptide("ARSENIC"), 6, null);
var crosslinkMod = new ExplicitMod(3, crosslinkerDef).ChangeLinkedPeptide(linkedPeptide);
var explicitModsWithCrosslink = new ExplicitMods(mainPeptide, new[] { crosslinkMod }, new TypedExplicitModifications[0]);
var transitionGroupDocNode = new TransitionGroupDocNode(transitionGroup, Annotations.EMPTY, srmSettings,
explicitModsWithCrosslink, null, ExplicitTransitionGroupValues.EMPTY, null, null, false);
var choices = transitionGroupDocNode.GetPrecursorChoices(srmSettings, explicitModsWithCrosslink, true)
.Cast <TransitionDocNode>().ToArray();
var complexFragmentIons = choices.Select(transition => transition.ComplexFragmentIon.GetName()).ToArray();
Assert.AreNotEqual(0, complexFragmentIons.Length);
}
public PeptideDocNode CreateDocNodeFromSettings(LibKey key, Peptide peptide, SrmSettingsDiff diff, out TransitionGroupDocNode nodeGroupMatched)
{
if (!key.Target.IsProteomic)
{
// Scan the spectral lib entry for top N ranked (for now, that's just by intensity with high mz as tie breaker) fragments,
// add those as mass-only fragments, or with more detail if peak annotations are present.
foreach (var nodePep in peptide.CreateDocNodes(Settings, new MaxModFilter(0)))
{
SpectrumHeaderInfo libInfo;
if (nodePep != null && Settings.PeptideSettings.Libraries.TryGetLibInfo(key, out libInfo))
{
var isotopeLabelType = key.Adduct.HasIsotopeLabels ? IsotopeLabelType.heavy : IsotopeLabelType.light;
var group = new TransitionGroup(peptide, key.Adduct, isotopeLabelType);
nodeGroupMatched = new TransitionGroupDocNode(group, Annotations.EMPTY, Settings, null, libInfo, ExplicitTransitionGroupValues.EMPTY, null, null, false);
SpectrumPeaksInfo spectrum;
if (Settings.PeptideSettings.Libraries.TryLoadSpectrum(key, out spectrum))
{
// Add fragment and precursor transitions as needed
var transitionDocNodes =
Settings.TransitionSettings.Filter.SmallMoleculeIonTypes.Contains(IonType.precursor)
? nodeGroupMatched.GetPrecursorChoices(Settings, null, true) // Gives list of precursors
: new List <DocNode>();
if (Settings.TransitionSettings.Filter.SmallMoleculeIonTypes.Contains(IonType.custom))
{
GetSmallMoleculeFragments(key, nodeGroupMatched, spectrum, transitionDocNodes);
}
nodeGroupMatched = (TransitionGroupDocNode)nodeGroupMatched.ChangeChildren(transitionDocNodes);
return((PeptideDocNode)nodePep.ChangeChildren(new List <DocNode>()
{
nodeGroupMatched
}));
}
}
}
nodeGroupMatched = null;
return(null);
}
return(CreateDocNodeFromSettings(key.Target, peptide, diff, out nodeGroupMatched));
}
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);
}
public static Size RenderTip(PeptideDocNode nodePep,
TransitionGroupDocNode nodeGroup,
TransitionDocNode nodeTranSelected,
SrmSettings settings,
Graphics g,
Size sizeMax,
bool draw)
{
if (nodeGroup.TransitionGroup.IsCustomIon) // TODO(bspratt) this seems to leave out a lot of detail
{
var customTable = new TableDesc();
using (RenderTools rt = new RenderTools())
{
