private void TestReports(SrmDocument doc1, string msg = null)
{
// Verify reports working for CCS
var row = 0;
var documentGrid = ShowDialog <DocumentGridForm>(() => SkylineWindow.ShowDocumentGrid(true));
EnableDocumentGridColumns(documentGrid,
Resources.SkylineViewContext_GetTransitionListReportSpec_Small_Molecule_Transition_List,
doc1.PeptideTransitionCount * doc1.MeasuredResults.Chromatograms.Count,
new[]
{
"Proteins!*.Peptides!*.Precursors!*.Results!*.Value.CollisionalCrossSection",
"Proteins!*.Peptides!*.Precursors!*.Results!*.Value.IonMobilityMS1",
"Proteins!*.Peptides!*.Precursors!*.Results!*.Value.IonMobilityFragment",
"Proteins!*.Peptides!*.Precursors!*.Results!*.Value.IonMobilityUnits",
"Proteins!*.Peptides!*.Precursors!*.Results!*.Value.IonMobilityWindow"
});
CheckFieldByName(documentGrid, "IonMobilityMS1", row, 0.832, msg);
CheckFieldByName(documentGrid, "IonMobilityFragment", row, (double?)null, msg); // Document is all precursor
CheckFieldByName(documentGrid, "IonMobilityUnits", row, IonMobilityValue.GetUnitsString(eIonMobilityUnits.inverse_K0_Vsec_per_cm2), msg);
CheckFieldByName(documentGrid, "IonMobilityWindow", row, 0.04, msg);
CheckFieldByName(documentGrid, "CollisionalCrossSection", row, 474.26, msg);
// And clean up after ourselves
RunUI(() => documentGrid.Close());
}
public bool IsSimSpectrum(MsDataSpectrum dataSpectrum, MsDataSpectrum[] spectra)
{
if (!EnabledMs || _mseLevel > 0)
{
return(false);
}
bool isSimSpectrum = dataSpectrum.Level == 1 &&
IsSimIsolation(GetIsolationWindows(dataSpectrum.Precursors).FirstOrDefault());
if (isSimSpectrum && spectra.Length > 1)
{
// If this is actually a run of IMS bins, look at the aggregate isolation window
var rt = spectra[0].RetentionTime;
var win = GetIsolationWindows(spectra[0].Precursors).FirstOrDefault();
double mzLow = win.IsolationMz.Value - win.IsolationWidth.Value / 2;
double mzHigh = win.IsolationMz.Value + win.IsolationWidth.Value / 2;
for (var i = 1; i < spectra.Length; i++)
{
var spec = spectra[i];
if (!Equals(spec.RetentionTime, rt) || !IonMobilityValue.IsExpectedValueOrdering(spectra[i - 1].IonMobility, spec.IonMobility))
{
return(true); // Not a run of IMS bins, must have been actual SIM scan
}
win = GetIsolationWindows(spec.Precursors).FirstOrDefault();
mzLow = Math.Min(mzLow, win.IsolationMz.Value - win.IsolationWidth.Value / 2);
mzHigh = Math.Max(mzHigh, win.IsolationMz.Value + win.IsolationWidth.Value / 2);
}
var width = mzHigh - mzLow;
isSimSpectrum = IsSimIsolation(new IsolationWindowFilter(new SignedMz(mzLow + width / 2), width));
}
return(isSimSpectrum);
}
private void TestReports(SrmDocument doc1, int row, double expectedDtWindow, string msg = null)
{
// Verify reports working for CCS
var documentGrid = ShowDialog <DocumentGridForm>(() => SkylineWindow.ShowDocumentGrid(true));
EnableDocumentGridColumns(documentGrid,
Resources.SkylineViewContext_GetTransitionListReportSpec_Small_Molecule_Transition_List,
doc1.PeptideTransitionCount * doc1.MeasuredResults.Chromatograms.Count,
new[]
{
"Proteins!*.Peptides!*.Precursors!*.Results!*.Value.CollisionalCrossSection",
"Proteins!*.Peptides!*.Precursors!*.Results!*.Value.IonMobilityMS1",
"Proteins!*.Peptides!*.Precursors!*.Results!*.Value.IonMobilityFragment",
"Proteins!*.Peptides!*.Precursors!*.Results!*.Value.IonMobilityUnits",
"Proteins!*.Peptides!*.Precursors!*.Results!*.Value.IonMobilityWindow"
});
CheckFieldByName(documentGrid, "IonMobilityMS1", row, _testCase == 1 ? 18.43 : 23.50, msg);
CheckFieldByName(documentGrid, "IonMobilityFragment", row, (double?)null, msg); // Document is all precursor
CheckFieldByName(documentGrid, "IonMobilityUnits", row, IonMobilityValue.GetUnitsString(eIonMobilityUnits.drift_time_msec), msg);
CheckFieldByName(documentGrid, "IonMobilityWindow", row, expectedDtWindow, msg);
CheckFieldByName(documentGrid, "CollisionalCrossSection", row, _testCase == 1 ? 292.4 : 333.34, msg);
// And clean up after ourselves
RunUI(() => documentGrid.Close());
}
public double?CCSFromIonMobility(IonMobilityValue ionMobilityValue, double mz, int charge)
{
if (_dataFile == null)
{
return(null);
}
return(_dataFile.CCSFromIonMobilityValue(ionMobilityValue, mz, charge));
}
/// <summary>
/// Return a collisional cross section for this ion mobility at this mz, if reader supports this
/// </summary>
public double?CCSFromIonMobility(IonMobilityValue ionMobility, double mz, int charge)
{
if (_scanProvider == null)
{
return(null);
}
return(_scanProvider.CCSFromIonMobility(ionMobility, mz, charge));
}
public double CCSFromIonMobility(IonMobilityValue im, double mz, int charge)
{
if (ProvidesCollisionalCrossSectionConverter)
{
return(_ionMobilityFunctionsProvider.CCSFromIonMobility(im, mz, charge));
}
Assume.IsNotNull(_ionMobilityFunctionsProvider, "No ion mobility to CCS translation is possible for this data set"); // Not L10N
return(0);
}
public bool ContainsIonMobilityValue(IonMobilityValue ionMobility, double highEnergyOffset)
{
if (!ionMobility.HasValue)
{
return(true); // It doesn't NOT have the ion mobility, since there isn't one
}
