public override string ToString()
{
if (IsPrecursor())
{
return(Resources.Transition_ToString_precursor + GetChargeIndicator(Charge) +
GetMassIndexText(MassIndex));
}
if (IsCustom())
{
var text = CustomIon.ToString();
// Was there enough information to generate a string more distinctive that just "Ion"?
if (String.IsNullOrEmpty(CustomIon.Name) &&
String.IsNullOrEmpty(CustomIon.Formula))
{
// No, add mz and charge to whatever generic text was used to describe it
var mz = BioMassCalc.CalculateIonMz(CustomIon.MonoisotopicMass, Charge);
return(string.Format("{0} {1:F04}{2}", // Not L10N
text, mz, GetChargeIndicator(Charge)));
}
return(text);
}
return(string.Format("{0} - {1}{2}{3}{4}", // Not L10N
AA,
IonType.ToString().ToLowerInvariant(),
Ordinal,
GetDecoyText(DecoyMassShift),
GetChargeIndicator(Charge)));
}
public void TestParseMass()
{
var bioMassCalc = new BioMassCalc(MassType.Monoisotopic);
string description = "C'2";
Assert.AreEqual(26, bioMassCalc.ParseMass(ref description), .01);
Assert.AreEqual(string.Empty, description);
description = "-C'2";
Assert.AreEqual(0, bioMassCalc.ParseMass(ref description));
Assert.AreEqual("-C'2", description);
description = "C'2-C2";
Assert.AreEqual(26, bioMassCalc.ParseMass(ref description), .01);
Assert.AreEqual("-C2", description);
description = "C'2";
Assert.AreEqual(26, bioMassCalc.ParseMassExpression(ref description), .01);
Assert.AreEqual(string.Empty, description);
description = "C'2-C2";
Assert.AreEqual(2, bioMassCalc.ParseMassExpression(ref description), .01);
Assert.AreEqual(string.Empty, description);
description = "C'2-C2-N2";
Assert.AreEqual(2, bioMassCalc.ParseMassExpression(ref description), .01);
Assert.AreEqual("-N2", description);
Assert.AreEqual(2, bioMassCalc.CalculateMassFromFormula("C'2-C2"), .01);
AssertEx.ThrowsException <ArgumentException>(() => bioMassCalc.CalculateMassFromFormula("C'2-C2-N2"));
}
public TransitionDocNode(Transition id,
Annotations annotations,
TransitionLosses losses,
double massH,
TransitionIsotopeDistInfo isotopeDistInfo,
TransitionLibInfo libInfo,
Results <TransitionChromInfo> results)
: base(id, annotations)
{
Losses = losses;
if (losses != null)
{
massH -= losses.Mass;
}
if (id.IsCustom())
{
Mz = new SignedMz(BioMassCalc.CalculateIonMz(massH, id.Charge), id.IsNegative());
}
else
{
Mz = new SignedMz(SequenceMassCalc.GetMZ(massH, id.Charge) + SequenceMassCalc.GetPeptideInterval(id.DecoyMassShift), id.IsNegative());
}
IsotopeDistInfo = isotopeDistInfo;
LibInfo = libInfo;
Results = results;
}
public void TestParseModParts()
{
var bioMassCalc = new BioMassCalc(MassType.Monoisotopic);
CollectionAssert.AreEqual(new[] { "C'2", "" }, SequenceMassCalc.ParseModParts(bioMassCalc, "C'2"));
CollectionAssert.AreEqual(new[] { "", "C2" }, SequenceMassCalc.ParseModParts(bioMassCalc, "-C2"));
CollectionAssert.AreEqual(new[] { "C'2", "C2" }, SequenceMassCalc.ParseModParts(bioMassCalc, "C'2-C2"));
}
private static void TestEditingTransition()
{
double massPrecisionTolerance = Math.Pow(10, -SequenceMassCalc.MassPrecision);
var doc = SkylineWindow.Document;
RunUI(() =>
{
SkylineWindow.ExpandPrecursors();
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0].FirstNode.FirstNode.FirstNode;
});
var editMoleculeDlg =
ShowDialog <EditCustomMoleculeDlg>(
() => SkylineWindow.ModifyTransition((TransitionTreeNode)SkylineWindow.SequenceTree.SelectedNode));
RunUI(() =>
{
Assert.AreEqual(C12H12, editMoleculeDlg.FormulaBox.Formula);
Assert.AreEqual(BioMassCalc.MONOISOTOPIC.CalculateMassFromFormula(C12H12), editMoleculeDlg.FormulaBox.MonoMass ?? -1, massPrecisionTolerance);
Assert.AreEqual(BioMassCalc.AVERAGE.CalculateMassFromFormula(C12H12), editMoleculeDlg.FormulaBox.AverageMass ?? -1, massPrecisionTolerance);
editMoleculeDlg.FormulaBox.Formula = null;
editMoleculeDlg.Charge = 2; // If we set this after we set the mass, the mass will change since m/z is the actual input
editMoleculeDlg.FormulaBox.AverageMass = 800;
editMoleculeDlg.FormulaBox.MonoMass = 805;
editMoleculeDlg.NameText = "Fragment";
});
OkDialog(editMoleculeDlg, editMoleculeDlg.OkDialog);
var newdoc = WaitForDocumentChange(doc);
Assert.AreEqual("Fragment", newdoc.MoleculeTransitions.ElementAt(0).Transition.CustomIon.ToString());
Assert.AreEqual(BioMassCalc.CalculateIonMz(805, 2), newdoc.MoleculeTransitions.ElementAt(0).Mz, massPrecisionTolerance);
Assert.IsFalse(ReferenceEquals(doc.MoleculeTransitions.ElementAt(0).Id, newdoc.MoleculeTransitions.ElementAt(0).Id)); // Changing the mass changes the Id
// Verify that tree selection doesn't change just because we changed an ID object
// (formerly the tree node would collapse and focus would jump up a level)
RunUI(() =>
{
Assert.AreEqual(SkylineWindow.SequenceTree.SelectedNode, SkylineWindow.SequenceTree.Nodes[0].FirstNode.FirstNode.FirstNode);
});
// And test undo/redo
RunUI(() => SkylineWindow.Undo());
newdoc = WaitForDocumentChange(newdoc);
Assert.AreNotEqual("Fragment", newdoc.MoleculeTransitions.ElementAt(0).Transition.CustomIon.ToString());
Assert.AreNotEqual(BioMassCalc.CalculateIonMz(805, 2), newdoc.MoleculeTransitions.ElementAt(0).Mz, massPrecisionTolerance);
Assert.IsTrue(ReferenceEquals(doc.MoleculeTransitions.ElementAt(0).Id, newdoc.MoleculeTransitions.ElementAt(0).Id));
RunUI(() => SkylineWindow.Redo());
newdoc = WaitForDocumentChange(newdoc);
Assert.AreEqual("Fragment", newdoc.MoleculeTransitions.ElementAt(0).Transition.CustomIon.ToString());
Assert.AreEqual(BioMassCalc.CalculateIonMz(805, 2), newdoc.MoleculeTransitions.ElementAt(0).Mz, massPrecisionTolerance);
// Verify that tree selection doesn't change just because we changed an ID object
// (formerly the tree node would collapse and focus would jump up a level)
RunUI(() =>
{
Assert.AreEqual(SkylineWindow.SequenceTree.SelectedNode, SkylineWindow.SequenceTree.Nodes[0].FirstNode.FirstNode.FirstNode);
});
}
private void DoValidate()
{
if (!BioMassCalc.IsSkylineHeavySymbol(IsotopeSymbol)) // e.g. accept H' but not D
{
throw new InvalidDataException(string.Format(Resources.IsotopeEnrichmentItem_DoValidate_Isotope_enrichment_is_not_supported_for_the_symbol__0__, IsotopeSymbol));
}
if (MIN_ATOM_PERCENT_ENRICHMENT > AtomPercentEnrichment ||
AtomPercentEnrichment > MAX_ATOM_PERCENT_ENRICHMENT)
{
throw new InvalidDataException(string.Format(Resources.IsotopeEnrichmentItem_DoValidate_Atom_percent_enrichment__0__must_be_between__1__and__2__,
AtomPercentEnrichment, MIN_ATOM_PERCENT_ENRICHMENT, MAX_ATOM_PERCENT_ENRICHMENT));
}
}
private void DoValidate()
{
var isotopes = BioMassCalc.DEFAULT_ABUNDANCES;
var dictSymDist = _isotopeEnrichments.ToDictionary(e => e.IsotopeSymbol,
e => e.CalcDistribution(isotopes));
// Make sure all heavy symbols used in Skyline are represented.