customTable.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Molecule, nodeGroup.CustomMolecule.Name, rt);
customTable.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Precursor_charge,
nodeGroup.TransitionGroup.PrecursorAdduct.AdductCharge.ToString(LocalizationHelper.CurrentCulture), rt);
customTable.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Precursor_mz,
string.Format(@"{0:F04}", nodeGroup.PrecursorMz), rt);
if (nodeGroup.CustomMolecule.Formula != null)
{
customTable.AddDetailRow(Resources.TransitionTreeNode_RenderTip_Formula,
nodeGroup.CustomMolecule.Formula + nodeGroup.TransitionGroup.PrecursorAdduct.AdductFormula.ToString(LocalizationHelper.CurrentCulture), rt);
}
SizeF size = customTable.CalcDimensions(g);
customTable.Draw(g);
return(new Size((int)size.Width + 2, (int)size.Height + 2));
}
}
ExplicitMods mods = (nodePep != null ? nodePep.ExplicitMods : null);
IEnumerable <DocNode> choices = nodeGroup.GetPrecursorChoices(settings, mods, true).ToArray();
HashSet <DocNode> chosen = new HashSet <DocNode>(nodeGroup.Children);
// Make sure all chosen peptides get listed
HashSet <DocNode> setChoices = new HashSet <DocNode>(choices);
setChoices.UnionWith(chosen);
choices = setChoices.ToArray();
Transition tranSelected = (nodeTranSelected != null ? nodeTranSelected.Transition : null);
IFragmentMassCalc calc = settings.GetFragmentCalc(nodeGroup.TransitionGroup.LabelType, mods);
var aa = nodeGroup.TransitionGroup.Peptide.Target.Sequence; // We handled custom ions above, and returned
var masses = calc.GetFragmentIonMasses(nodeGroup.TransitionGroup.Peptide.Target);
var filter = settings.TransitionSettings.Filter;
// Get charges and type pairs, making sure all chosen charges are included
var setCharges = new HashSet <Adduct>(filter.PeptideProductCharges.Where(charge =>
Math.Abs(charge.AdductCharge) <= Math.Abs(nodeGroup.TransitionGroup.PrecursorCharge) &&
Math.Sign(charge.AdductCharge) == Math.Sign(nodeGroup.TransitionGroup.PrecursorCharge)));
HashSet <IonType> setTypes = new HashSet <IonType>(filter.PeptideIonTypes);
foreach (TransitionDocNode nodTran in chosen)
{
var type = nodTran.Transition.IonType;
if (!Transition.IsPeptideFragment(type))
{
continue;
}
setCharges.Add(nodTran.Transition.Adduct);
setTypes.Add(type);
}
setTypes.RemoveWhere(t => !Transition.IsPeptideFragment(t));
var charges = setCharges.Where(c => c.IsProteomic).ToArray();
Array.Sort(charges);
IonType[] types = Transition.GetTypePairs(setTypes);
var tableDetails = new TableDesc();
var table = new TableDesc();
using (RenderTools rt = new RenderTools())
{
var seqModified = GetModifiedSequence(nodePep, nodeGroup, settings);
if (!Equals(seqModified, nodeGroup.TransitionGroup.Peptide.Target))
{
tableDetails.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Modified, seqModified.Sequence, rt);
}
var precursorCharge = nodeGroup.TransitionGroup.PrecursorAdduct;
var precursorMz = nodeGroup.PrecursorMz;
tableDetails.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Precursor_charge,