return((!MinIonMobilityValue.HasValue || MinIonMobilityValue.Value + highEnergyOffset <= ionMobility.Mobility) &&
(!MaxIonMobilityValue.HasValue || MaxIonMobilityValue.Value + highEnergyOffset >= ionMobility.Mobility));
}
// TODO(bspratt) either upgrade this for all ion mobility types, or rip out this code altogether
public IonMobilityAndCCS GetDriftTimeInfo(LibKey key, ChargeRegressionLine regression)
{
DbIonMobilityPeptide pep;
if (DictLibrary.TryGetValue(key, out pep))
{
return(IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.GetIonMobilityValue(regression.GetY(pep.CollisionalCrossSection), eIonMobilityUnits.drift_time_msec), pep.CollisionalCrossSection, pep.HighEnergyDriftTimeOffsetMsec));
}
return(null);
}
public Dictionary <LibKey, IonMobilityAndCCS> GetTableMeasuredIonMobility(bool useHighEnergyOffsets, MsDataFileImpl.eIonMobilityUnits units)
{
var e = new CancelEventArgs();
var dict = new Dictionary <LibKey, IonMobilityAndCCS>();
foreach (DataGridViewRow row in _gridMeasuredDriftTimePeptides.Rows)
{
if (row.IsNewRow)
{
continue;
}
string seq;
if (!ValidateSequence(e, row.Cells[EditDriftTimePredictorDlg.COLUMN_SEQUENCE], out seq))
{
return(null);
}
Adduct charge;
if (!ValidateCharge(e, row.Cells[EditDriftTimePredictorDlg.COLUMN_CHARGE], out charge))
{
return(null);
}
double mobility;
if (!ValidateDriftTime(e, row.Cells[EditDriftTimePredictorDlg.COLUMN_ION_MOBILITY], out mobility))
{
return(null);
}
double?ccs;
if (!ValidateCCS(e, row.Cells[EditDriftTimePredictorDlg.COLUMN_CCS], out ccs))
{
return(null);
}
double highEnergyOffset = 0; // Set default value in case user does not provide one
if (useHighEnergyOffsets && !ValidateHighEnergyDriftTimeOffset(e, row.Cells[EditDriftTimePredictorDlg.COLUMN_HIGH_ENERGY_OFFSET], out highEnergyOffset))
{
return(null);
}
var ionMobility = IonMobilityValue.GetIonMobilityValue(mobility, units);
try
{
dict.Add(new LibKey(seq, charge.AdductCharge), IonMobilityAndCCS.GetIonMobilityAndCCS(ionMobility, ccs, highEnergyOffset));
}
// ReSharper disable once EmptyGeneralCatchClause
catch
{
// just take the first seen
}
}
return(dict);
}
public bool ContainsIonMobilityValue(IonMobilityValue ionMobility, bool highEnergy)
{
if (!ionMobility.HasValue)
{
return(true); // It doesn't NOT have the ion mobility, since there isn't one
}
double offset = highEnergy ? HighEnergyIonMobilityValueOffset : 0;
return((!MinIonMobilityValue.HasValue || MinIonMobilityValue.Value + offset <= ionMobility.Mobility) &&
(!MaxIonMobilityValue.HasValue || MaxIonMobilityValue.Value + offset >= ionMobility.Mobility));
}
public IonMobilityFilter GetIonMobilityWindow()
{
if (MinIonMobilityValue.HasValue && MaxIonMobilityValue.HasValue)
{
// High energy (product ion) scans may have a faster ion mobility, as in Waters MsE, that gets applied elsewhere
var width = MaxIonMobilityValue.Value - MinIonMobilityValue.Value;
var center = MinIonMobilityValue.Value + 0.5 * width;
return(IonMobilityFilter.GetIonMobilityFilter(IonMobilityValue.GetIonMobilityValue(center, IonMobilityInfo.IonMobility.Units), width, IonMobilityInfo.CollisionalCrossSectionSqA));
}
else
{
return(IonMobilityFilter.EMPTY);
}
}
public IonMobilityFilter GetIonMobilityWindow(bool highEnergy)
{
if (MinIonMobilityValue.HasValue && MaxIonMobilityValue.HasValue)
{
// High energy (product ion) scans may have a faster ion mobility, as in Waters MsE
double offset = highEnergy ? HighEnergyIonMobilityValueOffset : 0;
var width = MaxIonMobilityValue.Value - MinIonMobilityValue.Value;
var center = offset + MinIonMobilityValue.Value + 0.5 * width;
return(IonMobilityFilter.GetIonMobilityFilter(IonMobilityValue.GetIonMobilityValue(center, IonMobilityInfo.IonMobility.Units), width, IonMobilityInfo.CollisionalCrossSectionSqA));
}
else
{
return(IonMobilityFilter.EMPTY);
}
}
private void TestReports(SrmDocument doc1, string msg = null)
{
// Verify reports working for CCS
var row = 0;
var documentGrid = ShowDialog <DocumentGridForm>(() => SkylineWindow.ShowDocumentGrid(true));
EnableDocumentGridColumns(documentGrid,
Resources.SkylineViewContext_GetTransitionListReportSpec_Small_Molecule_Transition_List,
doc1.PeptideTransitionCount,
new[]
{
"Proteins!*.Peptides!*.Precursors!*.Results!*.Value.CollisionalCrossSection",
"Proteins!*.Peptides!*.Precursors!*.Results!*.Value.IonMobilityMS1",
"Proteins!*.Peptides!*.Precursors!*.Results!*.Value.IonMobilityFragment",
"Proteins!*.Peptides!*.Precursors!*.Results!*.Value.IonMobilityUnits",
"Proteins!*.Peptides!*.Precursors!*.Results!*.Value.IonMobilityWindow"
});
CheckFieldByName(documentGrid, "PrecursorResult.IonMobilityMS1", row, 1.1732, msg);
CheckFieldByName(documentGrid, "PrecursorResult.IonMobilityFragment", row, 1.1732, msg);
CheckFieldByName(documentGrid, "PrecursorResult.IonMobilityUnits", row, IonMobilityValue.GetUnitsString(eIonMobilityUnits.inverse_K0_Vsec_per_cm2), msg);
CheckFieldByName(documentGrid, "PrecursorResult.IonMobilityWindow", row, 0.12, msg);
CheckFieldByName(documentGrid, "PrecursorResult.CollisionalCrossSection", row, 666.9175, msg);
EnableDocumentGridColumns(documentGrid,
Resources.ReportSpecList_GetDefaults_Peptide_RT_Results,
