public bool ValidateProductResMz(MessageBoxHelper helper, out double?productResMz)
{
FullScanAcquisitionMethod acquisitionMethod = AcquisitionMethod;
productResMz = null;
if (acquisitionMethod != FullScanAcquisitionMethod.None)
{
if (IsResMzAnalyzer(ProductMassAnalyzer))
{
double prodResMz;
bool valid = helper.ValidateDecimalTextBox(textProductAt,
TransitionFullScan.MIN_RES_MZ,
TransitionFullScan.MAX_RES_MZ, out prodResMz);
if (!valid)
{
return(false);
}
productResMz = prodResMz;
}
}
return(true);
}
public bool ValidateProductRes(MessageBoxHelper helper, out double?productRes, TabControl tabControl = null, int tabIndex = -1)
{
FullScanAcquisitionMethod acquisitionMethod = AcquisitionMethod;
productRes = null;
if (acquisitionMethod != FullScanAcquisitionMethod.None)
{
double minFilt, maxFilt;
GetFilterMinMax(ProductMassAnalyzer, out minFilt, out maxFilt);
double prodRes;
bool valid;
if (null != tabControl)
{
valid = helper.ValidateDecimalTextBox(tabControl, (int)TransitionSettingsUI.TABS.FullScan,
textProductRes, minFilt, maxFilt, out prodRes);
}
else
{
valid = helper.ValidateDecimalTextBox(textProductRes, minFilt, maxFilt, out prodRes);
}
if (!valid)
{
return(false);
}
productRes = prodRes;
}
return(true);
}
public bool ValidateProductRes(MessageBoxHelper helper, out double?productRes)
{
FullScanAcquisitionMethod acquisitionMethod = AcquisitionMethod;
productRes = null;
if (acquisitionMethod != FullScanAcquisitionMethod.None)
{
double minFilt, maxFilt;
GetFilterMinMax(ProductMassAnalyzer, out minFilt, out maxFilt);
double prodRes;
bool valid = helper.ValidateDecimalTextBox(textProductRes, minFilt, maxFilt, out prodRes);
if (!valid)
{
return(false);
}
productRes = prodRes;
}
return(true);
}
private void ExportIsolationList(
string csvFilename, string instrumentType, FullScanAcquisitionMethod acquisitionMethod,
ExportMethodType methodType, params string[] checkStrings)
{
// Set acquisition method, mass analyzer type, resolution, etc.
if (Equals(instrumentType, ExportInstrumentType.AGILENT_TOF))
{
RunUI(() => SkylineWindow.ModifyDocument("Set TOF full-scan settings", doc => doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs => fs
.ChangePrecursorResolution(FullScanMassAnalyzerType.tof, 10000, null)
.ChangeProductResolution(FullScanMassAnalyzerType.tof, 10000, null)
.ChangeAcquisitionMethod(acquisitionMethod, null)))));
}
else
{
RunUI(() => SkylineWindow.ModifyDocument("Set Orbitrap full-scan settings", doc => doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs => fs
.ChangePrecursorResolution(FullScanMassAnalyzerType.orbitrap, 60000, 400)
.ChangeProductResolution(FullScanMassAnalyzerType.orbitrap, 60000, 400)
.ChangeAcquisitionMethod(acquisitionMethod, null)))));
}
// Open Export Method dialog, and set method to scheduled or standard.
string csvPath = TestContext.GetTestPath(csvFilename);
var exportMethodDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.IsolationList));
RunUI(() =>
{
exportMethodDlg.InstrumentType = instrumentType;
exportMethodDlg.MethodType = methodType;
exportMethodDlg.UseSlens = WithSLens;
Assert.IsFalse(exportMethodDlg.IsOptimizeTypeEnabled);
Assert.IsTrue(exportMethodDlg.IsTargetTypeEnabled);
Assert.IsFalse(exportMethodDlg.IsDwellTimeVisible);
Assert.IsFalse(exportMethodDlg.IsMaxTransitionsEnabled);
});
if (methodType == ExportMethodType.Standard)
{
// Simply close the dialog.
OkDialog(exportMethodDlg, () => exportMethodDlg.OkDialog(csvPath));
}
else
{
// Close the SchedulingOptionsDlg, then wait for export dialog to close.