foreach (string symbol in BioMassCalc.HeavySymbols.Where(symbol => !dictSymDist.ContainsKey(symbol)))
{
dictSymDist.Add(symbol, new IsotopeEnrichmentItem(symbol, 1.0).CalcDistribution(isotopes));
}
IsotopeAbundances = BioMassCalc.AddHeavyNicknames(isotopes.SetAbundances(dictSymDist));
}
private string GetTextFromMass(double?mass)
{
if (!mass.HasValue)
{
return(string.Empty);
}
double result = mass.Value;
if (Charge.HasValue)
{
// We want to show this as an m/z value, rounded to a reasonable length
result = SequenceMassCalc.PersistentMZ(BioMassCalc.CalculateIonMz(result, Charge.Value));
}
return(result.ToString(CultureInfo.CurrentCulture));
}
private void ProposeMoleculeWithCommonFormula(Peptide peptide)
{
// Examine any provided formulas (including parent molecule and/or precursor ions) and find common basis
ProposedMolecule = peptide.CustomMolecule;
var precursorsWithFormulas = _precursorRawDetails.Where(d => !string.IsNullOrEmpty(d._formulaUnlabeled)).ToList();
var parentFormula = peptide.CustomMolecule.UnlabeledFormula;
var commonFormula = string.IsNullOrEmpty(parentFormula)
? BioMassCalc.MONOISOTOPIC.FindFormulaIntersectionUnlabeled(
precursorsWithFormulas.Select(p => p._formulaUnlabeled))
: parentFormula;
// Check for consistent and correctly declared precursor formula+adduct
var precursorsWithFormulasAndAdducts = precursorsWithFormulas.Where(d => !Adduct.IsNullOrEmpty(d._nominalAdduct)).ToList();
if (precursorsWithFormulasAndAdducts.Any() &&
precursorsWithFormulas.All(
d => d._formulaUnlabeled.Equals(precursorsWithFormulasAndAdducts[0]._formulaUnlabeled)))
{
commonFormula = precursorsWithFormulasAndAdducts[0]._formulaUnlabeled;
}
if (!string.IsNullOrEmpty(commonFormula))
{
var parentComposition = Molecule.ParseExpression(commonFormula);
// Check for children proposing to label more atoms than parent provides, adjust parent as needed
foreach (var precursor in _precursorRawDetails.Where(d => d._labels != null))
{
foreach (var kvpIsotopeCount in precursor._labels)
{
var unlabeled = BioMassCalc.UnlabeledFromIsotopeSymbol(kvpIsotopeCount.Key);
int parentCount;
parentComposition.TryGetValue(unlabeled, out parentCount);
if (kvpIsotopeCount.Value > parentCount)
{
// Child proposes to label more of an atom than the parent possesses (seen in the wild) - update the parent
commonFormula =
Molecule.AdjustElementCount(commonFormula, unlabeled, kvpIsotopeCount.Value - parentCount);
parentComposition = Molecule.ParseExpression(commonFormula);
}
}
}
if (!Equals(peptide.CustomMolecule.Formula, commonFormula))
{
ProposedMolecule = new CustomMolecule(commonFormula, peptide.CustomMolecule.Name);
}
}
}
protected virtual void ReadAttributes(XmlReader reader, out Adduct embeddedAdduct)
{
var formula = reader.GetAttribute(ATTR.formula);
if (!string.IsNullOrEmpty(formula))
{
formula = BioMassCalc.AddH(formula); // Update this old style formula to current by adding the hydrogen we formerly left out due to assuming protonation
}
else
{
var text = reader.GetAttribute(ATTR.ion_formula) ?? reader.GetAttribute(ATTR.neutral_formula);
if (text != null)
{
text = text.Trim(); // We've seen some trailing spaces in the wild
}
formula = text;
}
string neutralFormula;
Molecule mol;
// We commonly see the adduct inline with the neutral formula ("C12H5[M+Na]"), so be ready to preserve that
if (IonInfo.IsFormulaWithAdduct(formula, out mol, out embeddedAdduct, out neutralFormula))
{
formula = neutralFormula;
}
else
{
embeddedAdduct = Adduct.EMPTY;
}
if (string.IsNullOrEmpty(formula))
{
AverageMass = ReadAverageMass(reader);
MonoisotopicMass = ReadMonoisotopicMass(reader);
}
Formula = formula;
Name = reader.GetAttribute(ATTR.custom_ion_name);
if (string.IsNullOrEmpty(Name))
{
Name = reader.GetAttribute(ATTR.name) ?? string.Empty;
}
AccessionNumbers = MoleculeAccessionNumbers.FromSerializableString(reader.GetAttribute(ATTR.id));
Validate();
}
protected virtual void ReadAttributes(XmlReader reader)
{
Formula = reader.GetAttribute(ATTR.formula);
if (!string.IsNullOrEmpty(Formula))
{
Formula = BioMassCalc.AddH(Formula); // Update this old style formula to current by adding the hydrogen we formerly left out due to assuming protonation
}
else
{
Formula = reader.GetAttribute(ATTR.ion_formula);
}
if (string.IsNullOrEmpty(Formula))
{
AverageMass = reader.GetDoubleAttribute(ATTR.mass_average);
MonoisotopicMass = reader.GetDoubleAttribute(ATTR.mass_monoisotopic);
}
Validate();
}
public void TestGetHeavyFormula()
{
Assert.AreEqual("C'O2", SequenceMassCalc.GetHeavyFormula("CO2", LabelAtoms.C13));
Assert.AreEqual("C'O2", SequenceMassCalc.GetHeavyFormula("C'O2", LabelAtoms.C13));
Assert.AreEqual("C'", SequenceMassCalc.GetHeavyFormula("C", LabelAtoms.C13));
Assert.AreEqual("N'", SequenceMassCalc.GetHeavyFormula("N", LabelAtoms.N15));
Assert.AreEqual("O'", SequenceMassCalc.GetHeavyFormula("O", LabelAtoms.O18));
Assert.AreEqual("H'", SequenceMassCalc.GetHeavyFormula("H", LabelAtoms.H2));
Assert.AreEqual("Cl'", SequenceMassCalc.GetHeavyFormula("Cl", LabelAtoms.Cl37));
Assert.AreEqual("Br'", SequenceMassCalc.GetHeavyFormula("Br", LabelAtoms.Br81));
Assert.AreEqual("P'", SequenceMassCalc.GetHeavyFormula("P", LabelAtoms.P32));
Assert.AreEqual("S'", SequenceMassCalc.GetHeavyFormula("S", LabelAtoms.S34));
// Make sure IUPAC nicknames don't find their way into our list of heavy symbols
Assume.IsTrue(BioMassCalc.IsSkylineHeavySymbol("H'"));
Assume.IsFalse(BioMassCalc.IsSkylineHeavySymbol("D"));
Assume.IsFalse(BioMassCalc.IsSkylineHeavySymbol("T"));
}
private void TestTaxolAdduct(string adductText, double expectedMz, int expectedCharge, HashSet <string> coverage)
{
// See http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator/
var Taxol = "C47H51NO14"; // M=853.33089 (agrees with chemspider)
var calcMass = BioMassCalc.MONOISOTOPIC.CalculateMassFromFormula(Taxol);
Assert.AreEqual(massTaxol, calcMass, .0001);
var adduct = Adduct.FromStringAssumeProtonated(adductText);
Assert.AreEqual(expectedCharge, adduct.AdductCharge);
var mz = BioMassCalc.CalculateIonMz(calcMass, adduct);
Assert.AreEqual(expectedMz, mz, .001);
var massWithIsotopes = adduct.MassFromMz(mz, MassType.Monoisotopic);
Assert.AreEqual(massTaxol, massWithIsotopes - adduct.GetIsotopesIncrementalMonoisotopicMass() / adduct.GetMassMultiplier(), .0001);
coverage.Add(adduct.AsFormula());
}
/// <summary>
/// Calculates the matching charge within a tolerance for a mass.
/// </summary>
/// <param name="massH">The mass to calculate charge for</param>
/// <param name="mz">The desired m/z value the charge should produce</param>
/// <param name="tolerance">How far off the actual m/z is allowed to be</param>
/// <param name="isCustomIon">Is this a custom ion formula?</param>
/// <param name="minCharge">Minimum charge to consider</param>
/// <param name="maxCharge">Maximum charge to consider</param>
/// <param name="massShifts">Possible mass shifts that may have been applied to decoys</param>
/// <param name="massShiftType"></param>
/// <param name="massShift">Mass shift required to to achieve this charge state or zero</param>
/// <param name="nearestCharge">closest matching charge, useful when return value is null</param>
/// <returns>A matching charge or null, in which case the closest non-matching charge can be found in the nearestCharge value.</returns>
public static int?CalcCharge(double massH, double mz, double tolerance, bool isCustomIon, int minCharge, int maxCharge,
ICollection <int> massShifts, MassShiftType massShiftType, out int massShift, out int nearestCharge)
{
Assume.IsTrue(minCharge <= maxCharge);
massShift = 0;
nearestCharge = 0;
double nearestDelta = double.MaxValue;
for (int i = minCharge; i <= maxCharge; i++)
{
if (i != 0) // Avoid z=0 if we're entertaining negative charge states
{
double delta = mz - (isCustomIon ? BioMassCalc.CalculateIonMz(massH, i) : SequenceMassCalc.GetMZ(massH, i));
double deltaAbs = Math.Abs(delta);
int potentialShift = (int)Math.Round(deltaAbs);
double fractionalDelta = deltaAbs - potentialShift;
if (MatchMz(fractionalDelta, tolerance) && MatchMassShift(potentialShift, massShifts, massShiftType))
{
massShift = potentialShift;
if (delta < 0)
{
massShift = -massShift;
}
int?result = i;
nearestCharge = i;
return(result);
}
if (deltaAbs < nearestDelta)
{
nearestDelta = deltaAbs;
nearestCharge = i;
}
}
}
Debug.Assert(nearestCharge != 0); // Could only happen if min > max
return(null);
}
/// <summary>
/// Get a mass value from the text string, treating the string as m/z info if we have a charge state
/// </summary>
private double?GetMassFromText(string text)
{
try
{
if (String.IsNullOrEmpty(text))
{
return(null);
}
else
{
double parsed = double.Parse(text);
if (Charge.HasValue)
{
// Convert from m/z to mass
return(BioMassCalc.CalculateIonMassFromMz(parsed, Charge.Value));
}
return(parsed);
}
}
catch (Exception)
{
return(null);
}
}
public void DoFullScanSettingsTest(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules,
out List <SrmDocument> docCheckPoints)
{
docCheckPoints = new List <SrmDocument>();
var doc0 = ResultsUtil.DeserializeDocument("MultiLabel.sky", GetType());
var refine = new RefinementSettings();
var docSM = refine.ConvertToSmallMolecules(doc0, ".", asSmallMolecules);
docCheckPoints.Add(docSM);
Assert.IsFalse(docSM.MoleculeTransitionGroups.Any(nodeGroup => nodeGroup.IsotopeDist != null));
AssertEx.Serializable(docSM, AssertEx.Cloned);
double c13Delta = BioMassCalc.MONOISOTOPIC.GetMass(BioMassCalc.C13) -
BioMassCalc.MONOISOTOPIC.GetMass(BioMassCalc.C);
double n15Delta = BioMassCalc.MONOISOTOPIC.GetMass(BioMassCalc.N15) -
BioMassCalc.MONOISOTOPIC.GetMass(BioMassCalc.N);
// Verify isotope distributions calculated when MS1 filtering enabled
var enrichments = IsotopeEnrichmentsList.DEFAULT;
var docIsotopes = docSM.ChangeSettings(docSM.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count, 3, enrichments)));
docCheckPoints.Add(docIsotopes);
Assert.AreEqual(FullScanMassAnalyzerType.tof,
docIsotopes.Settings.TransitionSettings.FullScan.PrecursorMassAnalyzer);
Assert.IsFalse(docIsotopes.MoleculeTransitionGroups.Any(nodeGroup => nodeGroup.IsotopeDist == null));
foreach (var nodeGroup in docIsotopes.MoleculeTransitionGroups)
{
Assert.AreEqual(3, nodeGroup.Children.Count);
var isotopePeaks = nodeGroup.IsotopeDist;
Assert.IsNotNull(isotopePeaks);
Assert.IsTrue(nodeGroup.HasIsotopeDist);
// The peaks should always includ at least M-1
Assume.IsTrue(isotopePeaks.MassIndexToPeakIndex(0) > 0);
// Within 2.5% of 100% of the entire isotope distribution
Assert.AreEqual(1.0, isotopePeaks.ExpectedProportions.Sum(), 0.025);
// Precursor mass and m/z values are expected to match exactly (well, within XML roundtrip accuracy anyway)
Assert.AreEqual(nodeGroup.PrecursorMz, nodeGroup.IsotopeDist.GetMZI(0), SequenceMassCalc.MassTolerance);
Assert.AreEqual(nodeGroup.PrecursorMz, nodeGroup.TransitionGroup.IsCustomIon ?