doc1.PeptideCount * doc1.MeasuredResults.Chromatograms.Count, null);
foreach (var rt in new[] {
14.35, 14.34, 14.33, 14.33, 14.15, 14.12, 14.11, 14.11, 14.63, 14.61, 14.61, 14.61, 14.75, 14.74, 14.72, 14.73, 14.06, 14.04,
14.03, 14.03, 14.43, 14.43, 14.42, 14.43, 14.36, 14.37, 14.35, 14.35, 14.31, 14.31, 14.29, 14.28, 14.48, 14.49, 14.47, 14.48,
14.69, 14.67, 14.67, 14.67, 14.61, 14.34, 14.34, 14.35, 14.25, 14.25, 14.22, 14.23, 14.37, 14.36, 14.35, 14.35, 14.51, 14.52,
14.5, 14.5, 14.24, 14.25, 14.22, 14.23, 14.81, 14.78, 14.78, 14.78, 14.63, 14.61, 14.61, 14.61, 14.48, 14.46, 14.46, 14.47,
14.52, 14.49, 14.49, 14.49, 14.67, 14.65, 14.65, 14.65, 14.46, 14.45, 14.45, 14.45, 14.44, 14.43, 14.42, 14.43, 14.24, 14.24,
14.25, 14.25, 14.48, 14.46, 14.45, 14.44, 14.19, 14.16, 14.16, 14.17, 14.38, 14.34, 14.34, 14.36, 14.88, 14.86, 14.86, 14.85,
14.22, 14.22, 14.21, 14.21, 14.19, 14.19, 14.18, 14.18, 14.11, 14.09, 14.09, 14.1, 14.72, 14.7, 14.71, 14.71, 14.64, 14.61,
14.62, 14.61, 14.12, 14.1, 14.1, 14.1, 14.23, 14.21, 14.2, 14.2
})
{
CheckFieldByName(documentGrid, "PeptideRetentionTime", row++, rt, msg, true);
}
// And clean up after ourselves
RunUI(() => documentGrid.Close());
}
private MsDataSpectrum GetSpectrumFromJObject(JObject jObject, int msLevel)
{
// ReSharper disable NonLocalizedString
string strMzs = jObject["mzs-base64"].ToString();
string strIntensities = jObject["intensities-base64"].ToString();
byte[] mzBytes = Convert.FromBase64String(strMzs);
byte[] intensityBytes = Convert.FromBase64String(strIntensities);
double[] mzs = PrimitiveArrays.FromBytes <double>(
PrimitiveArrays.ReverseBytesInBlocks(mzBytes, sizeof(double)));
float[] intensityFloats = PrimitiveArrays.FromBytes <float>(
PrimitiveArrays.ReverseBytesInBlocks(intensityBytes, sizeof(float)));
double[] intensities = intensityFloats.Select(f => (double)f).ToArray();
IonMobilityValue ionMobility = IonMobilityValue.EMPTY;
JToken jDriftTime;
if (jObject.TryGetValue("driftTime", out jDriftTime))
{
var driftTime = jDriftTime.ToObject <double>();
if (driftTime != 0)
{
ionMobility = IonMobilityValue.GetIonMobilityValue(driftTime, MsDataFileImpl.eIonMobilityUnits.drift_time_msec);
}
}
MsDataSpectrum spectrum = new MsDataSpectrum
{
Index = jObject["index"].ToObject <int>(),
RetentionTime = jObject["rt"].ToObject <double>(),
Mzs = mzs,
Intensities = intensities,
IonMobility = ionMobility,
};
return(spectrum);
// ReSharper restore NonLocalizedString
}
public Dictionary <LibKey, IonMobilityAndCCS> GetTableMeasuredIonMobility(bool useHighEnergyOffsets, eIonMobilityUnits units)
{
var e = new CancelEventArgs();
var dict = new Dictionary <LibKey, IonMobilityAndCCS>();
foreach (DataGridViewRow row in _gridMeasuredDriftTimePeptides.Rows)
{
if (row.IsNewRow)
{
continue;
}
string seq;
if (!ValidateSequence(e, row.Cells[EditDriftTimePredictorDlg.COLUMN_SEQUENCE], out seq))
{
return(null);
}
// OK, we have a non-empty "sequence" string, but is that actually a peptide or a molecule?
// See if there's anything in the document whose text representation matches what's in the list
var target = _targetResolver.ResolveTarget(seq);
if (target == null || target.IsEmpty)
{
return(null);
}
Adduct charge;
if (!ValidateCharge(e, row.Cells[EditDriftTimePredictorDlg.COLUMN_CHARGE], target.IsProteomic, out charge))
{
return(null);
}
double mobility;
if (!ValidateDriftTime(e, row.Cells[EditDriftTimePredictorDlg.COLUMN_ION_MOBILITY], out mobility))
{
return(null);
}
double?ccs;
if (!ValidateCCS(e, row.Cells[EditDriftTimePredictorDlg.COLUMN_CCS], out ccs))
{
return(null);
}
double highEnergyOffset = 0; // Set default value in case user does not provide one
if (useHighEnergyOffsets && !ValidateHighEnergyDriftTimeOffset(e, row.Cells[EditDriftTimePredictorDlg.COLUMN_HIGH_ENERGY_OFFSET], out highEnergyOffset))
{
return(null);
}
var ionMobility = IonMobilityValue.GetIonMobilityValue(mobility, units);
try
{
dict.Add(new LibKey(target, charge), IonMobilityAndCCS.GetIonMobilityAndCCS(ionMobility, ccs, highEnergyOffset));
}
// ReSharper disable once EmptyGeneralCatchClause
catch
{
// just take the first seen
}
}
return(dict);
}
public virtual IonMobilityAndCCS GetIonMobilityAndCCS()
{
return(IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.GetIonMobilityValue(IonMobilityNullable,
IonMobilityUnits), CollisionalCrossSectionNullable, HighEnergyIonMobilityOffset));
}
private void EvaluateBestIonMobilityValue(int msLevel, LibKey libKey, float tolerance, List <TransitionFullScanInfo> transitions)
{
IonMobilityValue ionMobilityValue = IonMobilityValue.EMPTY;
double maxIntensity = 0;
// Avoid picking MS2 ion mobility values wildly different from MS1 valuess
IonMobilityValue ms1IonMobilityBest;
if ((msLevel == 2) && _ms1IonMobilities.ContainsKey(libKey))
{
ms1IonMobilityBest =
_ms1IonMobilities[libKey].OrderByDescending(p => p.Intensity)
.FirstOrDefault()
.IonMobility.IonMobility;
}
else
{
ms1IonMobilityBest = IonMobilityValue.EMPTY;
}
double maxHighEnergyDriftOffsetMsec = UseHighEnergyOffset ? 2 : 0; // CONSIDER(bspratt): user definable? or dynamically set by looking at scan to scan drift delta? Or resolving power?