RunDlg <SchedulingOptionsDlg>(() => exportMethodDlg.OkDialog(csvPath), schedulingOptionsDlg => schedulingOptionsDlg.OkDialog());
WaitForClosedForm(exportMethodDlg);
}
// Check for expected output.
string csvOut = File.ReadAllText(csvPath);
AssertEx.Contains(csvOut, checkStrings);
}
public bool ValidateProductResMz(MessageBoxHelper helper, out double?productResMz, TabControl tabControl = null, int tabIndex = -1)
{
FullScanAcquisitionMethod acquisitionMethod = AcquisitionMethod;
productResMz = null;
if (acquisitionMethod != FullScanAcquisitionMethod.None)
{
if (IsResMzAnalyzer(ProductMassAnalyzer))
{
double prodResMz;
bool valid;
if (null != tabControl)
{
valid = helper.ValidateDecimalTextBox(tabControl, (int)TransitionSettingsUI.TABS.FullScan,
textProductAt,
TransitionFullScan.MIN_RES_MZ,
TransitionFullScan.MAX_RES_MZ, out prodResMz);
}
else
{
valid = helper.ValidateDecimalTextBox(textProductAt,
TransitionFullScan.MIN_RES_MZ,
TransitionFullScan.MAX_RES_MZ, out prodResMz);
}
if (!valid)
{
return(false);
}
productResMz = prodResMz;
}
}
return(true);
}
private void ExportIsolationList(
string csvFilename, string instrumentType, FullScanAcquisitionMethod acquisitionMethod,
ExportMethodType methodType, params string[] checkStrings)
{
// Set acquisition method, mass analyzer type, resolution, etc.
if (Equals(instrumentType, ExportInstrumentType.AGILENT_TOF))
{
RunUI(() => SkylineWindow.ModifyDocument("Set TOF full-scan settings", doc => doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs => fs
.ChangePrecursorResolution(FullScanMassAnalyzerType.tof, 10000, null)
.ChangeProductResolution(FullScanMassAnalyzerType.tof, 10000, null)
.ChangeAcquisitionMethod(acquisitionMethod, null)))));
}
else
{
RunUI(() => SkylineWindow.ModifyDocument("Set Orbitrap full-scan settings", doc => doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs => fs
.ChangePrecursorResolution(FullScanMassAnalyzerType.orbitrap, 60000, 400)
.ChangeProductResolution(FullScanMassAnalyzerType.orbitrap, 60000, 400)
.ChangeAcquisitionMethod(acquisitionMethod, null)))));
}
// Open Export Method dialog, and set method to scheduled or standard.
string csvPath = TestFilesDirs[0].GetTestPath(csvFilename);
var exportMethodDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.IsolationList));
var exportPolarityFilter =
AsSmallMoleculesNegativeMode != RefinementSettings.ConvertToSmallMoleculesChargesMode.none &&
SkylineWindow.Document.IsMixedPolarity() ?
ExportPolarity.separate :
ExportPolarity.all;
RunUI(() =>
{
exportMethodDlg.InstrumentType = instrumentType;
exportMethodDlg.MethodType = methodType;
exportMethodDlg.UseSlens = WithSLens;
exportMethodDlg.PolarityFilter = exportPolarityFilter;
Assert.IsFalse(exportMethodDlg.IsOptimizeTypeEnabled);
Assert.IsTrue(exportMethodDlg.IsTargetTypeEnabled);
Assert.IsFalse(exportMethodDlg.IsDwellTimeVisible);
Assert.IsFalse(exportMethodDlg.IsMaxTransitionsEnabled);
});
if (methodType == ExportMethodType.Standard)
{
// Simply close the dialog.
OkDialog(exportMethodDlg, () => exportMethodDlg.OkDialog(csvPath));
}
else
{
// Close the SchedulingOptionsDlg, then wait for export dialog to close.
RunDlg <SchedulingOptionsDlg>(() => exportMethodDlg.OkDialog(csvPath), schedulingOptionsDlg => schedulingOptionsDlg.OkDialog());
WaitForClosedForm(exportMethodDlg);
}
// Check for expected output.
var csvResult = csvPath;
if (exportPolarityFilter == ExportPolarity.separate)
{
// We will have emitted two docs, one for pos and one for neg
var ext = csvPath.Substring(csvPath.LastIndexOf('.'));
csvResult = csvPath.Replace(ext, string.Format("_{0}_0001{1}", ExportPolarity.negative, ext));
var csvPos = File.ReadAllText(csvPath.Replace(ext, string.Format("_{0}_0001{1}", ExportPolarity.positive, ext)));
var csvNeg = File.ReadAllText(csvResult);
Assert.IsFalse(csvNeg.Equals(csvPos));
}
string csvOut = File.ReadAllText(csvResult);
AssertEx.Contains(csvOut, checkStrings);
}
private IEnumerable <SpectrumFilterPair> FindFilterPairs(IsolationWindowFilter isoWin,
FullScanAcquisitionMethod acquisitionMethod, bool ignoreIsolationScheme = false)
{
if (!isoWin.IsolationMz.HasValue)
{
return(new SpectrumFilterPair[0]); // empty
}
// Return cached value from dictionary if we've seen this target previously.