BioMassCalc.CalculateIonMz(nodeGroup.IsotopeDist.GetMassI(0),
nodeGroup.TransitionGroup.PrecursorAdduct.Unlabeled) :
SequenceMassCalc.GetMZ(nodeGroup.IsotopeDist.GetMassI(0),
nodeGroup.TransitionGroup.PrecursorAdduct), SequenceMassCalc.MassTolerance);
// Check isotope distribution masses
for (int i = 1; i < isotopePeaks.CountPeaks; i++)
{
int massIndex = isotopePeaks.PeakIndexToMassIndex(i);
Assert.IsTrue(isotopePeaks.GetMZI(massIndex - 1) < isotopePeaks.GetMZI(massIndex));
double massDelta = GetMassDelta(isotopePeaks, massIndex);
if (nodeGroup.TransitionGroup.LabelType.IsLight)
{
// All positive should be close to 13C - C, and 0 should be the same as the next delta
double expectedDelta = (massIndex > 0 ? c13Delta : GetMassDelta(isotopePeaks, massIndex + 1));
Assert.AreEqual(expectedDelta, massDelta, 0.001);
}
else if (nodeGroup.TransitionGroup.LabelType.Name.Contains("15N"))
{
// All positive should be close to 13C, and all negative 15N
double expectedDelta = (massIndex > 0 ? c13Delta : n15Delta);
Assert.AreEqual(expectedDelta, massDelta, 0.0015);
}
else if (massIndex == 0)
{
double expectedDelta = (isotopePeaks.GetProportionI(massIndex - 1) == 0
? GetMassDelta(isotopePeaks, massIndex + 1)
: 1.0017);
Assert.AreEqual(expectedDelta, massDelta, 0.001);
}
else
{
Assert.AreEqual(c13Delta, massDelta, 0.001);
}
}
}
AssertEx.Serializable(docIsotopes, AssertEx.Cloned);
// Narrow the resolution, and verify that predicted proportion of the isotope
// distribution captured is reduced for all precursors
var docIsotopesFt = docIsotopes.ChangeSettings(docIsotopes.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorResolution(FullScanMassAnalyzerType.ft_icr, 500 * 1000, 400)));
docCheckPoints.Add(docIsotopesFt);
var tranGroupsOld = docIsotopes.MoleculeTransitionGroups.ToArray();
var tranGroupsNew = docIsotopesFt.MoleculeTransitionGroups.ToArray();
Assume.AreEqual(tranGroupsOld.Length, tranGroupsNew.Length);
for (int i = 0; i < tranGroupsOld.Length; i++)
{
Assert.AreNotSame(tranGroupsOld[i], tranGroupsNew[i]);
Assert.AreNotSame(tranGroupsOld[i].IsotopeDist, tranGroupsNew[i].IsotopeDist);
Assert.IsTrue(tranGroupsOld[i].IsotopeDist.ExpectedProportions.Sum() >
tranGroupsNew[i].IsotopeDist.ExpectedProportions.Sum());
}
// Use Min % of base peak and verify variation in transitions used
const float minPercent1 = 10;
var docIsotopesP1 = docIsotopes.ChangeSettings(docIsotopes.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Percent, minPercent1, enrichments)));
docCheckPoints.Add(docIsotopesP1);
tranGroupsNew = docIsotopesP1.MoleculeTransitionGroups.ToArray();
int maxTran = 0;
for (int i = 0; i < tranGroupsOld.Length; i++)
{
// Isotope distributions should not have changed
var isotopePeaks = tranGroupsNew[i].IsotopeDist;
Assert.AreSame(tranGroupsOld[i].IsotopeDist, isotopePeaks);
// Expected transitions should be present
maxTran = Math.Max(maxTran, tranGroupsNew[i].Children.Count);
foreach (TransitionDocNode nodeTran in tranGroupsNew[i].Children)
{
int massIndex = nodeTran.Transition.MassIndex;
Assume.IsTrue(minPercent1 <= isotopePeaks.GetProportionI(massIndex) * 100.0 / isotopePeaks.BaseMassPercent);
}
}
Assume.AreEqual(5, maxTran);
AssertEx.Serializable(docIsotopesP1, AssertEx.Cloned); // Express any failure in terms of XML diffs
// Use 10%, and check that 15N modifications all have M-1
const float minPercent2 = 5;
var docIsotopesP2 = docIsotopesP1.ChangeSettings(docIsotopesP1.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Percent, minPercent2, enrichments)));
docCheckPoints.Add(docIsotopesP2);
foreach (var nodeGroup in docIsotopesP2.MoleculeTransitionGroups)
{
var firstChild = (TransitionDocNode)nodeGroup.Children[0];
if (nodeGroup.TransitionGroup.LabelType.Name.EndsWith("15N"))
{
Assume.AreEqual(-1, firstChild.Transition.MassIndex);
}
else
{
Assume.AreNotEqual(-1, firstChild.Transition.MassIndex);
}
}
AssertEx.Serializable(docIsotopesP2, AssertEx.Cloned);
// Use lower enrichment of 13C, and verify that this add M-1 for 13C labeled precursors
var enrichmentsLow13C = enrichments.ChangeEnrichment(new IsotopeEnrichmentItem(BioMassCalc.C13, 0.9));
var docIsotopesLow13C = docIsotopesP1.ChangeSettings(docIsotopesP1.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Percent, minPercent2, enrichmentsLow13C)));
tranGroupsNew = docIsotopesLow13C.MoleculeTransitionGroups.ToArray();
for (int i = 0; i < tranGroupsOld.Length; i++)
{
var nodeGroup = tranGroupsNew[i];
if (!Equals(nodeGroup.TransitionGroup.LabelType.Name, "heavy"))
{
Assert.AreSame(tranGroupsOld[i].IsotopeDist, nodeGroup.IsotopeDist);
}
else
{
var firstChild = (TransitionDocNode)nodeGroup.Children[0];
Assert.IsTrue(firstChild.Transition.MassIndex < 0);
}
}
AssertEx.Serializable(docIsotopesLow13C, AssertEx.Cloned); // Express any failure as XML diffs
// Use 0%, and check that everything has M-1 and lower
var enrichmentsLow = enrichmentsLow13C.ChangeEnrichment(new IsotopeEnrichmentItem(BioMassCalc.N15, 0.97));
var docIsotopesLowP0 = docIsotopesP1.ChangeSettings(docIsotopesP1.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Percent, 0, enrichmentsLow)));
docCheckPoints.Add(docIsotopesLowP0);
foreach (var nodeGroup in docIsotopesLowP0.MoleculeTransitionGroups)
{
Assume.AreEqual(nodeGroup.IsotopeDist.CountPeaks, nodeGroup.Children.Count);
var firstChild = (TransitionDocNode)nodeGroup.Children[0];
if (nodeGroup.TransitionGroup.LabelType.IsLight)
{
Assert.AreEqual(-1, firstChild.Transition.MassIndex);
}
else
{
Assert.IsTrue(-1 > firstChild.Transition.MassIndex);
}
}
AssertEx.Serializable(docIsotopesLowP0, AssertEx.Cloned);
// Test a document with variable and heavy modifications, which caused problems for
// the original implementation
var docVariable = ResultsUtil.DeserializeDocument("HeavyVariable.sky", GetType());
Assert.IsFalse(docVariable.MoleculeTransitionGroups.Any(nodeGroup => nodeGroup.IsotopeDist == null));
foreach (var nodeGroup in docVariable.MoleculeTransitionGroups)
{
var isotopePeaks = nodeGroup.IsotopeDist;
Assert.IsNotNull(isotopePeaks);
// The peaks should always includ at least M-1
Assert.IsTrue(isotopePeaks.MassIndexToPeakIndex(0) > 0);
// Precursor mass and m/z values are expected to match exactly (well, within XML roundtrip tolerance anyway)
var mzI = nodeGroup.IsotopeDist.GetMZI(0);
Assert.AreEqual(nodeGroup.PrecursorMz, mzI, SequenceMassCalc.MassTolerance);
// Check isotope distribution masses
for (int i = 1; i < isotopePeaks.CountPeaks; i++)
{
int massIndex = isotopePeaks.PeakIndexToMassIndex(i);
Assert.IsTrue(isotopePeaks.GetMZI(massIndex - 1) < isotopePeaks.GetMZI(massIndex));
double massDelta = GetMassDelta(isotopePeaks, massIndex);
bool containsSulfur = nodeGroup.TransitionGroup.Peptide.IsCustomMolecule
? (nodeGroup.CustomMolecule.Formula.IndexOfAny("S".ToCharArray()) != -1)
: (nodeGroup.TransitionGroup.Peptide.Sequence.IndexOfAny("CM".ToCharArray()) != -1);
if (massIndex == 0)
{
double expectedDelta = (isotopePeaks.GetProportionI(massIndex - 1) == 0
? GetMassDelta(isotopePeaks, massIndex + 1)
: 1.0017);
Assert.AreEqual(expectedDelta, massDelta, 0.001);
}
else if (!containsSulfur || massIndex == 1)
{
Assert.AreEqual(c13Delta, massDelta, 0.001);
}
else
{
Assert.AreEqual(1.00075, massDelta, 0.001);
}
}
}
docCheckPoints.Add(docVariable);
}
public void AdductParserTest()
{
TestAdductOperators();
var coverage = new HashSet <string>();
TestPentaneAdduct("[M+2NH4]", "C5H20N2", 2, coverage); // multiple of a group
TestPentaneAdduct("[M+2(NH4)]", "C5H20N2", 2, coverage); // multiple of a group in parenthesis
TestPentaneAdduct("[M+2H]", "C5H14", 2, coverage);
TestPentaneAdduct("[M2C13+2H]", "C3C'2H14", 2, coverage); // Labeled
TestPentaneAdduct("[2M2C13+2H]", "C6C'4H26", 2, coverage); // Labeled dimer
TestPentaneAdduct("[2M2C14+2H]", "C6C\"4H26", 2, coverage); // Labeled dimer
TestPentaneAdduct("[M2C13]", "C3C'2H12", 0, coverage); // Labeled no charge
TestPentaneAdduct("[2M2C13]", "C6C'4H24", 0, coverage); // Labeled, dimer, no charge
TestPentaneAdduct("[2M]", "C10H24", 0, coverage); // dimer no charge
TestPentaneAdduct("[2M2C13+3]", "C6C'4H24", 3, coverage); // Labeled, dimer, charge only
TestPentaneAdduct("[2M2C13]+3", "C6C'4H24", 3, coverage); // Labeled, dimer, charge only
TestPentaneAdduct("[2M2C13+++]", "C6C'4H24", 3, coverage); // Labeled, dimer, charge only
TestPentaneAdduct("[2M2C13]+++", "C6C'4H24", 3, coverage); // Labeled, dimer, charge only
TestPentaneAdduct("[2M+3]", "C10H24", 3, coverage); // dimer charge only
TestPentaneAdduct("[2M]+3", "C10H24", 3, coverage); // dimer charge only
TestPentaneAdduct("[2M+++]", "C10H24", 3, coverage); // dimer charge only
TestPentaneAdduct("[2M]+++", "C10H24", 3, coverage); // dimer charge only
TestPentaneAdduct("[2M2C13-3]", "C6C'4H24", -3, coverage); // Labeled, dimer, charge only
TestPentaneAdduct("[2M2C13---]", "C6C'4H24", -3, coverage); // Labeled, dimer, charge only
TestPentaneAdduct("[2M-3]", "C10H24", -3, coverage); // dimer charge only
TestPentaneAdduct("[2M---]", "C10H24", -3, coverage); // dimer charge only
TestPentaneAdduct("[2M2C133H2+2H]", "C6C'4H20H'6", 2, coverage); // Labeled with some complexity, multiplied
TestPentaneAdduct("M+H", "C5H13", 1, coverage);
TestPentaneAdduct("M+", PENTANE, 1, coverage);
TestPentaneAdduct("M+2", PENTANE, 2, coverage);
TestPentaneAdduct("M+3", PENTANE, 3, coverage);
TestPentaneAdduct("M-", PENTANE, -1, coverage);
TestPentaneAdduct("M-2", PENTANE, -2, coverage);
TestPentaneAdduct("M-3", PENTANE, -3, coverage);
TestPentaneAdduct("M++", PENTANE, 2, coverage);
TestPentaneAdduct("M--", PENTANE, -2, coverage);
TestPentaneAdduct("M", PENTANE, 0, coverage); // Trivial non-adduct
TestPentaneAdduct("M+CH3COO", "C7H15O2", -1, coverage); // From XCMS
TestPentaneAdduct("[M+H]1+", "C5H13", 1, coverage);
TestPentaneAdduct("[M-H]1-", "C5H11", -1, coverage);
TestPentaneAdduct("[M-2H]", "C5H10", -2, coverage);
TestPentaneAdduct("[M-2H]2-", "C5H10", -2, coverage);
TestPentaneAdduct("[M+2H]++", "C5H14", 2, coverage);
TestPentaneAdduct("[MH2+2H]++", "C5H13H'", 2, coverage); // Isotope
TestPentaneAdduct("[MH3+2H]++", "C5H13H\"", 2, coverage); // Isotope
TestPentaneAdduct("[MD+2H]++", "C5H13H'", 2, coverage); // Isotope
TestPentaneAdduct("[MD+DMSO+2H]++", "C7H19H'OS", 2, coverage); // Check handling of Deuterium and DMSO together
TestPentaneAdduct("[MT+DMSO+2H]++", "C7H19H\"OS", 2, coverage); // Check handling of Tritium
TestPentaneAdduct("[M+DMSO+2H]++", "C7H20OS", 2, coverage);
TestPentaneAdduct("[M+DMSO+2H]2+", "C7H20OS", 2, coverage);
TestPentaneAdduct("[M+MeOH-H]", "C6H15O", -1, coverage); // Methanol "CH3OH"
TestPentaneAdduct("[M+MeOX-H]", "C6H14N", -1, coverage); // Methoxamine "CH3N"
TestPentaneAdduct("[M+TMS-H]", "C8H19Si", -1, coverage); // MSTFA(N-methyl-N-trimethylsilytrifluoroacetamide) "C3H8Si"
TestPentaneAdduct("[M+TMS+MeOX]-", "C9H23NSi", -1, coverage);
TestPentaneAdduct("[M+HCOO]", "C6H13O2", -1, coverage);
TestPentaneAdduct("[M+NOS]5+", "C5H12NOS", 5, coverage); // Not a real adduct, but be ready for adducts we just don't know about
TestPentaneAdduct("[M+NOS]5", "C5H12NOS", 5, coverage); // Not a real adduct, but be ready for adducts we just don't know about
TestPentaneAdduct("[M+NOS]5-", "C5H12NOS", -5, coverage); // Not a real adduct, but be ready for adducts we just don't know about
// See http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator/
// There you will find an excel spreadsheet from which I pulled these numbers, which as it turns out has several errors in it.