foreach (var scan in _msDataFileScanHelper.MsDataSpectra.Where(scan => scan != null))
{
if (!scan.IonMobility.HasValue || !scan.Mzs.Any())
{
continue;
}
if (ms1IonMobilityBest.HasValue &&
(scan.IonMobility.Mobility <
ms1IonMobilityBest.Mobility - maxHighEnergyDriftOffsetMsec ||
scan.IonMobility.Mobility >
ms1IonMobilityBest.Mobility + maxHighEnergyDriftOffsetMsec))
{
continue;
}
// Get the total intensity for all transitions of current msLevel
double totalIntensity = 0;
foreach (var t in transitions)
{
Assume.IsTrue(t.ProductMz.IsNegative == scan.NegativeCharge); // It would be strange if associated scan did not have same polarity
var mzPeak = t.ProductMz;
var halfwin = (t.ExtractionWidth ?? tolerance) / 2;
var mzLow = mzPeak - halfwin;
var mzHigh = mzPeak + halfwin;
var first = Array.BinarySearch(scan.Mzs, mzLow);
if (first < 0)
{
first = ~first;
}
for (var i = first; i < scan.Mzs.Length; i++)
{
if (scan.Mzs[i] > mzHigh)
{
break;
}
totalIntensity += scan.Intensities[i];
}
}
if (maxIntensity < totalIntensity)
{
ionMobilityValue = scan.IonMobility;
maxIntensity = totalIntensity;
}
}
if (ionMobilityValue.HasValue)
{
var dict = (msLevel == 1) ? _ms1IonMobilities : _ms2IonMobilities;
var ccs = msLevel == 1 && _msDataFileScanHelper.ProvidesCollisionalCrossSectionConverter ? _msDataFileScanHelper.CCSFromIonMobility(ionMobilityValue, transitions.First().PrecursorMz, libKey.Charge) : null;
var result = new IonMobilityIntensityPair
{
IonMobility = IonMobilityAndCCS.GetIonMobilityAndCCS(ionMobilityValue, ccs, 0),
Intensity = maxIntensity
};
List <IonMobilityIntensityPair> listPairs;
if (!dict.TryGetValue(libKey, out listPairs))
{
listPairs = new List <IonMobilityIntensityPair>();
dict.Add(libKey, listPairs);
}
listPairs.Add(result);
}
}
public void TestLibIonMobilityInfo()
{
const string caffeineFormula = "C8H10N4O2";
const string caffeineInChiKey = "RYYVLZVUVIJVGH-UHFFFAOYSA-N";
const string caffeineHMDB = "HMDB01847";
const double HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC = -.01;
var dbIon1 = new DbIonMobilityPeptide(new Target("JKLMN"), Adduct.SINGLY_PROTONATED, 1.2, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC)
{
Id = 12345
};
for (var loop = 0; loop < 2; loop++)
{
var dbIon2 = new DbIonMobilityPeptide(dbIon1);
DbIonMobilityPeptide dbIon3 = null;
Assert.AreEqual(dbIon1.GetHashCode(), dbIon2.GetHashCode());
Assert.IsFalse(dbIon1.Equals(null));
Assert.IsTrue(dbIon1.Equals(dbIon2 as object));
// ReSharper disable once ExpressionIsAlwaysNull
Assert.IsFalse(dbIon1.Equals(dbIon3 as object));
Assert.IsTrue(dbIon1.Equals(dbIon1));
Assert.IsTrue(dbIon1.Equals(dbIon1 as object));
Assert.IsTrue(dbIon1.Equals(dbIon2));
dbIon1.CollisionalCrossSection = 1.3;
Assert.AreNotEqual(dbIon1.CollisionalCrossSection, dbIon2.CollisionalCrossSection);
if (loop == 1)
{
dbIon1.ModifiedTarget = new Target("foo");
Assert.AreNotEqual(dbIon1.Target, dbIon2.Target);
Assert.AreNotEqual(dbIon1.ModifiedTarget, dbIon2.ModifiedTarget);
}
else
{
Assert.AreEqual(dbIon1.ModifiedTarget, dbIon2.ModifiedTarget);
Assert.AreEqual(dbIon1.ModifiedTarget.Molecule, dbIon2.ModifiedTarget.Molecule);
}
dbIon1 = new DbIonMobilityPeptide(
SmallMoleculeLibraryAttributes.Create("caffeine", caffeineFormula, caffeineInChiKey, caffeineHMDB),
Adduct.FromStringAssumeProtonated("M+Na"),
1.2, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC)
{
Id = 12345
};
}
var dictCCS1 = new Dictionary <LibKey, IonMobilityAndCCS[]>();
var ccs1 = new List <IonMobilityAndCCS> {
IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.EMPTY, 1, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC), IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.EMPTY, 2, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC)
}; // Collisional cross sections
var ccs2 = new List <IonMobilityAndCCS> {
IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.EMPTY, 3, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC), IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.EMPTY, 4, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC)
}; // Collisional cross sections
const string seq1 = "JKLM";
const string seq2 = "KLMN";
dictCCS1.Add(new LibKey(seq1, 1), ccs1.ToArray());
dictCCS1.Add(new LibKey(seq2, 1), ccs2.ToArray());
var lib = new List <LibraryIonMobilityInfo> {
new LibraryIonMobilityInfo("test", dictCCS1)
};
var peptideTimes = CollisionalCrossSectionGridViewDriver.ConvertDriftTimesToCollisionalCrossSections(null,
lib, 1, null);
var validatingIonMobilityPeptides = peptideTimes as ValidatingIonMobilityPeptide[] ?? peptideTimes.ToArray();
Assert.AreEqual(2, validatingIonMobilityPeptides.Length);
Assert.AreEqual(1.5, validatingIonMobilityPeptides[0].CollisionalCrossSection);
Assert.AreEqual(3.5, validatingIonMobilityPeptides[1].CollisionalCrossSection);
Assert.AreEqual(HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC, validatingIonMobilityPeptides[1].HighEnergyDriftTimeOffsetMsec);
// Test serialization of molecule with '$' in it, which we use as a tab replacement against XML parser variability
var molser = new CustomMolecule(SmallMoleculeLibraryAttributes.Create("caffeine$", caffeineFormula, caffeineInChiKey, caffeineHMDB));
var text = molser.ToSerializableString();
Assert.AreEqual(molser, CustomMolecule.FromSerializableString(text));
var dictCCS2 = new Dictionary <LibKey, IonMobilityAndCCS[]>();
var ccs3 = new List <IonMobilityAndCCS> {
IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.GetIonMobilityValue(4, eIonMobilityUnits.drift_time_msec), null, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC), IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.GetIonMobilityValue(5, eIonMobilityUnits.drift_time_msec), null, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC)
}; // Drift times
const string seq3 = "KLMNJ";
dictCCS2.Add(new LibKey(seq3, Adduct.SINGLY_PROTONATED), ccs3.ToArray());
lib.Add(new LibraryIonMobilityInfo("test2", dictCCS2));
List <LibraryIonMobilityInfo> lib1 = lib;
AssertEx.ThrowsException <Exception>(() => CollisionalCrossSectionGridViewDriver.ConvertDriftTimesToCollisionalCrossSections(null,
lib1, 2, null),
String.Format(
Resources.CollisionalCrossSectionGridViewDriver_ProcessIonMobilityValues_Cannot_import_measured_ion_mobility_for_sequence__0___no_collisional_cross_section_conversion_parameters_were_provided_for_charge_state__1__,
seq3, 1));
var regressions = new Dictionary <int, RegressionLine> {
{ 1, new RegressionLine(2, 1) }
};
lib = new List <LibraryIonMobilityInfo> {
new LibraryIonMobilityInfo("test", dictCCS2)
};
peptideTimes = CollisionalCrossSectionGridViewDriver.ConvertDriftTimesToCollisionalCrossSections(null,
lib, 1, regressions);
validatingIonMobilityPeptides = peptideTimes as ValidatingIonMobilityPeptide[] ?? peptideTimes.ToArray();
Assert.AreEqual(1, validatingIonMobilityPeptides.Length);
Assert.AreEqual(1.75, validatingIonMobilityPeptides[0].CollisionalCrossSection);
}
public void TestLibIonMobilityInfo()
{
const string caffeineFormula = "C8H10N4O2";
const string caffeineInChiKey = "RYYVLZVUVIJVGH-UHFFFAOYSA-N";
const string caffeineHMDB = "HMDB01847";