precursorCharge.AdductCharge.ToString(LocalizationHelper.CurrentCulture), rt);
tableDetails.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Precursor_mz,
string.Format(@"{0:F04}", precursorMz), rt);
tableDetails.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Precursor_mh,
string.Format(@"{0:F04}", nodeGroup.GetPrecursorIonMass()),
rt);
int?decoyMassShift = nodeGroup.TransitionGroup.DecoyMassShift;
if (decoyMassShift.HasValue)
{
tableDetails.AddDetailRow(Resources.TransitionGroupTreeNode_RenderTip_Decoy_Mass_Shift,
decoyMassShift.Value.ToString(LocalizationHelper.CurrentCulture), rt);
}
if (nodeGroup.HasLibInfo)
{
foreach (KeyValuePair <PeptideRankId, string> pair in nodeGroup.LibInfo.RankValues)
{
tableDetails.AddDetailRow(pair.Key.Label, pair.Value, rt);
}
}
if (charges.Length > 0 && types.Length > 0)
{
var headers = new RowDesc
{
CreateHead(@"#", rt),
CreateHead(@"AA", rt),
CreateHead(@"#", rt)
};
foreach (var charge in charges)
{
string plusSub = Transition.GetChargeIndicator(charge);
foreach (IonType type in types)
{
CellDesc cell = CreateHead(type.ToString().ToLower() + plusSub, rt);
if (Transition.IsNTerminal(type))
{
headers.Insert(0, cell);
}
else
{
headers.Add(cell);
}
}
}
table.Add(headers);
int len = aa.Length;
for (int i = 0; i < len; i++)
{
CellDesc cellAA = CreateRowLabel(aa.Substring(i, 1), rt);
cellAA.Align = StringAlignment.Center;
var row = new RowDesc
{
CreateRowLabel(i == len - 1 ? string.Empty : (i + 1).ToString(CultureInfo.InvariantCulture), rt),
cellAA,
CreateRowLabel(i == 0 ? string.Empty : (len - i).ToString(CultureInfo.InvariantCulture), rt)
};
foreach (var charge in charges)
{
foreach (IonType type in types)
{
CellDesc cell;
if (Transition.IsNTerminal(type))
{
if (i == len - 1)
{
cell = CreateData(string.Empty, rt);
}
else
{
var massH = masses[type, i];
cell = CreateIon(type, i + 1, massH, charge, choices, chosen, tranSelected, rt);
}
row.Insert(0, cell);
}
else
{
if (i == 0)
{
cell = CreateData(string.Empty, rt);
}
else
{
var massH = masses[type, i - 1];
cell = CreateIon(type, len - i, massH, charge, choices, chosen, tranSelected, rt);
}
row.Add(cell);
}
}
}
table.Add(row);
}
}
SizeF sizeDetails = tableDetails.CalcDimensions(g);
sizeDetails.Height += TableDesc.TABLE_SPACING; // Spacing between details and fragments
SizeF size = table.CalcDimensions(g);
if (draw)
{
tableDetails.Draw(g);
g.TranslateTransform(0, sizeDetails.Height);
table.Draw(g);
g.TranslateTransform(0, -sizeDetails.Height);
}
int width = (int)Math.Round(Math.Max(sizeDetails.Width, size.Width));
int height = (int)Math.Round(sizeDetails.Height + size.Height);
return(new Size(width + 2, height + 2));
}
}
public void ReporterIonTest()
{
// Test the code that updates old-style formulas
Assert.AreEqual("C5C'H13N2", BioMassCalc.AddH("C5C'H12N2"));
Assert.AreEqual("CO2H", BioMassCalc.AddH("CO2"));
var docOriginal = new SrmDocument(SrmSettingsList.GetDefault().ChangeTransitionInstrument(instrument => instrument.ChangeMinMz(10))); // H2O2 is not very heavy!