// There is also a table in the web page itself that contains the same values and some unmarked corrections.
// Sadly that faulty spreadsheet is copied all over the internet. I've let the author know what we found. - bspratt
TestTaxolAdduct("M+3H", 285.450928, 3, coverage);
TestTaxolAdduct("M+2H+Na", 292.778220, 3, coverage);
TestTaxolAdduct("M+H+2Na", 300.105557, 3, coverage); // Spreadsheet and table both say 300.209820, but also says adduct "mass" = 15.766190, I get 15.6618987 using their H and Na masses (and this is clearly m/z, not mass)
TestTaxolAdduct("M+3Na", 307.432848, 3, coverage);
TestTaxolAdduct("M+2H", 427.672721, 2, coverage);
TestTaxolAdduct("M+H+NH4", 436.185995, 2, coverage);
TestTaxolAdduct("M+H+Na", 438.663692, 2, coverage);
TestTaxolAdduct("M+H+K", 446.650662, 2, coverage);
TestTaxolAdduct("M+ACN+2H", 448.185995, 2, coverage);
TestTaxolAdduct("M+2Na", 449.654663, 2, coverage);
TestTaxolAdduct("M+2ACN+2H", 468.699268, 2, coverage);
TestTaxolAdduct("M+3ACN+2H", 489.212542, 2, coverage);
TestTaxolAdduct("M+H", 854.338166, 1, coverage);
TestTaxolAdduct("M+NH4", 871.364713, 1, coverage);
TestTaxolAdduct("M+Na", 876.320108, 1, coverage);
TestTaxolAdduct("M+CH3OH+H", 886.364379, 1, coverage);
TestTaxolAdduct("M+K", 892.294048, 1, coverage);
TestTaxolAdduct("M+ACN+H", 895.364713, 1, coverage);
TestTaxolAdduct("M+2Na-H", 898.302050, 1, coverage);
TestTaxolAdduct("M+IsoProp+H", 914.396230, 1, coverage);
TestTaxolAdduct("M+ACN+Na", 917.346655, 1, coverage);
TestTaxolAdduct("M+2K-H", 930.249930, 1, coverage); // Spreadsheet and table disagree - spreadsheet says "M+2K+H" but that's 3+, not 1+, and this fits the mz value
TestTaxolAdduct("M+DMSO+H", 932.352110, 1, coverage);
TestTaxolAdduct("M+2ACN+H", 936.391260, 1, coverage);
TestTaxolAdduct("M+IsoProp+Na+H", 468.692724, 2, coverage); // Spreadsheet and table both say mz=937.386000 z=1 (does Isoprop interact somehow to eliminate half the ionization?)
TestTaxolAdduct("2M+H", 1707.669056, 1, coverage);
TestTaxolAdduct("2M+NH4", 1724.695603, 1, coverage);
TestTaxolAdduct("2M+Na", 1729.650998, 1, coverage);
TestTaxolAdduct("2M+3H2O+2H", 881.354, 2, coverage); // Does not appear in table. Charge agrees but spreadsheet says mz= 1734.684900
TestTaxolAdduct("2M+K", 1745.624938, 1, coverage);
TestTaxolAdduct("2M+ACN+H", 1748.695603, 1, coverage);
TestTaxolAdduct("2M+ACN+Na", 1770.677545, 1, coverage);
TestTaxolAdduct("M-3H", 283.436354, -3, coverage);
TestTaxolAdduct("M-2H", 425.658169, -2, coverage);
TestTaxolAdduct("M-H2O-H", 834.312500, -1, coverage);
TestTaxolAdduct("M+-H2O-H", 834.312500, -1, coverage); // Tolerate empty atom description ("+-")
TestTaxolAdduct("M-H", 852.323614, -1, coverage);
TestTaxolAdduct("M+Na-2H", 874.305556, -1, coverage);
TestTaxolAdduct("M+Cl", 888.300292, -1, coverage);
TestTaxolAdduct("M+K-2H", 890.279496, -1, coverage);
TestTaxolAdduct("M+FA-H", 898.329091, -1, coverage);
TestTaxolAdduct("M+Hac-H", 912.344741, -1, coverage);
TestTaxolAdduct("M+Br", 932.249775, -1, coverage);
TestTaxolAdduct("MT+TFA-H", 968.324767, -1, coverage); // Tritium label + TFA
TestTaxolAdduct("M+TFA-H", 966.316476, -1, coverage);
TestTaxolAdduct("2M-H", 1705.654504, -1, coverage);
TestTaxolAdduct("2M+FA-H", 1751.659981, -1, coverage);
TestTaxolAdduct("2M+Hac-H", 1765.675631, -1, coverage);
TestTaxolAdduct("3M-H", 2558.985394, -1, coverage); // Spreadsheet and table give mz as 2560.999946 -but also gives adduct "mass" as 1.007276, should be -1.007276
// A couple more simple ones we support with statics
TestTaxolAdduct("M+4H", 214.3400149, 4, coverage);
TestTaxolAdduct("M+5H", 171.6734671, 5, coverage);
// And a few of our own to exercise the interaction of multiplier and isotope
var dC13 = BioMassCalc.MONOISOTOPIC.GetMass(BioMassCalc.C13) - BioMassCalc.MONOISOTOPIC.GetMass(BioMassCalc.C);
TestTaxolAdduct("M2C13+3H", 285.450928 + (2 * dC13) / 3.0, 3, coverage);
TestTaxolAdduct("M2C13+2H+Na", 292.778220 + (2 * dC13) / 3.0, 3, coverage);
TestTaxolAdduct("2M2C13+3H", 285.450906 + (massTaxol + 4 * dC13) / 3.0, 3, coverage);
TestTaxolAdduct("2M2C13+2H+Na", 292.778220 + (massTaxol + 4 * dC13) / 3.0, 3, coverage);
var dC14 = BioMassCalc.MONOISOTOPIC.GetMass(BioMassCalc.C14) - BioMassCalc.MONOISOTOPIC.GetMass(BioMassCalc.C);
TestTaxolAdduct("M2C14+3H", 285.450928 + (2 * dC14) / 3.0, 3, coverage);
TestTaxolAdduct("M2C14+2H+Na", 292.778220 + (2 * dC14) / 3.0, 3, coverage);
TestTaxolAdduct("2M2C14+3H", 285.450906 + (massTaxol + 4 * dC14) / 3.0, 3, coverage);
TestTaxolAdduct("2M2C14+2H+Na", 292.778220 + (massTaxol + 4 * dC14) / 3.0, 3, coverage);
// Using example adducts from
// https://gnps.ucsd.edu/ProteoSAFe/gnpslibrary.jsp?library=GNPS-LIBRARY#%7B%22Library_Class_input%22%3A%221%7C%7C2%7C%7C3%7C%7CEXACT%22%7D
var Hectochlorin = "C27H34Cl2N2O9S2";
var massHectochlorin = 664.108276; // http://www.chemspider.com/Chemical-Structure.552449.html?rid=3a7c08af-0886-4e82-9e4f-5211b8efb373
var adduct = Adduct.FromStringAssumeProtonated("M+H");
var mol = IonInfo.ApplyAdductToFormula(Hectochlorin, adduct).ToString();
var mass = BioMassCalc.MONOISOTOPIC.CalculateMassFromFormula(mol);
Assert.AreEqual(massHectochlorin + BioMassCalc.MONOISOTOPIC.CalculateMassFromFormula("H"), mass, 0.00001);
var mz = BioMassCalc.CalculateIonMz(BioMassCalc.MONOISOTOPIC.CalculateMassFromFormula(Hectochlorin), adduct);
Assert.AreEqual(665.11555415, mz, .000001); // GNPS says 665.0 for Hectochlorin M+H
mol = IonInfo.ApplyAdductToFormula(Hectochlorin, Adduct.FromStringAssumeProtonated("MCl37+H")).ToString();
Assert.AreEqual("C27ClCl'H35N2O9S2", mol);
mass = BioMassCalc.MONOISOTOPIC.CalculateMassFromFormula(mol);
Assert.AreEqual(667.11315, mass, .00001);
mol = IonInfo.ApplyAdductToFormula(Hectochlorin, Adduct.FromStringAssumeProtonated("M2Cl37+H")).ToString();
Assert.AreEqual("C27Cl'2H35N2O9S2", mol);
// Test ability to describe isotope label by mass only
var heavy = Adduct.FromStringAssumeProtonated("2M1.2345+H");
mz = BioMassCalc.CalculateIonMz(new TypedMass(massHectochlorin, MassType.Monoisotopic), heavy);
heavy = Adduct.FromStringAssumeProtonated("2M1.2345");
mz = BioMassCalc.CalculateIonMass(new TypedMass(massHectochlorin, MassType.Monoisotopic), heavy);
Assert.AreEqual(2 * (massHectochlorin + 1.23456), mz, .001);
heavy = Adduct.FromStringAssumeProtonated("M1.2345");
mz = BioMassCalc.CalculateIonMass(new TypedMass(massHectochlorin, MassType.Monoisotopic), heavy);
Assert.AreEqual(massHectochlorin + 1.23456, mz, .001);
heavy = Adduct.FromStringAssumeProtonated("2M(-1.2345)+H");
mz = BioMassCalc.CalculateIonMz(new TypedMass(massHectochlorin, MassType.Monoisotopic), heavy);
Assert.AreEqual((2 * (massHectochlorin - 1.23456) + BioMassCalc.MONOISOTOPIC.CalculateMassFromFormula("H")), mz, .001);
heavy = Adduct.FromStringAssumeProtonated("2M(-1.2345)");
mz = BioMassCalc.CalculateIonMass(new TypedMass(massHectochlorin, MassType.Monoisotopic), heavy);
Assert.AreEqual(2 * (massHectochlorin - 1.23456), mz, .001);
heavy = Adduct.FromStringAssumeProtonated("2M(1.2345)+H");
mz = BioMassCalc.CalculateIonMz(new TypedMass(massHectochlorin, MassType.Monoisotopic), heavy);
Assert.AreEqual((2 * (massHectochlorin + 1.23456) + BioMassCalc.MONOISOTOPIC.CalculateMassFromFormula("H")), mz, .001);
heavy = Adduct.FromStringAssumeProtonated("2M(1.2345)");
mz = BioMassCalc.CalculateIonMass(new TypedMass(massHectochlorin, MassType.Monoisotopic), heavy);
Assert.AreEqual(2 * (massHectochlorin + 1.23456), mz, .001);
TestException(Hectochlorin, "M3Cl37+H"); // Trying to label more chlorines than exist in the molecule
TestException(Hectochlorin, "M-3Cl+H"); // Trying to remove more chlorines than exist in the molecule
TestException(PENTANE, "M+foo+H"); // Unknown adduct
TestException(PENTANE, "M2Cl37H+H"); // nonsense label ("2Cl37H2" would make sense, but regular H doesn't belong)
TestException(PENTANE, "M+2H+"); // Trailing sign - we now understand this as a charge state declaration, but this one doesn't match described charge
TestException(PENTANE, "[M-2H]3-"); // Declared charge doesn't match described charge
// Test label stripping
Assert.AreEqual("C5H9NO2S", (new IonInfo("C5H9H'3NO2S[M-3H]")).UnlabeledFormula);
// Peptide representations
Assert.AreEqual("C40H65N11O16", (new SequenceMassCalc(MassType.Average)).GetNeutralFormula("PEPTIDER", null));
// Figuring out adducts from old style skyline doc ion molecules and ion precursors
var adductDiff = Adduct.FromFormulaDiff("C6H27NO2Si2C'5", "C'5H11NO2", 3);
Assert.AreEqual("[M+C6H16Si2]3+", adductDiff.AdductFormula);
Assert.AreEqual(3, adductDiff.AdductCharge);
Assert.AreEqual(Adduct.FromString("[M+C6H16Si2]3+", Adduct.ADDUCT_TYPE.non_proteomic, null), adductDiff);
adductDiff = Adduct.FromFormulaDiff("C6H27NO2", "C6H27NO2", 3);
Assert.AreEqual("[M+3]", adductDiff.AdductFormula);
Assert.AreEqual(3, adductDiff.AdductCharge);
adductDiff = Adduct.ProtonatedFromFormulaDiff("C6H27NO2Si2C'5", "C'5H11NO2", 3);
var expectedFromProtonatedDiff = "[M+C6H13Si2+3H]";
Assert.AreEqual(expectedFromProtonatedDiff, adductDiff.AdductFormula);
Assert.AreEqual(3, adductDiff.AdductCharge);
Assert.AreEqual(Adduct.FromString(expectedFromProtonatedDiff, Adduct.ADDUCT_TYPE.non_proteomic, null), adductDiff);
adductDiff = Adduct.ProtonatedFromFormulaDiff("C6H27NO2", "C6H27NO2", 3);
Assert.AreEqual("[M+3H]", adductDiff.AdductFormula);
Assert.AreEqual(3, adductDiff.AdductCharge);
// Implied positive mode
TestPentaneAdduct("MH", "C5H13", 1, coverage); // implied pos mode seems to be fairly common in the wild
TestPentaneAdduct("MH+", "C5H13", 1, coverage); // implied pos mode seems to be fairly common in the wild
TestPentaneAdduct("MNH4", "C5H16N", 1, coverage); // implied pos mode seems to be fairly common in the wild
TestPentaneAdduct("MNH4+", "C5H16N", 1, coverage); // implied pos mode seems to be fairly common in the wild
TestPentaneAdduct("2MNH4+", "C10H28N", 1, coverage); // implied pos mode seems to be fairly common in the wild
// Explict charge states within the adduct
TestPentaneAdduct("[M+S+]", "C5H12S", 1, coverage); // We're trusting the user to declare charge
TestPentaneAdduct("[3M+S+]", "C15H36S", 1, coverage); // We're trusting the user to declare charge
TestPentaneAdduct("[M+S++]", "C5H12S", 2, coverage); // We're trusting the user to declare charge
TestPentaneAdduct("[MS+]", "C5H12S", 1, coverage); // We're trusting the user to declare charge
TestPentaneAdduct("[MS++]", "C5H12S", 2, coverage); // We're trusting the user to declare charge
TestPentaneAdduct("[M+S+2]", "C5H12S", 2, coverage); // We're trusting the user to declare charge
TestPentaneAdduct("[M+S]2+", "C5H12S", 2, coverage); // We're trusting the user to declare charge
TestPentaneAdduct("[M+S-]", "C5H12S", -1, coverage); // We're trusting the user to declare charge
TestPentaneAdduct("[M+S--]", "C5H12S", -2, coverage); // We're trusting the user to declare charge
TestPentaneAdduct("[M-3H-3]", "C5H9", -3, coverage); // We're trusting the user to declare charge
TestPentaneAdduct("[M+S-2]", "C5H12S", -2, coverage); // We're trusting the user to declare charge
TestPentaneAdduct("[M+S]2-", "C5H12S", -2, coverage); // We're trusting the user to declare charge
// Did we test all the adducts we claim to support?