const double HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC = -.01;
var dbMolecule = new DbMolecule(new Target("JKLMN"))
{
Id = 123456
};
var dbPrecursorIon = new DbPrecursorIon(dbMolecule, Adduct.SINGLY_PROTONATED)
{
Id = 1234567
};
var dbIonMobilityValue = new DbPrecursorAndIonMobility(dbPrecursorIon,
1.2, 2.3, eIonMobilityUnits.drift_time_msec, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC)
{
Id = 12345
};
DbPrecursorAndIonMobility dbPrecursorAndIonMobilityValue2 = new DbPrecursorAndIonMobility(dbIonMobilityValue);
for (var loop = 0; loop < 2; loop++)
{
Assert.AreEqual(dbIonMobilityValue.GetHashCode(), dbPrecursorAndIonMobilityValue2.GetHashCode());
Assert.IsFalse(dbIonMobilityValue.Equals(null));
Assert.IsTrue(dbIonMobilityValue.Equals(dbPrecursorAndIonMobilityValue2 as object));
Assert.IsTrue(dbIonMobilityValue.Equals(dbIonMobilityValue));
Assert.IsTrue(dbIonMobilityValue.Equals(dbIonMobilityValue as object));
Assert.IsTrue(dbPrecursorAndIonMobilityValue2.Equals(dbIonMobilityValue));
dbIonMobilityValue.CollisionalCrossSectionSqA = 1.3;
Assert.AreNotEqual(dbIonMobilityValue.CollisionalCrossSectionSqA, dbPrecursorAndIonMobilityValue2.CollisionalCrossSectionSqA);
if (loop == 1)
{
dbIonMobilityValue.DbPrecursorIon = new DbPrecursorIon(new Target("foo"), Adduct.SINGLY_PROTONATED)
{
Id = 1234567
};
Assert.AreNotEqual(dbIonMobilityValue.DbPrecursorIon.GetTarget(), dbMolecule);
}
else
{
Assert.AreEqual(dbIonMobilityValue.DbPrecursorIon.DbMolecule, dbMolecule);
}
dbIonMobilityValue = new DbPrecursorAndIonMobility(
new DbPrecursorIon(
SmallMoleculeLibraryAttributes.Create("caffeine", caffeineFormula, caffeineInChiKey, caffeineHMDB),
Adduct.FromStringAssumeProtonated("M+Na"))
{
Id = 23456
},
1.2, 2.3, eIonMobilityUnits.drift_time_msec, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC)
{
Id = 12345
};
dbPrecursorAndIonMobilityValue2 = new DbPrecursorAndIonMobility(dbIonMobilityValue);
}
var dictCCS1 = new Dictionary <LibKey, IonMobilityAndCCS[]>();
var im = IonMobilityValue.GetIonMobilityValue(12, eIonMobilityUnits.drift_time_msec);
var ccs1 = new List <IonMobilityAndCCS> {
IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.EMPTY, 1, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC), IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.EMPTY, 2, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC)
}; // Collisional cross sections
var ccs2 = new List <IonMobilityAndCCS> {
IonMobilityAndCCS.GetIonMobilityAndCCS(im, 3, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC), IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.EMPTY, 4, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC)
}; // Collisional cross sections
const string seq1 = "JKLM";
const string seq2 = "KLMN";
dictCCS1.Add(new LibKey(seq1, 1), ccs1.ToArray());
dictCCS1.Add(new LibKey(seq2, 1), ccs2.ToArray());
var lib = new List <LibraryIonMobilityInfo> {
new LibraryIonMobilityInfo("test", false, dictCCS1)
};
var peptideTimes = CollisionalCrossSectionGridViewDriver.CollectIonMobilitiesAndCollisionalCrossSections(null,
lib, 1);
var validatingIonMobilityPeptides = peptideTimes as ValidatingIonMobilityPrecursor[] ?? peptideTimes.ToArray();
Assert.AreEqual(2, validatingIonMobilityPeptides.Length);
Assert.AreEqual(1.5, validatingIonMobilityPeptides[0].CollisionalCrossSectionSqA);
Assert.AreEqual(3.5, validatingIonMobilityPeptides[1].CollisionalCrossSectionSqA);
Assert.AreEqual(HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC, validatingIonMobilityPeptides[1].HighEnergyIonMobilityOffset);
// This time with multiple CCS conformers supported
lib = new List <LibraryIonMobilityInfo> {
new LibraryIonMobilityInfo("test", true, dictCCS1)
};
peptideTimes = CollisionalCrossSectionGridViewDriver.CollectIonMobilitiesAndCollisionalCrossSections(null,
lib, 1);
validatingIonMobilityPeptides = peptideTimes as ValidatingIonMobilityPrecursor[] ?? peptideTimes.ToArray();
Assert.AreEqual(4, validatingIonMobilityPeptides.Length);
Assert.AreEqual(1, validatingIonMobilityPeptides[0].CollisionalCrossSectionSqA);
Assert.AreEqual(2, validatingIonMobilityPeptides[1].CollisionalCrossSectionSqA);
Assert.AreEqual(3, validatingIonMobilityPeptides[2].CollisionalCrossSectionSqA);
Assert.AreEqual(4, validatingIonMobilityPeptides[3].CollisionalCrossSectionSqA);
Assert.AreEqual(HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC, validatingIonMobilityPeptides[1].HighEnergyIonMobilityOffset);
// Test serialization of molecule with '$' in it, which we use as a tab replacement against XML parser variability
var molser = CustomMolecule.FromSmallMoleculeLibraryAttributes(SmallMoleculeLibraryAttributes.Create("caffeine$", caffeineFormula, caffeineInChiKey, caffeineHMDB));
var text = molser.ToSerializableString();
Assert.AreEqual(molser, CustomMolecule.FromSerializableString(text));
// Test handling of SmallMoleculeLibraryAttributes for mass-only descriptions
var molserB = CustomMolecule.FromSmallMoleculeLibraryAttributes(SmallMoleculeLibraryAttributes.Create("caffeine$", null, new TypedMass(123.4, MassType.Monoisotopic), new TypedMass(123.45, MassType.Average), caffeineInChiKey, caffeineHMDB));
var textB = molserB.ToSerializableString();
Assert.AreEqual(molserB, CustomMolecule.FromSerializableString(textB));
var dictCCS2 = new Dictionary <LibKey, IonMobilityAndCCS[]>();
var ccs3 = new List <IonMobilityAndCCS> {
IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.GetIonMobilityValue(4, eIonMobilityUnits.drift_time_msec), 1.75, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC), IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.GetIonMobilityValue(5, eIonMobilityUnits.drift_time_msec), null, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC)
}; // Drift times
const string seq3 = "KLMNJ";
dictCCS2.Add(new LibKey(seq3, Adduct.SINGLY_PROTONATED), ccs3.ToArray());
lib = new List <LibraryIonMobilityInfo> {
new LibraryIonMobilityInfo("test", false, dictCCS2)
};
peptideTimes = CollisionalCrossSectionGridViewDriver.CollectIonMobilitiesAndCollisionalCrossSections(null,
lib, 1);
validatingIonMobilityPeptides = peptideTimes as ValidatingIonMobilityPrecursor[] ?? peptideTimes.ToArray();
Assert.AreEqual(1, validatingIonMobilityPeptides.Length);
Assert.AreEqual(1.75, validatingIonMobilityPeptides[0].CollisionalCrossSectionSqA);
}
protected override void DoTest()
{
// IsPauseForScreenShots = true; // For a quick demo when you need it
string skyFile = TestFilesDir.GetTestPath("test_measured_drift_times_perf.sky");
Program.ExtraRawFileSearchFolder = TestFilesDir.PersistentFilesDir; // So we don't have to reload the raw files, which have moved relative to skyd file
RunUI(() => SkylineWindow.OpenFile(skyFile));
var document = WaitForDocumentLoaded(240000); // If it decides to remake chromatograms this can take awhile
AssertEx.IsDocumentState(document, null, 1, 34, 38, 398);
RunUI(() =>
{
SkylineWindow.SaveDocument(TestFilesDir.GetTestPath("local.sky")); // Avoid "document changed since last edit" message
document = SkylineWindow.DocumentUI;
});