IdentityPath path;
SrmDocument docPeptide = docOriginal.ImportFasta(new StringReader(">peptide1\nPEPMCIDEPR"),
true, IdentityPath.ROOT, out path);
// One of the prolines should have caused an extra transition
Assert.AreEqual(4, docPeptide.PeptideTransitionCount);
Assert.IsTrue(docPeptide.PeptideTransitions.Contains(nodeTran => nodeTran.Transition.Ordinal == 8));
const string formula = "H2O2"; // This was H2O, but that falls below mz=10 at z > 1
const string hydrogenPeroxide = "Hydrogen Perxoide";
var reporterIons = new[] { new MeasuredIon(hydrogenPeroxide, formula, null, null, Adduct.SINGLY_PROTONATED), new MeasuredIon(hydrogenPeroxide, formula, null, null, Adduct.DOUBLY_PROTONATED), new MeasuredIon(hydrogenPeroxide, formula, null, null, Adduct.TRIPLY_PROTONATED), MeasuredIonList.NTERM_PROLINE };
SrmDocument docReporterIon = docPeptide.ChangeSettings(docPeptide.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(reporterIons)));
AssertEx.IsDocumentTransitionCount(docReporterIon, 7);
//Check With Monoisotopic
var mass = BioMassCalc.MONOISOTOPIC.CalculateMassFromFormula(formula);
for (int i = 0; i < 3; i++)
{
TransitionDocNode tranNode = docReporterIon.MoleculeTransitions.ElementAt(i);
Transition tran = tranNode.Transition;
Assert.AreEqual(reporterIons[i].SettingsCustomIon, tran.CustomIon);
Assert.AreEqual(tran.Charge, i + 1);
Assert.AreEqual(BioMassCalc.CalculateIonMz(mass, tran.Adduct), tranNode.Mz, BioMassCalc.MassElectron / 100);
}
//Check with Average
TransitionPrediction predSettings =
docReporterIon.Settings.TransitionSettings.Prediction.ChangeFragmentMassType(MassType.Average);
TransitionSettings tranSettings = docReporterIon.Settings.TransitionSettings.ChangePrediction(predSettings);
SrmSettings srmSettings = docReporterIon.Settings.ChangeTransitionSettings(tranSettings);
SrmDocument averageDocument = docReporterIon.ChangeSettings(srmSettings);
mass = BioMassCalc.AVERAGE.CalculateMassFromFormula(formula);
for (int i = 0; i < 3; i++)
{
TransitionDocNode tranNode = averageDocument.MoleculeTransitions.ElementAt(i);
Transition tran = tranNode.Transition;
Assert.AreEqual(reporterIons[i].SettingsCustomIon, tran.CustomIon);
Assert.AreEqual(tran.Charge, i + 1);
Assert.AreEqual(BioMassCalc.CalculateIonMz(mass, tran.Adduct), tranNode.Mz, BioMassCalc.MassElectron / 100);
}
//Make sure the rest of the transitions aren't reporter ions
for (int i = 3; i < 7; i++)
{
Transition tran = docReporterIon.MoleculeTransitions.ElementAt(i).Transition;
Assert.AreNotEqual(tran.CustomIon, reporterIons);
}
var optionalIon = new MeasuredIon(hydrogenPeroxide, formula, null, null, Adduct.SINGLY_PROTONATED, true);
SrmDocument optionalDoc = docPeptide.ChangeSettings(docPeptide.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(new[] { optionalIon })));
Assert.AreEqual(3, optionalDoc.PeptideTransitionCount);
optionalDoc = optionalDoc.ChangeSettings(optionalDoc.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(new[] { optionalIon.ChangeIsOptional(false) })));
AssertEx.IsDocumentTransitionCount(optionalDoc, 4);
Assert.AreEqual(optionalIon.ChangeIsOptional(false).SettingsCustomIon,
optionalDoc.MoleculeTransitions.ElementAt(0).Transition.CustomIon);
optionalDoc =
optionalDoc.ChangeSettings(
optionalDoc.Settings.ChangeTransitionFilter(
filter => filter.ChangeMeasuredIons(new[] { optionalIon.ChangeIsOptional(true) })));
TransitionGroupDocNode nodeGroup = optionalDoc.MoleculeTransitionGroups.ElementAt(0);
var filteredNodes =
nodeGroup.GetPrecursorChoices(optionalDoc.Settings,
optionalDoc.Molecules.ElementAt(0).ExplicitMods, true)
.Cast <TransitionDocNode>()
.Where(node => Equals(node.Transition.CustomIon, optionalIon.SettingsCustomIon));
var unfilteredNodes =
nodeGroup.GetPrecursorChoices(optionalDoc.Settings,
optionalDoc.Molecules.ElementAt(0).ExplicitMods, false)
.Cast <TransitionDocNode>()
.Where(node => Equals(node.Transition.CustomIon, optionalIon.SettingsCustomIon));
Assert.AreEqual(0, filteredNodes.Count());
Assert.AreEqual(1, unfilteredNodes.Count());
}