foreach (var adducts in new[] {
Adduct.DEFACTO_STANDARD_ADDUCTS,
Adduct.COMMON_CHARGEONLY_ADDUCTS,
Adduct.COMMON_SMALL_MOL_ADDUCTS.Select(a => a.AdductFormula),
Adduct.COMMON_PROTONATED_ADDUCTS.Select(a => a.AdductFormula),
})
{
foreach (var adductText in adducts)
{
if (!coverage.Contains(adductText))
{
Assert.Fail("Need to add a test for adduct {0}", adductText);
}
}
}
}
public IEnumerable <TransitionDocNode> GetPrecursorTransitions(SrmSettings settings,
ExplicitMods mods,
IPrecursorMassCalc calcFilterPre,
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;
MassType massType = tranSettings.Prediction.FragmentMassType;
int minMz = tranSettings.Instrument.GetMinMz(precursorMz);
int maxMz = tranSettings.Instrument.MaxMz;
bool precursorMS1 = fullScan.IsEnabledMs;
if (IsCustomIon)
{
var ionMz =
BioMassCalc.CalculateIonMz(
CustomIon.GetMass(settings.TransitionSettings.Prediction.PrecursorMassType),
PrecursorCharge);
if (!useFilter ||
!libraryFilter ||
IsMatched(transitionRanks,
ionMz, IonType.precursor,
PrecursorCharge, null))
{
if (precursorMS1 && isotopeDist != null)
{
foreach (int i in fullScan.SelectMassIndices(isotopeDist, useFilter))
{
double precursorMS1Mass = isotopeDist.GetMassI(i);
ionMz = BioMassCalc.CalculateIonMz(precursorMS1Mass, PrecursorCharge);
if (minMz > ionMz || ionMz > maxMz)
{
continue;
}
var isotopeDistInfo = new TransitionIsotopeDistInfo(isotopeDist.GetRankI(i), isotopeDist.GetProportionI(i));
yield return(CreateTransitionNode(i, precursorMS1Mass, isotopeDistInfo, null, transitionRanks, CustomIon));
}
}
else
{
var transition = new Transition(this, PrecursorCharge, null, CustomIon, IonType.precursor);
double massH = CustomIon.GetMass(settings.TransitionSettings.Prediction.PrecursorMassType);
yield return(new TransitionDocNode(transition, null, massH, null, null));
}
}
yield break;
}
string sequence = Peptide.Sequence;
bool precursorNoProducts = precursorMS1 && !fullScan.IsEnabledMsMs &&
tranSettings.Filter.IonTypes.Count == 1 && tranSettings.Filter.IonTypes[0] == IonType.precursor;
double precursorMassPredict = calcPredict.GetPrecursorFragmentMass(sequence);
foreach (var losses in CalcTransitionLosses(IonType.precursor, 0, massType, potentialLosses))
{
double ionMz = SequenceMassCalc.GetMZ(Transition.CalcMass(precursorMassPredict, losses), PrecursorCharge);
if (losses == null)
{
if (precursorMS1 && isotopeDist != null)
{
foreach (int i in fullScan.SelectMassIndices(isotopeDist, useFilter))
{
double precursorMS1Mass = isotopeDist.GetMassI(i, DecoyMassShift);
ionMz = SequenceMassCalc.GetMZ(precursorMS1Mass, PrecursorCharge);
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,
PrecursorCharge, losses))
{
yield return(CreateTransitionNode(0, precursorMassPredict, null, losses,
precursorIsProduct ? transitionRanks : null));
}
}
}
public IEnumerable <TransitionDocNode> GetTransitions(SrmSettings settings,
TransitionGroupDocNode groupDocNode,
ExplicitMods mods,
double precursorMz,
IsotopeDistInfo isotopeDist,
SpectrumHeaderInfo libInfo,
IDictionary <double, LibraryRankedSpectrumInfo.RankedMI> transitionRanks,
bool useFilter)
{
Assume.IsTrue(ReferenceEquals(groupDocNode.TransitionGroup, this));
// Get necessary mass calculators and masses
var calcFilterPre = settings.GetPrecursorCalc(IsotopeLabelType.light, mods);
var calcFilter = settings.GetFragmentCalc(IsotopeLabelType.light, mods);
var calcPredict = settings.GetFragmentCalc(LabelType, mods);
string sequence = Peptide.Sequence;
// Save the true precursor m/z for TranstionSettings.Accept() now that all isotope types are
// checked. This is more correct than just using the light precursor m/z for precursor window
// exclusion.
double precursorMzAccept = precursorMz;
if (!ReferenceEquals(calcFilter, calcPredict))
{
// Get the normal precursor m/z for filtering, so that light and heavy ion picks will match.
precursorMz = IsCustomIon ?
BioMassCalc.CalculateIonMz(calcFilterPre.GetPrecursorMass(groupDocNode.CustomIon), groupDocNode.TransitionGroup.PrecursorCharge) :
SequenceMassCalc.GetMZ(calcFilterPre.GetPrecursorMass(sequence), groupDocNode.TransitionGroup.PrecursorCharge);
}
if (!IsAvoidMismatchedIsotopeTransitions)
{
precursorMzAccept = precursorMz;
}
var tranSettings = settings.TransitionSettings;
var filter = tranSettings.Filter;
var charges = filter.ProductCharges;
var startFinder = filter.FragmentRangeFirst;
var endFinder = filter.FragmentRangeLast;
double precursorMzWindow = filter.PrecursorMzWindow;
var types = filter.IonTypes;
MassType massType = tranSettings.Prediction.FragmentMassType;
int minMz = tranSettings.Instrument.GetMinMz(precursorMzAccept);
int maxMz = tranSettings.Instrument.MaxMz;
var pepMods = settings.PeptideSettings.Modifications;
var potentialLosses = CalcPotentialLosses(sequence, pepMods, mods, massType);
// A start m/z will need to be calculated if the start fragment
// finder uses m/z and their are losses to consider. If the filter
// is set to only consider fragments with m/z greater than the
// precursor, the code below needs to also prevent loss fragments
// from being under that m/z.
double startMz = 0;
// Get library settings
var pick = tranSettings.Libraries.Pick;
if (!useFilter)
{
pick = TransitionLibraryPick.all;
var listAll = Transition.ALL_CHARGES.ToList();
listAll.AddRange(charges.Where(c => !Transition.ALL_CHARGES.Contains(c)));
listAll.Sort();
charges = listAll.ToArray();
types = Transition.ALL_TYPES;
}
// If there are no libraries or no library information, then
// picking cannot use library information
else if (!settings.PeptideSettings.Libraries.HasLibraries || libInfo == null)
{
pick = TransitionLibraryPick.none;
}
// If filtering without library picking
if (potentialLosses != null)
{
if (pick == TransitionLibraryPick.none)
{
// Only include loss combinations where all losses are included always
potentialLosses = potentialLosses.Where(losses =>
losses.All(loss => loss.TransitionLoss.Loss.Inclusion == LossInclusion.Always)).ToArray();
}
else if (useFilter)
{
// Exclude all losses which should never be included by default
potentialLosses = potentialLosses.Where(losses =>
losses.All(loss => loss.TransitionLoss.Loss.Inclusion != LossInclusion.Never)).ToArray();
}
if (!potentialLosses.Any())
{
potentialLosses = null;
}
}
// Return precursor ions
if (!useFilter || types.Contains(IonType.precursor))
{
bool libraryFilter = (pick == TransitionLibraryPick.all || pick == TransitionLibraryPick.filter);
foreach (var nodeTran in GetPrecursorTransitions(settings, mods, calcFilterPre, calcPredict,
precursorMz, isotopeDist, potentialLosses, transitionRanks, libraryFilter, useFilter))
{
if (minMz <= nodeTran.Mz && nodeTran.Mz <= maxMz)
{
yield return(nodeTran);
}
}
}
// Return special ions from settings, if this is a peptide
if (!IsCustomIon)
{
// This is a peptide, but it may have custom transitions (reporter ions), check those
foreach (var measuredIon in tranSettings.Filter.MeasuredIons.Where(m => m.IsCustom))
{
if (useFilter && measuredIon.IsOptional)
{
continue;
}
var tran = new Transition(this, measuredIon.Charge, null, measuredIon.CustomIon);
double mass = settings.GetFragmentMass(IsotopeLabelType.light, null, tran, null);
var nodeTran = new TransitionDocNode(tran, null, mass, null, null);
if (minMz <= nodeTran.Mz && nodeTran.Mz <= maxMz)
{
yield return(nodeTran);
}
}
}
// For small molecules we can't generate new nodes, so just mz filter those we have
foreach (var nodeTran in groupDocNode.Transitions.Where(tran => tran.Transition.IsNonPrecursorNonReporterCustomIon()))
{
if (minMz <= nodeTran.Mz && nodeTran.Mz <= maxMz)
{
yield return(nodeTran);
}
}
if (sequence == null) // Completely custom
{
yield break;
}
// If picking relies on library information
if (useFilter && pick != TransitionLibraryPick.none)
{
// If it is not yet loaded, or nothing got ranked, return an empty enumeration
if (!settings.PeptideSettings.Libraries.IsLoaded ||
(transitionRanks != null && transitionRanks.Count == 0))
{
yield break;
}
}
double[,] massesPredict = calcPredict.GetFragmentIonMasses(sequence);
int len = massesPredict.GetLength(1);
if (len == 0)
{
yield break;
}
double[,] massesFilter = massesPredict;
if (!ReferenceEquals(calcFilter, calcPredict))
{
// Get the normal m/z values for filtering, so that light and heavy
// ion picks will match.