List <ValidatingIonMobilityPrecursor> curatedDTs = null;
var measuredDTs = new List <List <ValidatingIonMobilityPrecursor> >();
var precursors = new LibKeyIndex(document.MoleculePrecursorPairs.Select(
p => p.NodePep.ModifiedTarget.GetLibKey(p.NodeGroup.PrecursorAdduct).LibraryKey));
PauseForScreenShot(@"Legacy ion mobility values loaded, placed in .imsdb database file"); // For a quick demo when you need it
for (var pass = 0; pass < 2; pass++)
{
// Verify ability to extract predictions from raw data
var transitionSettingsDlg = ShowDialog <TransitionSettingsUI>(
() => SkylineWindow.ShowTransitionSettingsUI(TransitionSettingsUI.TABS.IonMobility));
PauseForScreenShot("new Transition Settings tab"); // For a quick demo when you need it
// Simulate user picking Edit Current from the Ion Mobility Library combo control
var ionMobilityLibraryDlg = ShowDialog <EditIonMobilityLibraryDlg>(transitionSettingsDlg.IonMobilityControl.EditIonMobilityLibrary);
PauseForScreenShot("next, we'll update values with 'Use Results' button"); // For a quick demo when you need it
RunUI(() =>
{
if (curatedDTs == null)
{
curatedDTs = ionMobilityLibraryDlg.LibraryMobilitiesFlat.ToList();
}
ionMobilityLibraryDlg.SetOffsetHighEnergySpectraCheckbox(true);
ionMobilityLibraryDlg.GetIonMobilitiesFromResults();
});
PauseForScreenShot("values updated");// For a quick demo when you need it
RunUI(() =>
{
measuredDTs.Add(ionMobilityLibraryDlg.LibraryMobilitiesFlat.ToList());
ionMobilityLibraryDlg.OkDialog();
});
WaitForClosedForm(ionMobilityLibraryDlg);
RunUI(() =>
{
transitionSettingsDlg.OkDialog();
});
WaitForClosedForm(transitionSettingsDlg);
document = SkylineWindow.Document;
var count = 0;
for (var n = 0; n < curatedDTs.Count; n++)
{
var cdt = curatedDTs[n];
var key = cdt.Precursor;
var indexM = measuredDTs[pass].FindIndex(m => m.Precursor.Equals(key));
var measured = measuredDTs[pass][indexM];
var measuredDT = measured.IonMobility;
var measuredHEO = measured.HighEnergyIonMobilityOffset;
if (precursors.ItemsMatching(key, true).Any())
{
count++;
AssertEx.AreNotEqual(cdt.IonMobility, measuredDT, "measured drift time should differ somewhat for " + measured.Precursor);
}
AssertEx.AreEqual(cdt.IonMobility, measuredDT, 1.0, "measured drift time differs too much for " + key);
AssertEx.AreEqual(cdt.HighEnergyIonMobilityOffset, measuredHEO, 2.0, "measured drift time high energy offset differs too much for " + key);
}
AssertEx.AreEqual(document.MoleculeTransitionGroupCount, count, "did not find drift times for all precursors"); // Expect to find a value for each precursor
if (pass == 1)
{
break;
}
// Verify that we select based on strongest results by removing the training set and relying on the other noisier set
RunDlg <ManageResultsDlg>(SkylineWindow.ManageResults, dlg =>
{
var chromatograms = document.Settings.MeasuredResults.Chromatograms;
var chromTraining = chromatograms[0];
var chroms = new[] { chromTraining };
dlg.SelectedChromatograms = chroms; // Passing this chromatograms[0] results in the other set being deleted - compiler problem?
dlg.RemoveReplicates();
dlg.OkDialog();
});
document = WaitForDocumentChange(document);
AssertEx.AreEqual(1, document.Settings.MeasuredResults.Chromatograms.Count);
}
// Results should be slightly different without the training set of chromatograms to contain a potentially stronger peak
var ccount = 0;
var noChange = new List <LibKey>();
for (var n = 0; n < measuredDTs[0].Count; n++)
{
var validatingIonMobilityPeptide0 = measuredDTs[0][n];
var validatingIonMobilityPeptide1 = measuredDTs[1][n];
var key = measuredDTs[0][n].Precursor;
if (precursors.ItemsMatching(key, true).Any())
{
ccount++;
if (validatingIonMobilityPeptide0.HighEnergyIonMobilityOffset == validatingIonMobilityPeptide1.HighEnergyIonMobilityOffset)
{
noChange.Add(key);
}
}
AssertEx.AreEqual(validatingIonMobilityPeptide0.IonMobility, validatingIonMobilityPeptide1.IonMobility, 1.0, "averaged measured drift time differs for " + key);
AssertEx.AreEqual(validatingIonMobilityPeptide0.HighEnergyIonMobilityOffset, validatingIonMobilityPeptide1.HighEnergyIonMobilityOffset, 2.0, "averaged measured drift time high energy offset differs for " + key);
AssertEx.AreEqual(validatingIonMobilityPeptide0.CollisionalCrossSectionSqA, validatingIonMobilityPeptide1.CollisionalCrossSectionSqA, 1.0, "averaged measured CCS differs for " + key);
}
AssertEx.AreEqual(document.MoleculeTransitionGroupCount, ccount, "did not find drift times for all precursors"); // Expect to find a value for each precursor
AssertEx.IsTrue(noChange.Count < ccount / 2, "expected most values to shift a little without the nice clean training data");
// And finally verify ability to reimport with altered drift filter (would formerly fail on an erroneous Assume)
// Simulate user picking Edit Current from the Ion Mobility Library combo control, and messing with all the measured drift time values
var transitionSettingsDlg2 = ShowDialog <TransitionSettingsUI>(
() => SkylineWindow.ShowTransitionSettingsUI(TransitionSettingsUI.TABS.Prediction));
var editIonMobilityLibraryDlg = ShowDialog <EditIonMobilityLibraryDlg>(transitionSettingsDlg2.IonMobilityControl.EditIonMobilityLibrary);
RunUI(() =>
{
var revised = new List <ValidatingIonMobilityPrecursor>();
foreach (var item in editIonMobilityLibraryDlg.LibraryMobilitiesFlat)
{
var im = item.IonMobility;
var heo = item.HighEnergyIonMobilityOffset;
revised.Add(new ValidatingIonMobilityPrecursor(item.Precursor,
IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.GetIonMobilityValue(im * 1.02, item.IonMobilityUnits),
item.CollisionalCrossSectionSqA * 1.02, heo * 1.02)));
}
editIonMobilityLibraryDlg.LibraryMobilitiesFlat = revised;
editIonMobilityLibraryDlg.OkDialog();
});
WaitForClosedForm(editIonMobilityLibraryDlg);
RunUI(() =>
{
transitionSettingsDlg2.OkDialog();
});
WaitForClosedForm(transitionSettingsDlg2);
var docChangedDriftTimePredictor = WaitForDocumentChange(document);
// Reimport data for a replicate - without the fix this will throw
RunDlg <ManageResultsDlg>(SkylineWindow.ManageResults, dlg =>
{
var chromatograms = docChangedDriftTimePredictor.Settings.MeasuredResults.Chromatograms;
dlg.SelectedChromatograms = new[] { chromatograms[0] };
dlg.ReimportResults();
dlg.OkDialog();
});
WaitForDocumentChangeLoaded(docChangedDriftTimePredictor, WAIT_TIME * 2);
}
private void PerformTestMeasuredDriftValues(bool asSmallMolecules)
{
if (asSmallMolecules)
{
if (!RunSmallMoleculeTestVersions)
{
Console.Write(MSG_SKIPPING_SMALLMOLECULE_TEST_VERSION);
return;
}
TestSmallMolecules = false; // No need to add the magic small molecule test node
}
var testFilesDir = new TestFilesDir(TestContext, @"Test\Results\BlibDriftTimeTest.zip"); // Re-used from BlibDriftTimeTest
// Open document with some peptides but no results
var docPath = testFilesDir.GetTestPath("BlibDriftTimeTest.sky");
// This was a malformed document, which caused problems after a fix to not recalculate
// document library settings on open. To avoid rewriting this test for the document
// which now contains 2 precursors, the first precursor is removed immediately.
SrmDocument docOriginal = ResultsUtil.DeserializeDocument(docPath);
var pathFirstPeptide = docOriginal.GetPathTo((int)SrmDocument.Level.Molecules, 0);
var nodeFirstPeptide = (DocNodeParent)docOriginal.FindNode(pathFirstPeptide);
docOriginal = (SrmDocument)docOriginal.RemoveChild(pathFirstPeptide, nodeFirstPeptide.Children[0]);
if (asSmallMolecules)
{
var refine = new RefinementSettings();
docOriginal = refine.ConvertToSmallMolecules(docOriginal, testFilesDir.FullPath);
}
using (var docContainer = new ResultsTestDocumentContainer(docOriginal, docPath))
{
var doc = docContainer.Document;
// Import an mz5 file that contains drift info
const string replicateName = "ID12692_01_UCA168_3727_040714";
var chromSets = new[]
{
new ChromatogramSet(replicateName, new[]
{ new MsDataFilePath(testFilesDir.GetTestPath("ID12692_01_UCA168_3727_040714" + ExtensionTestContext.ExtMz5)), }),
};
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(chromSets));
Assert.IsTrue(docContainer.SetDocument(docResults, docOriginal, true));
docContainer.AssertComplete();
var document = docContainer.Document;
document = document.ChangeSettings(document.Settings.ChangePeptidePrediction(prediction => new PeptidePrediction(null, IonMobilityPredictor.EMPTY)));
// Verify ability to extract predictions from raw data
var newPred = document.Settings.PeptideSettings.Prediction.IonMobilityPredictor.ChangeMeasuredIonMobilityValuesFromResults(
document, docContainer.DocumentFilePath);
var result = newPred.MeasuredMobilityIons;
Assert.AreEqual(TestSmallMolecules ? 2 : 1, result.Count);
const double expectedDT = 4.0019;
var expectedOffset = .4829;
Assert.AreEqual(expectedDT, result.Values.First().IonMobility.Mobility.Value, .001);
Assert.AreEqual(expectedOffset, result.Values.First().HighEnergyIonMobilityValueOffset, .001);
// Check ability to update, and to preserve unchanged
var revised = new Dictionary <LibKey, IonMobilityAndCCS>();
var libKey = result.Keys.First();
revised.Add(libKey, IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.GetIonMobilityValue(4, eIonMobilityUnits.drift_time_msec), null, 0.234)); // N.B. CCS handling would require actual raw data in this test, it's covered in a perf test
var libKey2 = new LibKey("DEADEELS", asSmallMolecules ? Adduct.NonProteomicProtonatedFromCharge(2) : Adduct.DOUBLY_PROTONATED);
revised.Add(libKey2, IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.GetIonMobilityValue(5, eIonMobilityUnits.drift_time_msec), null, 0.123));
document =
document.ChangeSettings(
document.Settings.ChangePeptidePrediction(prediction => new PeptidePrediction(null, new IonMobilityPredictor("test", revised, null, null, IonMobilityWindowWidthCalculator.IonMobilityPeakWidthType.resolving_power, 40, 0, 0))));
newPred = document.Settings.PeptideSettings.Prediction.ChangeDriftTimePredictor(
document.Settings.PeptideSettings.Prediction.IonMobilityPredictor.ChangeMeasuredIonMobilityValuesFromResults(
document, docContainer.DocumentFilePath)).IonMobilityPredictor;
result = newPred.MeasuredMobilityIons;
Assert.AreEqual(TestSmallMolecules ? 3 : 2, result.Count);
Assert.AreEqual(expectedDT, result[libKey].IonMobility.Mobility.Value, .001);
Assert.AreEqual(expectedOffset, result[libKey].HighEnergyIonMobilityValueOffset, .001);
Assert.AreEqual(5, result[libKey2].IonMobility.Mobility.Value, .001);
Assert.AreEqual(0.123, result[libKey2].HighEnergyIonMobilityValueOffset, .001);
}
}
public bool ContainsIonMobilityValue(IonMobilityValue ionMobility, double highEnergyOffset)
{
return(!ionMobility.HasValue || ContainsIonMobilityValue(ionMobility.Mobility.Value, highEnergyOffset));
}
private void PerformTestMeasuredDriftValues(bool asSmallMolecules)
{
if (asSmallMolecules)
{
if (!RunSmallMoleculeTestVersions)
{
Console.Write(MSG_SKIPPING_SMALLMOLECULE_TEST_VERSION);
return;
}
}
var testFilesDir = new TestFilesDir(TestContext, @"TestData\Results\BlibDriftTimeTest.zip"); // Re-used from BlibDriftTimeTest
// Open document with some peptides but no results
var docPath = testFilesDir.GetTestPath("BlibDriftTimeTest.sky");
// This was a malformed document, which caused problems after a fix to not recalculate
// document library settings on open. To avoid rewriting this test for the document
// which now contains 2 precursors, the first precursor is removed immediately.