massesFilter = calcFilter.GetFragmentIonMasses(sequence);
}
// Get types other than this to make sure matches are possible for all types
var listOtherTypes = new List <Tuple <TransitionGroupDocNode, IFragmentMassCalc> >();
foreach (var labelType in settings.PeptideSettings.Modifications.GetModificationTypes())
{
if (Equals(labelType, LabelType))
{
continue;
}
var calc = settings.GetFragmentCalc(labelType, mods);
if (calc == null)
{
continue;
}
var tranGroupOther = new TransitionGroup(Peptide, PrecursorCharge, labelType, false, DecoyMassShift);
var nodeGroupOther = new TransitionGroupDocNode(tranGroupOther, Annotations.EMPTY, settings, mods,
libInfo, ExplicitTransitionGroupValues.EMPTY, null, new TransitionDocNode[0], false);
listOtherTypes.Add(new Tuple <TransitionGroupDocNode, IFragmentMassCalc>(nodeGroupOther, calc));
}
// Loop over potential product ions picking transitions
foreach (IonType type in types)
{
// Precursor type is handled above.
if (type == IonType.precursor)
{
continue;
}
foreach (int charge in charges)
{
// Precursor charge can never be lower than product ion charge.
if (Math.Abs(PrecursorCharge) < Math.Abs(charge))
{
continue;
}
int start = 0, end = 0;
if (pick != TransitionLibraryPick.all)
{
start = startFinder.FindStartFragment(massesFilter, type, charge,
precursorMz, precursorMzWindow, out startMz);
end = endFinder.FindEndFragment(type, start, len);
if (Transition.IsCTerminal(type))
{
Helpers.Swap(ref start, ref end);
}
}
for (int i = 0; i < len; i++)
{
// Get the predicted m/z that would be used in the transition
double massH = massesPredict[(int)type, i];
foreach (var losses in CalcTransitionLosses(type, i, massType, potentialLosses))
{
double ionMz = SequenceMassCalc.GetMZ(Transition.CalcMass(massH, losses), charge);
// Make sure the fragment m/z value falls within the valid instrument range.
// CONSIDER: This means that a heavy transition might excede the instrument
// range where a light one is accepted, leading to a disparity
// between heavy and light transtions picked.
if (minMz > ionMz || ionMz > maxMz)
{
continue;
}
TransitionDocNode nodeTranReturn = null;
bool accept = true;
if (pick == TransitionLibraryPick.all || pick == TransitionLibraryPick.all_plus)
{
if (!useFilter)
{
nodeTranReturn = CreateTransitionNode(type, i, charge, massH, losses, transitionRanks);
accept = false;
}
else
{
if (IsMatched(transitionRanks, ionMz, type, charge, losses))
{
nodeTranReturn = CreateTransitionNode(type, i, charge, massH, losses, transitionRanks);
accept = false;
}
// If allowing library or filter, check the filter to decide whether to accept
else if (pick == TransitionLibraryPick.all_plus &&
tranSettings.Accept(sequence, precursorMzAccept, type, i, ionMz, start, end, startMz))
{
nodeTranReturn = CreateTransitionNode(type, i, charge, massH, losses, transitionRanks);
}
}
}
else if (tranSettings.Accept(sequence, precursorMzAccept, type, i, ionMz, start, end, startMz))
{
if (pick == TransitionLibraryPick.none)
{
nodeTranReturn = CreateTransitionNode(type, i, charge, massH, losses, transitionRanks);
}
else
{
if (IsMatched(transitionRanks, ionMz, type, charge, losses))
{
nodeTranReturn = CreateTransitionNode(type, i, charge, massH, losses, transitionRanks);
}
}
}
if (nodeTranReturn != null)
{
if (IsAvoidMismatchedIsotopeTransitions &&
!OtherLabelTypesAllowed(settings, minMz, maxMz, start, end, startMz, accept,
groupDocNode, nodeTranReturn, listOtherTypes))
{
continue;
}
Assume.IsTrue(minMz <= nodeTranReturn.Mz && nodeTranReturn.Mz <= maxMz);
yield return(nodeTranReturn);
}
}
}
}
}
}
private static void TestEditingTransition()
{
double massPrecisionTolerance = Math.Pow(10, -SequenceMassCalc.MassPrecision);
var doc = SkylineWindow.Document;
RunUI(() =>
{
SkylineWindow.ExpandPrecursors();
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0].FirstNode.FirstNode.FirstNode;
});
var editMoleculeDlg =
ShowDialog <EditCustomMoleculeDlg>(
() => SkylineWindow.ModifyTransition((TransitionTreeNode)SkylineWindow.SequenceTree.SelectedNode));
var monoMass = new TypedMass(805, MassType.Monoisotopic);
RunUI(() =>
{
Assert.AreEqual(C12H12 + Adduct.NonProteomicProtonatedFromCharge(1).AdductFormula, editMoleculeDlg.FormulaBox.Formula);
Assert.AreEqual(BioMassCalc.MONOISOTOPIC.CalculateMassFromFormula(C12H12),
editMoleculeDlg.FormulaBox.MonoMass ?? -1, massPrecisionTolerance);
Assert.AreEqual(BioMassCalc.AVERAGE.CalculateMassFromFormula(C12H12),
editMoleculeDlg.FormulaBox.AverageMass ?? -1, massPrecisionTolerance);
Assert.AreEqual(Adduct.NonProteomicProtonatedFromCharge(1).AdductFormula, editMoleculeDlg.FormulaBox.Adduct.AdductFormula);
editMoleculeDlg.FormulaBox.Formula = editMoleculeDlg.FormulaBox.Adduct.AdductFormula; // Remove neutral formula, should leave masses unchanged
Assert.AreEqual(BioMassCalc.MONOISOTOPIC.CalculateMassFromFormula(C12H12),
editMoleculeDlg.FormulaBox.MonoMass ?? -1, massPrecisionTolerance);
Assert.AreEqual(BioMassCalc.AVERAGE.CalculateMassFromFormula(C12H12),
editMoleculeDlg.FormulaBox.AverageMass ?? -1, massPrecisionTolerance);
editMoleculeDlg.FormulaBox.AverageMass = 800;
editMoleculeDlg.FormulaBox.MonoMass = monoMass.Value;
editMoleculeDlg.NameText = "Fragment";
});
OkDialog(editMoleculeDlg, editMoleculeDlg.OkDialog);
var newdoc = WaitForDocumentChange(doc);
Assert.AreEqual("Fragment", newdoc.MoleculeTransitions.ElementAt(0).Transition.CustomIon.ToString());
Assert.AreEqual(BioMassCalc.CalculateIonMz(monoMass, editMoleculeDlg.Adduct), newdoc.MoleculeTransitions.ElementAt(0).Mz, massPrecisionTolerance);
Assert.IsFalse(ReferenceEquals(doc.MoleculeTransitions.ElementAt(0).Id, newdoc.MoleculeTransitions.ElementAt(0).Id)); // Changing the mass changes the Id
// Verify that tree selection doesn't change just because we changed an ID object
// (formerly the tree node would collapse and focus would jump up a level)
RunUI(() =>
{
Assert.AreEqual(SkylineWindow.SequenceTree.SelectedNode, SkylineWindow.SequenceTree.Nodes[0].FirstNode.FirstNode.FirstNode);
});
// And test undo/redo
RunUI(() => SkylineWindow.Undo());
newdoc = WaitForDocumentChange(newdoc);
Assert.AreNotEqual("Fragment", newdoc.MoleculeTransitions.ElementAt(0).Transition.CustomIon.ToString());
Assert.AreNotEqual(BioMassCalc.CalculateIonMz(monoMass, editMoleculeDlg.Adduct), newdoc.MoleculeTransitions.ElementAt(0).Mz, massPrecisionTolerance);
Assert.IsTrue(ReferenceEquals(doc.MoleculeTransitions.ElementAt(0).Id, newdoc.MoleculeTransitions.ElementAt(0).Id));
RunUI(() => SkylineWindow.Redo());
newdoc = WaitForDocumentChange(newdoc);
Assert.AreEqual("Fragment", newdoc.MoleculeTransitions.ElementAt(0).Transition.CustomIon.ToString());
Assert.AreEqual(BioMassCalc.CalculateIonMz(monoMass, editMoleculeDlg.Adduct), newdoc.MoleculeTransitions.ElementAt(0).Mz, massPrecisionTolerance);
// Verify that tree selection doesn't change just because we changed an ID object
// (formerly the tree node would collapse and focus would jump up a level)
RunUI(() =>
{
Assert.AreEqual(SkylineWindow.SequenceTree.SelectedNode, SkylineWindow.SequenceTree.Nodes[0].FirstNode.FirstNode.FirstNode);
});
}
public void OkDialog()
{
var helper = new MessageBoxHelper(this);
var charge = 0;
if (textCharge.Visible && !helper.ValidateSignedNumberTextBox(textCharge, _minCharge, _maxCharge, out charge))
{
return;
}
if (RetentionTimeWindow.HasValue && !RetentionTime.HasValue)
{
helper.ShowTextBoxError(textRetentionTimeWindow,
Resources.Peptide_ExplicitRetentionTimeWindow_Explicit_retention_time_window_requires_an_explicit_retention_time_value_);
return;
}
Charge = charge; // Note: order matters here, this settor indirectly updates _formulaBox.MonoMass when formula is empty
if (string.IsNullOrEmpty(_formulaBox.Formula))
{
// Can the text fields be understood as mz?
if (!_formulaBox.ValidateAverageText(helper))
{
return;
}
if (!_formulaBox.ValidateMonoText(helper))
{
return;
}
}
var formula = _formulaBox.Formula;
var monoMass = _formulaBox.MonoMass ?? 0;
var averageMass = _formulaBox.AverageMass ?? 0;
if (monoMass < CustomIon.MIN_MASS || averageMass < CustomIon.MIN_MASS)
{
_formulaBox.ShowTextBoxErrorFormula(helper,
string.Format(Resources.EditCustomMoleculeDlg_OkDialog_Custom_molecules_must_have_a_mass_greater_than_or_equal_to__0__,
CustomIon.MIN_MASS));
return;
}
if (monoMass > CustomIon.MAX_MASS || averageMass > CustomIon.MAX_MASS)
{
_formulaBox.ShowTextBoxErrorFormula(helper,
string.Format(Resources.EditCustomMoleculeDlg_OkDialog_Custom_molecules_must_have_a_mass_less_than_or_equal_to__0__, CustomIon.MAX_MASS));
return;
}
if ((_transitionSettings != null) &&
(!_transitionSettings.IsMeasurablePrecursor(BioMassCalc.CalculateIonMz(monoMass, charge)) ||
!_transitionSettings.IsMeasurablePrecursor(BioMassCalc.CalculateIonMz(averageMass, charge))))
{
_formulaBox.ShowTextBoxErrorFormula(helper, Resources.SkylineWindow_AddMolecule_The_precursor_m_z_for_this_molecule_is_out_of_range_for_your_instrument_settings_);
return;
}
if (!string.IsNullOrEmpty(_formulaBox.Formula))
{
try
{
ResultCustomIon = new DocNodeCustomIon(formula, textName.Text);
}
catch (InvalidDataException x)
{
_formulaBox.ShowTextBoxErrorFormula(helper, x.Message);
return;
}
}
else
{
ResultCustomIon = new DocNodeCustomIon(monoMass, averageMass, textName.Text);
}
// Did user change the list of heavy labels?
if (_driverLabelType != null)
{
PeptideModifications modifications = new PeptideModifications(
_peptideSettings.Modifications.StaticModifications,
_peptideSettings.Modifications.MaxVariableMods,
_peptideSettings.Modifications.MaxNeutralLosses,
_driverLabelType.GetHeavyModifications(), // This is the only thing the user may have altered
_peptideSettings.Modifications.InternalStandardTypes);
var settings = _peptideSettings.ChangeModifications(modifications);
// Only update if anything changed
if (!Equals(settings, _peptideSettings))
{
SrmSettings newSettings = _parent.DocumentUI.Settings.ChangePeptideSettings(settings);
if (!_parent.ChangeSettings(newSettings, true))
{
return;
}
_peptideSettings = newSettings.PeptideSettings;
}
}
// See if this combination of charge and label would conflict with any existing transition groups
if (_existingIds != null && _existingIds.Any(t =>
{
var transitionGroup = t as TransitionGroup;
return(transitionGroup != null && Equals(transitionGroup.LabelType, IsotopeLabelType) &&
Equals(transitionGroup.PrecursorCharge, Charge) && !ReferenceEquals(t, _initialId));
}))
{
helper.ShowTextBoxError(textName,
Resources.EditCustomMoleculeDlg_OkDialog_A_precursor_with_that_charge_and_label_type_already_exists_, textName.Text);
return;
}
// See if this would conflict with any existing transitions
if (_existingIds != null && (_existingIds.Any(t =>
{
var transition = t as Transition;
return(transition != null && ((transition.Charge == Charge) && Equals(transition.CustomIon, ResultCustomIon)) && !ReferenceEquals(t, _initialId));
})))
{
helper.ShowTextBoxError(textName,
Resources.EditCustomMoleculeDlg_OkDialog_A_similar_transition_already_exists_, textName.Text);
return;
}
DialogResult = DialogResult.OK;
}
public IsotopeEnrichmentItem(string isotopeSymbol)
: this(isotopeSymbol, BioMassCalc.GetIsotopeEnrichmentDefault(isotopeSymbol))
{
}
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());
}
protected override void DoTest()
{
const double precursorMzAtZNeg2 = 242.0373281;
const double productMzAtZNeg2 = 213.5097436;
const double precursorCE = 1.23;
const double precursorDT = 2.34;
const double highEnergyDtOffset = -.012;
const double slens = 6.789;
const double coneVoltage = 7.89;
const double compensationVoltage = 8.901;
const double declusteringPotential = 9.012;
const double precursorRT = 3.45;
const double precursorRTWindow = 4.567;
const string note = "noted!";
var docEmpty = SkylineWindow.Document;
TestLabelsNoFormulas();
TestPrecursorTransitions();
TestTransitionListArrangementAndReporting();
string line1 = "MyMolecule\tMyMol\tMyFrag\tC34H12O4\tC34H3O\t" + precursorMzAtZNeg2 + "\t" + productMzAtZNeg2 + "\t-2\t-2\tlight\t" +
precursorRT + "\t" + precursorRTWindow + "\t" + precursorCE + "\t" + note + "\t" + precursorDT + "\t" + highEnergyDtOffset + "\t" + slens + "\t" + coneVoltage +
"\t" + compensationVoltage + "\t" + declusteringPotential; // Legit
const string line2start = "\r\nMyMolecule2\tMyMol2\tMyFrag2\tCH12O4\tCH3O\t";
const string line3 = "\r\nMyMolecule2\tMyMol2\tMyFrag2\tCH12O4\tCHH500000000\t\t\t1\t1";
const string line4 = "\r\nMyMolecule3\tMyMol3\tMyFrag3\tH2\tH\t\t\t1\t1";
// Provoke some errors
TestError(line1.Replace("C34H12O4", "C77H12O4"), // mz and formula disagree
String.Format(Resources.PasteDlg_ReadPrecursorOrProductColumns_Error_on_line__0___Precursor_m_z__1__does_not_agree_with_value__2__as_calculated_from_ion_formula_and_charge_state__delta____3___Transition_Settings___Instrument___Method_match_tolerance_m_z____4_____Correct_the_m_z_value_in_the_table__or_leave_it_blank_and_Skyline_will_calculate_it_for_you_,
1, (float)precursorMzAtZNeg2, 500.0373, 258, docEmpty.Settings.TransitionSettings.Instrument.MzMatchTolerance));
TestError(line1.Replace("C34H3", "C76H3"), // mz and formula disagree
String.Format(Resources.PasteDlg_ReadPrecursorOrProductColumns_Error_on_line__0___Product_m_z__1__does_not_agree_with_value__2__as_calculated_from_ion_formula_and_charge_state__delta____3___Transition_Settings___Instrument___Method_match_tolerance_m_z____4_____Correct_the_m_z_value_in_the_table__or_leave_it_blank_and_Skyline_will_calculate_it_for_you_,
1, (float)productMzAtZNeg2, 465.5097, 252, docEmpty.Settings.TransitionSettings.Instrument.MzMatchTolerance));
var badcharge = Transition.MAX_PRODUCT_CHARGE + 1;
TestError(line1 + line2start + "\t\t1\t" + badcharge, // Excessively large charge for product
String.Format(Resources.Transition_Validate_Product_ion_charge__0__must_be_non_zero_and_between__1__and__2__,
badcharge, -Transition.MAX_PRODUCT_CHARGE, Transition.MAX_PRODUCT_CHARGE));
badcharge = 120;
TestError(line1 + line2start + "\t\t" + badcharge + "\t1", // Insanely large charge for precursor
String.Format(Resources.Transition_Validate_Precursor_charge__0__must_be_non_zero_and_between__1__and__2__,
badcharge, -TransitionGroup.MAX_PRECURSOR_CHARGE, TransitionGroup.MAX_PRECURSOR_CHARGE));
TestError(line1 + line2start + "\t\t1\t", // No mz or charge for product
String.Format(Resources.PasteDlg_ValidateEntry_Error_on_line__0___Product_needs_values_for_any_two_of__Formula__m_z_or_Charge_, 2));
TestError(line1 + line2start + "19\t5", // Precursor Formula and m/z don't make sense together
String.Format(Resources.PasteDlg_ValidateEntry_Error_on_line__0___Precursor_formula_and_m_z_value_do_not_agree_for_any_charge_state_, 2));
TestError(line1 + line2start + "\t5\t1", // Product Formula and m/z don't make sense together
String.Format(Resources.PasteDlg_ValidateEntry_Error_on_line__0___Product_formula_and_m_z_value_do_not_agree_for_any_charge_state_, 2));
TestError(line1 + line2start + "\t", // No mz or charge for precursor or product
String.Format(Resources.PasteDlg_ValidateEntry_Error_on_line__0___Precursor_needs_values_for_any_two_of__Formula__m_z_or_Charge_, 2));
TestError(line1 + line3, // Insanely large molecule
string.Format(Resources.CustomIon_Validate_The_mass_of_the_custom_ion_exceeeds_the_maximum_of__0_, CustomIon.MAX_MASS));
TestError(line1 + line4, // Insanely small molecule
string.Format(Resources.CustomIon_Validate_The_mass_of_the_custom_ion_is_less_than_the_minimum_of__0__, CustomIon.MIN_MASS));
TestError(line1 + line2start + +precursorMzAtZNeg2 + "\t" + productMzAtZNeg2 + "\t-2\t-2\t\t\t" + precursorRTWindow + "\t" + precursorCE + "\t" + precursorDT + "\t" + highEnergyDtOffset, // Explicit retention time window without retention time
Resources.Peptide_ExplicitRetentionTimeWindow_Explicit_retention_time_window_requires_an_explicit_retention_time_value_);
for (int withSpecials = 2; withSpecials-- > 0;)
{
// By default we don't show drift or other exotic columns
var columnOrder = (withSpecials == 0) ? null : new[]
{
PasteDlg.SmallMoleculeTransitionListColumnHeaders.moleculeGroup,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.namePrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.nameProduct,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.formulaPrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.formulaProduct,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.mzPrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.mzProduct,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.chargePrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.chargeProduct,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.labelType,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.rtPrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.rtWindowPrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.cePrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.note,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.dtPrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.dtHighEnergyOffset,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.slens,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.coneVoltage,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.compensationVoltage,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.declusteringPotential,
};
// Take a legit full paste and mess with each field in turn
string[] fields = { "MyMol", "MyPrecursor", "MyProduct", "C12H9O4", "C6H4O2", "217.049535420091", "108.020580420091", "1", "1", "heavy", "123", "5", "25", "this is a note", "7", "9", "88.5", "99.6", "77.3", "66.2" };
string[] badfields = { "", "", "", "123", "123", "fish", "-345", "cat", "pig", "12", "frog", "hamster", "boston", "foosball", "greasy", "mumble", "gumdrop", "dingle", "gorse", "AHHHHHRGH" };
var expectedErrors = new List <string>()
{
Resources.PasteDlg_ShowNoErrors_No_errors, Resources.PasteDlg_ShowNoErrors_No_errors, Resources.PasteDlg_ShowNoErrors_No_errors, // No name, no problem
BioMassCalc.MONOISOTOPIC.FormatArgumentExceptionMessage(badfields[3]),
BioMassCalc.MONOISOTOPIC.FormatArgumentExceptionMessage(badfields[4]),
string.Format(Resources.PasteDlg_ReadPrecursorOrProductColumns_Invalid_m_z_value__0_, badfields[5]),
string.Format(Resources.PasteDlg_ReadPrecursorOrProductColumns_Invalid_m_z_value__0_, badfields[6]),
string.Format(Resources.PasteDlg_ReadPrecursorOrProductColumns_Invalid_charge_value__0_, badfields[7]),
string.Format(Resources.PasteDlg_ReadPrecursorOrProductColumns_Invalid_charge_value__0_, badfields[8]),
string.Format(Resources.SrmDocument_ReadLabelType_The_isotope_modification_type__0__does_not_exist_in_the_document_settings, badfields[9]),
string.Format(Resources.PasteDlg_ReadPrecursorOrProductColumns_Invalid_retention_time_value__0_, badfields[10]),
string.Format(Resources.PasteDlg_ReadPrecursorOrProductColumns_Invalid_retention_time_window_value__0_, badfields[11]),
string.Format(Resources.PasteDlg_ReadPrecursorOrProductColumns_Invalid_collision_energy_value__0_, badfields[12]),
null // Notes are freeform, so any value is fine
};
if (withSpecials > 0)
{
var s = expectedErrors.Count;
expectedErrors.Add(
string.Format(Resources.PasteDlg_ReadPrecursorOrProductColumns_Invalid_drift_time_value__0_, badfields[s++]));
expectedErrors.Add(
string.Format(Resources.PasteDlg_ReadPrecursorOrProductColumns_Invalid_drift_time_high_energy_offset_value__0_, badfields[s++]));
expectedErrors.Add(
string.Format(Resources.PasteDlg_ReadPrecursorOrProductColumns_Invalid_S_Lens_value__0_, badfields[s++]));
expectedErrors.Add(
string.Format(Resources.PasteDlg_ReadPrecursorOrProductColumns_Invalid_cone_voltage_value__0_, badfields[s++]));
expectedErrors.Add(
string.Format(Resources.PasteDlg_ReadPrecursorOrProductColumns_Invalid_compensation_voltage__0_, badfields[s++]));
expectedErrors.Add(
string.Format(Resources.PasteDlg_ReadPrecursorOrProductColumns_Invalid_declustering_potential__0_, badfields[s++]));
}
expectedErrors.Add(Resources.PasteDlg_ShowNoErrors_No_errors); // N+1'th pass is unadulterated
for (var bad = 0; bad < expectedErrors.Count(); bad++)
{
var line = "";
for (var f = 0; f < expectedErrors.Count() - 1; f++)
{
line += ((bad == f) ? badfields[f] : fields[f]).Replace(".", LocalizationHelper.CurrentCulture.NumberFormat.NumberDecimalSeparator) + "\t";
}
if (!string.IsNullOrEmpty(expectedErrors[bad]))
{
TestError(line, expectedErrors[bad], columnOrder);
}
}
}
// Now load the document with a legit paste
TestError(line1 + line2start + "\t\t1\t1", String.Empty);
var docOrig = WaitForDocumentChange(docEmpty);
var testTransitionGroups = docOrig.MoleculeTransitionGroups.ToArray();
Assert.AreEqual(2, testTransitionGroups.Count());
var transitionGroup = testTransitionGroups[0];
var precursor = docOrig.Molecules.First();
var product = transitionGroup.Transitions.First();
Assert.AreEqual(precursorCE, transitionGroup.ExplicitValues.CollisionEnergy);
Assert.AreEqual(precursorDT, transitionGroup.ExplicitValues.DriftTimeMsec);
Assert.AreEqual(slens, transitionGroup.ExplicitValues.SLens);
Assert.AreEqual(coneVoltage, transitionGroup.ExplicitValues.ConeVoltage);
Assert.AreEqual(compensationVoltage, transitionGroup.ExplicitValues.CompensationVoltage);
Assert.AreEqual(declusteringPotential, transitionGroup.ExplicitValues.DeclusteringPotential);
Assert.AreEqual(note, product.Annotations.Note);
Assert.AreEqual(highEnergyDtOffset, transitionGroup.ExplicitValues.DriftTimeHighEnergyOffsetMsec.Value, 1E-7);
Assert.AreEqual(precursorRT, precursor.ExplicitRetentionTime.RetentionTime);
Assert.AreEqual(precursorRTWindow, precursor.ExplicitRetentionTime.RetentionTimeWindow);
Assert.IsTrue(ReferenceEquals(transitionGroup.TransitionGroup, product.Transition.Group));
Assert.AreEqual(precursorMzAtZNeg2, BioMassCalc.CalculateIonMz(precursor.CustomIon.MonoisotopicMass, transitionGroup.PrecursorCharge), 1E-7);
Assert.AreEqual(productMzAtZNeg2, BioMassCalc.CalculateIonMz(product.GetIonMass(), product.Transition.Charge), 1E-7);
// Does that produce the expected transition list file?