SrmDocument docOriginal = ResultsUtil.DeserializeDocument(docPath);
var pathFirstPeptide = docOriginal.GetPathTo((int)SrmDocument.Level.Molecules, 0);
var nodeFirstPeptide = (DocNodeParent)docOriginal.FindNode(pathFirstPeptide);
docOriginal = (SrmDocument)docOriginal.RemoveChild(pathFirstPeptide, nodeFirstPeptide.Children[0]);
if (asSmallMolecules)
{
var refine = new RefinementSettings();
docOriginal = refine.ConvertToSmallMolecules(docOriginal, testFilesDir.FullPath);
}
using (var docContainer = new ResultsTestDocumentContainer(docOriginal, docPath))
{
var doc = docContainer.Document;
// Import an mz5 file that contains drift info
const string replicateName = "ID12692_01_UCA168_3727_040714";
var chromSets = new[]
{
new ChromatogramSet(replicateName, new[]
{ new MsDataFilePath(testFilesDir.GetTestPath("ID12692_01_UCA168_3727_040714" + ExtensionTestContext.ExtMz5)), }),
};
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(chromSets));
Assert.IsTrue(docContainer.SetDocument(docResults, docOriginal, true));
docContainer.AssertComplete();
var document = docContainer.Document;
// Clear out any current settings
document = document.ChangeSettings(document.Settings.ChangeTransitionIonMobilityFiltering(s => TransitionIonMobilityFiltering.EMPTY));
// Verify ability to extract predictions from raw data
var libraryName0 = "test0";
var dbPath0 = testFilesDir.GetTestPath(libraryName0 + IonMobilityDb.EXT);
var newIMFiltering = document.Settings.TransitionSettings.IonMobilityFiltering.ChangeLibrary(
IonMobilityLibrary.CreateFromResults(
document, docContainer.DocumentFilePath, true,
libraryName0, dbPath0));
var result = newIMFiltering.IonMobilityLibrary.GetIonMobilityLibKeyMap().AsDictionary();
Assert.AreEqual(1, result.Count);
var expectedDT = 4.0019;
var expectedOffset = .4829;
Assert.AreEqual(expectedDT, result.Values.First().First().IonMobility.Mobility.Value, .001);
Assert.AreEqual(expectedOffset, result.Values.First().First().HighEnergyIonMobilityValueOffset ?? 0, .001);
// Check ability to update, and to preserve unchanged
var revised = new List <PrecursorIonMobilities>();
var libKey = result.Keys.First();
revised.Add(new PrecursorIonMobilities(libKey, IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.GetIonMobilityValue(expectedDT = 4, eIonMobilityUnits.drift_time_msec), null, expectedOffset = 0.234))); // N.B. CCS handling would require actual raw data in this test, it's covered in a perf test
var pepSequence = "DEADEELS";
var libKey2 = asSmallMolecules ?
new LibKey(SmallMoleculeLibraryAttributes.Create(pepSequence, "C12H5", null, null, null, null), Adduct.M_PLUS_2H) :
new LibKey(pepSequence, Adduct.DOUBLY_PROTONATED);
revised.Add(new PrecursorIonMobilities(libKey2, IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.GetIonMobilityValue(5, eIonMobilityUnits.drift_time_msec), null, 0.123)));
var libraryName = "test";
var dbPath = testFilesDir.GetTestPath(libraryName + IonMobilityDb.EXT);
var imsdb = IonMobilityDb.CreateIonMobilityDb(dbPath, libraryName, false, revised);
var newLibIM = new IonMobilityLibrary(libraryName, dbPath, imsdb);
var ionMobilityWindowWidthCalculator = new IonMobilityWindowWidthCalculator(
IonMobilityWindowWidthCalculator.IonMobilityWindowWidthType.resolving_power, 40, 0, 0, 0);
var calculator = ionMobilityWindowWidthCalculator;
document = document.ChangeSettings(
document.Settings.ChangeTransitionIonMobilityFiltering(
imf => imf.ChangeFilterWindowWidthCalculator(calculator).
ChangeLibrary(newLibIM)));
result = document.Settings.TransitionSettings.IonMobilityFiltering.IonMobilityLibrary.GetIonMobilityLibKeyMap().AsDictionary();
Assert.AreEqual(2, result.Count);
Assert.AreEqual(expectedDT, result[libKey].First().IonMobility.Mobility.Value, .001);
Assert.AreEqual(expectedOffset, result[libKey].First().HighEnergyIonMobilityValueOffset ?? 0, .001);
Assert.AreEqual(5, result[libKey2].First().IonMobility.Mobility.Value, .001);
Assert.AreEqual(0.123, result[libKey2].First().HighEnergyIonMobilityValueOffset ?? 0, .001);
ionMobilityWindowWidthCalculator = new IonMobilityWindowWidthCalculator(
IonMobilityWindowWidthCalculator.IonMobilityWindowWidthType.fixed_width, 40, 0, 0, 100);
document = document.ChangeSettings(
document.Settings.ChangeTransitionIonMobilityFiltering(
imf => imf.ChangeFilterWindowWidthCalculator(ionMobilityWindowWidthCalculator).
ChangeLibrary(newLibIM)));
result = document.Settings.TransitionSettings.IonMobilityFiltering.IonMobilityLibrary.GetIonMobilityLibKeyMap().AsDictionary();
Assert.AreEqual(2, result.Count);
Assert.AreEqual(expectedDT, result[libKey].First().IonMobility.Mobility.Value, .001);
Assert.AreEqual(expectedOffset, result[libKey].First().HighEnergyIonMobilityValueOffset ?? 0, .001);
Assert.AreEqual(5, result[libKey2].First().IonMobility.Mobility.Value, .001);
Assert.AreEqual(0.123, result[libKey2].First().HighEnergyIonMobilityValueOffset ?? 0, .001);
}
}
public Dictionary <LibKey, IonMobilityAndCCS> GetTableMeasuredIonMobility(bool useHighEnergyOffsets, eIonMobilityUnits units)
{
var e = new CancelEventArgs();
var dict = new Dictionary <LibKey, IonMobilityAndCCS>();
foreach (DataGridViewRow row in _gridMeasuredDriftTimePeptides.Rows)
{
if (row.IsNewRow)
{
continue;
}
string seq;
if (!ValidateSequence(e, row.Cells[EditDriftTimePredictorDlg.COLUMN_SEQUENCE], out seq))
{
return(null);
}
// OK, we have a non-empty "sequence" string, but is that actually a peptide or a molecule?
// See if there's anything in the document whose text representation matches what's in the list
var target = Program.MainWindow.Document.Molecules.Select(m => m.Target).FirstOrDefault(t => seq.Equals(t.ToString()));
if (target == null || target.IsEmpty)
{
// Does seq evaluate as a peptide?
target = !seq.All(c => char.IsUpper(c) || char.IsDigit(c) || @"[+-,.]()".Contains(c))
? new Target(CustomMolecule.FromSerializableString(seq))
: Target.FromSerializableString(seq);
}
Adduct charge;
if (!ValidateCharge(e, row.Cells[EditDriftTimePredictorDlg.COLUMN_CHARGE], target.IsProteomic, out charge))
{
return(null);
}
double mobility;
if (!ValidateDriftTime(e, row.Cells[EditDriftTimePredictorDlg.COLUMN_ION_MOBILITY], out mobility))
{
return(null);
}
double?ccs;
if (!ValidateCCS(e, row.Cells[EditDriftTimePredictorDlg.COLUMN_CCS], out ccs))
{
return(null);
}
double highEnergyOffset = 0; // Set default value in case user does not provide one
if (useHighEnergyOffsets && !ValidateHighEnergyDriftTimeOffset(e, row.Cells[EditDriftTimePredictorDlg.COLUMN_HIGH_ENERGY_OFFSET], out highEnergyOffset))
{
return(null);
}
var ionMobility = IonMobilityValue.GetIonMobilityValue(mobility, units);
try
{
dict.Add(new LibKey(target, charge), IonMobilityAndCCS.GetIonMobilityAndCCS(ionMobility, ccs, highEnergyOffset));
}
// ReSharper disable once EmptyGeneralCatchClause
catch
{
// just take the first seen
}
}
return(dict);
}
public double?CCSFromIonMobility(IonMobilityValue ionMobilityValue, double mz, int charge)
{
return(null); // Unsupported
}