TestTransitionListOutput(docOrig, "PasteMoleculeTinyTest.csv", "PasteMoleculeTinyTestExpected.csv", ExportFileType.IsolationList);
// Does serialization of imported values work properly?
AssertEx.Serializable(docOrig);
// Reset
RunUI(() =>
{
SkylineWindow.NewDocument(true);
docOrig = SkylineWindow.Document;
});
// Now a proper user data set
var pasteDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteTransitionListDlg);
PasteDlg dlg = pasteDlg;
RunUI(() =>
{
dlg.IsMolecule = true;
dlg.SetSmallMoleculeColumns(null); // Reset column headers to default selection and order
});
// Formerly SetExcelFileClipboardText(TestFilesDir.GetTestPath("MoleculeTransitionList.xlsx"),"sheet1",6,false); but TeamCity doesn't like that
SetCsvFileClipboardText(TestFilesDir.GetTestPath("MoleculeTransitionList.csv"));
RunUI(pasteDlg.PasteTransitions);
OkDialog(pasteDlg, pasteDlg.OkDialog);
var pastedDoc = WaitForDocumentChange(docOrig);
AssertEx.Serializable(pastedDoc);
RunUI(() => SkylineWindow.SaveDocument(TestFilesDir.GetTestPath("PasteMolecules.Sky")));
var paths = new []
{
"13417_02_WAA283_3805_071514" + ExtensionTestContext.ExtWatersRaw,
"13417_03_WAA283_3805_071514" + ExtensionTestContext.ExtWatersRaw,
"13418_02_WAA283_3805_071514" + ExtensionTestContext.ExtWatersRaw,
"13418_03_WAA283_3805_071514" + ExtensionTestContext.ExtWatersRaw,
};
var doc = SkylineWindow.Document;
RunUI(() => SkylineWindow.ChangeSettings(doc.Settings.
ChangeTransitionSettings(
doc.Settings.TransitionSettings.ChangeInstrument(
doc.Settings.TransitionSettings.Instrument.ChangeMzMatchTolerance(0.6))), true));
PasteMoleculesTestImportResults(paths);
var importDoc = SkylineWindow.Document;
var transitionCount = importDoc.MoleculeTransitionCount;
var tranWithResults = importDoc.MoleculeTransitions.Count(tran => tran.HasResults);
var tranWithPeaks = importDoc.MoleculeTransitions.Count(tran =>
{
for (int i = 0; i < 4; i++)
{
if (tran.GetPeakCountRatio(i) > 0)
{
return(true);
}
}
return(false);
});
// PauseTest(); // Pretty pictures!
Assert.AreEqual(98, transitionCount);
Assert.AreEqual(98, tranWithResults);
Assert.AreEqual(90, tranWithPeaks);
// Does that produce the expected transition list file?
TestTransitionListOutput(importDoc, "PasteMoleculeTest.csv", "PasteMoleculeTestExpected.csv", ExportFileType.List);
// Verify that MS1 filtering works properly
var pasteText =
"Steryl esters [ST0102],12:0 Cholesteryl ester,C39H68O2NH4,1\r\n" +
"Steryl esters [ST0102],14:0 Cholesteryl ester,C41H72O2NH4,1\r\n" +
"Steryl esters [ST0102],14:1 Cholesteryl ester,C41H70O2NH4,1\r\n" +
"Steryl esters [ST0102],15:1 Cholesteryl ester,C42H72O2NH4,1";
var columnOrderB = new[]
{
PasteDlg.SmallMoleculeTransitionListColumnHeaders.moleculeGroup,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.namePrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.formulaPrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.chargePrecursor,
};
// Doc is set for MS1 filtering, precursor transitions, charge=1, two peaks, should show M and M+1, M+2 after filter is invoked by changing to 3 peaks
RunUI(() => SkylineWindow.OpenFile(TestFilesDir.GetTestPath("small_molecule_missing_m1.sky")));
WaitForDocumentLoaded();
TestError(pasteText, String.Empty, columnOrderB);
var docB = SkylineWindow.Document;
Assert.AreEqual(4, docB.MoleculeTransitionCount); // Initial import is faithful to what's pasted
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.FullScan;
transitionSettingsUI.Peaks = 3;
});
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
docB = WaitForDocumentChange(docB);
Assert.AreEqual(12, docB.MoleculeTransitionCount);
// Verify that we can import heavy/light pairs
var columnOrderC = new[]
{
PasteDlg.SmallMoleculeTransitionListColumnHeaders.moleculeGroup,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.namePrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.formulaPrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.mzProduct,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.chargePrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.chargeProduct,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.labelType,
};
pasteText =
"A,27-HC,C36H57N2O3,135,1,1,light\r\n" +
"A,27-HC,C36H57N2O3,181,1,1,light\r\n" +
"A,27-HC,C36H57N2O3,367,1,1,light\r\n" +
"A,27-HC,C36H51H'6N2O3,135,1,1,heavy\r\n" +
"A,27-HC,C36H51H'6N2O3,181,1,1,heavy\r\n" +
"A,27-HC,C36H51H'6N2O3,215,1,1,heavy\r\n";
RunUI(() =>
{
SkylineWindow.NewDocument(true);
});
TestError(pasteText, String.Empty, columnOrderC);
var docC = SkylineWindow.Document;
Assert.AreEqual(1, docC.MoleculeGroupCount);
Assert.AreEqual(1, docC.MoleculeCount);
Assert.AreEqual(2, docC.MoleculeTransitionGroupCount);
}
public IsotopeDistInfo(MassDistribution massDistribution,
double monoisotopicMass,
bool isMassH, // Is monoisotopicMass M+H, or just M as in small molecule use?
int charge,
Func <double, double> calcFilterWindow,
double massResolution,
double minimumAbundance)
{
_monoisotopicMass = monoisotopicMass;
_charge = charge;
_isMassH = isMassH;
// Get peak center of mass values for the given resolution
var q1FilterValues = MassDistribution.NewInstance(massDistribution, massResolution, 0).Keys.ToList();
// Find the monoisotopic m/z and make sure it is exactly the expected number
double monoMz = isMassH ? SequenceMassCalc.GetMZ(_monoisotopicMass, _charge) : BioMassCalc.CalculateIonMz(_monoisotopicMass, _charge);
double monoMzDist = monoMz;
int monoMassIndex = 0;
for (int i = 0; i < q1FilterValues.Count; i++)
{
double peakCenterMz = q1FilterValues[i];
double filterWindow = calcFilterWindow(peakCenterMz);
double startMz = peakCenterMz - filterWindow / 2;
double endMz = startMz + filterWindow;
if (startMz < monoMz && monoMz < endMz)
{
monoMzDist = q1FilterValues[i];
q1FilterValues[i] = monoMz;
monoMassIndex = i;
break;
}
}
// Insert a M-1 peak, even if it is not expected in the isotope mass distribution
if (monoMassIndex == 0 && q1FilterValues.Count > 1)
{
// Use the delta from the original distribution monoMz to the next peak
q1FilterValues.Insert(0, monoMz + monoMzDist - q1FilterValues[1]);
monoMassIndex++;
}
if (!q1FilterValues.Any()) // As is small molecule docs with mz values only, no formulas
{
return;
}
// Use the filtering algorithm that will be used on real data to determine the
// expected proportions of the mass distribution that will end up filtered into
// peaks
// CONSIDER: Mass accuracy information is not calculated here
var key = new PrecursorTextId(q1FilterValues[monoMassIndex], null, ChromExtractor.summed);
var filter = new SpectrumFilterPair(key, PeptideDocNode.UNKNOWN_COLOR, 0, null, null, null, null, 0, false, false);
filter.AddQ1FilterValues(q1FilterValues, calcFilterWindow);
var expectedSpectrum = filter.FilterQ1SpectrumList(new[] { new MsDataSpectrum
{
Mzs = massDistribution.Keys.ToArray(), Intensities = massDistribution.Values.ToArray()
} });
int startIndex = expectedSpectrum.Intensities.IndexOf(inten => inten >= minimumAbundance);
if (startIndex == -1)
{
throw new InvalidOperationException(
string.Format(Resources.IsotopeDistInfo_IsotopeDistInfo_Minimum_abundance__0__too_high,
minimumAbundance));
}
// Always include the M-1 peak, even if it is expected to have zero intensity
if (startIndex > monoMassIndex - 1)
{
startIndex = monoMassIndex - 1;
}
if (startIndex < 0)
{
startIndex = 0;
}
int endIndex = expectedSpectrum.Intensities.LastIndexOf(inten => inten >= minimumAbundance) + 1;
int countPeaks = endIndex - startIndex;
var listProportionIndices = new List <KeyValuePair <float, int> >(countPeaks);
for (int i = 0; i < countPeaks; i++)
{
listProportionIndices.Add(new KeyValuePair <float, int>(
expectedSpectrum.Intensities[i + startIndex], i));
}
// Sort proportions descending.
listProportionIndices.Sort((p1, p2) => Comparer.Default.Compare(p2.Key, p1.Key));
// Set proportions and ranks back in the original locations
var expectedProportionRanks = new KeyValuePair <float, int> [countPeaks];
for (int i = 0; i < countPeaks; i++)
{
expectedProportionRanks[listProportionIndices[i].Value] =
new KeyValuePair <float, int>(listProportionIndices[i].Key, i + 1);
}
// TODO: Can this be discarded?
// MassDistribution = massDistribution;
MonoMassIndex = monoMassIndex - startIndex;
// Find the base peak and fill in the masses and proportions
var expectedPeaks = new List <MzRankProportion>();
for (int i = 0; i < countPeaks; i++)
{
float expectedProportion = expectedProportionRanks[i].Key;
int rank = expectedProportionRanks[i].Value;
expectedPeaks.Add(new MzRankProportion(q1FilterValues[i + startIndex], rank, expectedProportion));
if (expectedProportion > expectedProportionRanks[BaseMassIndex].Key)
{
BaseMassIndex = i;
}
}
ExpectedPeaks = expectedPeaks;
}
public double GetMassI(int massIndex, int?decoyMassShift = null)
{
// Return the original monoisotopic mass + H, if requested to maintain an exact match.
if (massIndex == 0 && !decoyMassShift.HasValue)
{
return(_monoisotopicMass);
}
// Otherwize use the charge to convert from the peak center m/z values
double shift = SequenceMassCalc.GetPeptideInterval(decoyMassShift); // Correct for shift applied to the distribution
return(_isMassH ? SequenceMassCalc.GetMH(ExpectedPeaks[MassIndexToPeakIndex(massIndex)].Mz - shift, _charge) : BioMassCalc.CalculateIonMassFromMz(ExpectedPeaks[MassIndexToPeakIndex(massIndex)].Mz - shift, _charge));
}
public double GetIonMass()
{
return(Transition.IsCustom()
? BioMassCalc.CalculateIonMassFromMz(Mz, Transition.Charge)
: SequenceMassCalc.GetMH(Mz, Transition.Charge));
}