var isoWinKey = isoWin;
IList <SpectrumFilterPair> filterPairsCached;
if (_filterPairDictionary.TryGetValue(isoWinKey, out filterPairsCached))
{
return(filterPairsCached);
}
var filterPairs = new List <SpectrumFilterPair>();
if (acquisitionMethod == FullScanAcquisitionMethod.DIA)
{
var isoTargMz = isoWin.IsolationMz;
double?isoTargWidth = isoWin.IsolationWidth;
if (!ignoreIsolationScheme)
{
CalcDiaIsolationValues(ref isoTargMz, ref isoTargWidth);
}
if (isoTargWidth.HasValue)
{
// For multiple case, find the first possible value, and iterate until
// no longer matching or the end of the array is encountered
int iFilter = IndexOfFilter(isoTargMz, isoTargWidth.Value);
if (iFilter != -1)
{
while (iFilter < _filterMzValues.Length && CompareMz(isoTargMz,
_filterMzValues[iFilter].Q1, isoTargWidth.Value) == 0)
{
filterPairs.Add(_filterMzValues[iFilter++]);
}
}
}
}
else
{
// For single (Targeted) case, review all possible matches for the one closest to the
// desired precursor m/z value.
// per "Issue 263: Too strict about choosing only one precursor for every MS/MS scan in Targeted MS/MS",
// if more than one match at this m/z value return a list
double minMzDelta = double.MaxValue;
double mzDeltaEpsilon = Math.Min(_instrument.MzMatchTolerance, .0001);
// Isolation width for single is based on the instrument m/z match tolerance
var isoTargMz = isoWin.IsolationMz;
var isoWinSingle = new IsolationWindowFilter(isoTargMz, _instrument.MzMatchTolerance * 2);
foreach (var filterPair in FindFilterPairs(isoWinSingle, FullScanAcquisitionMethod.DIA, true))
{
double mzDelta = Math.Abs(isoTargMz - filterPair.Q1);
if (mzDelta < minMzDelta) // new best match
{
minMzDelta = mzDelta;
// are any existing matches no longer within epsilion of new best match?
for (int n = filterPairs.Count; n-- > 0;)
{
if ((Math.Abs(isoTargMz - filterPairs[n].Q1) - minMzDelta) > mzDeltaEpsilon)
{
filterPairs.RemoveAt(n); // no longer a match by our new standard
}
}
filterPairs.Add(filterPair);
}
else if ((mzDelta - minMzDelta) <= mzDeltaEpsilon)
{
filterPairs.Add(filterPair); // not the best, but close to it
}
}
}
_filterPairDictionary[isoWinKey] = filterPairs;
return(filterPairs);
}
public SpectrumFilter(SrmDocument document, MsDataFileUri msDataFileUri, IFilterInstrumentInfo instrumentInfo,
IRetentionTimePredictor retentionTimePredictor = null, bool firstPass = false)
{
_fullScan = document.Settings.TransitionSettings.FullScan;
_instrument = document.Settings.TransitionSettings.Instrument;
_acquisitionMethod = _fullScan.AcquisitionMethod;
if (instrumentInfo != null)
{
_isWatersFile = instrumentInfo.IsWatersFile;
}
IsFirstPass = firstPass;
var comparer = PrecursorTextId.PrecursorTextIdComparerInstance;
var dictPrecursorMzToFilter = new SortedDictionary <PrecursorTextId, SpectrumFilterPair>(comparer);
if (EnabledMs || EnabledMsMs)
{
if (EnabledMs)
{
_isHighAccMsFilter = !Equals(_fullScan.PrecursorMassAnalyzer,
FullScanMassAnalyzerType.qit);
if (!firstPass)
{
var key = new PrecursorTextId(SignedMz.ZERO, null, ChromExtractor.summed); // TIC
dictPrecursorMzToFilter.Add(key, new SpectrumFilterPair(key, PeptideDocNode.UNKNOWN_COLOR, dictPrecursorMzToFilter.Count,
_instrument.MinTime, _instrument.MaxTime, null, null, 0, _isHighAccMsFilter, _isHighAccProductFilter));
key = new PrecursorTextId(SignedMz.ZERO, null, ChromExtractor.base_peak); // BPC
dictPrecursorMzToFilter.Add(key, new SpectrumFilterPair(key, PeptideDocNode.UNKNOWN_COLOR, dictPrecursorMzToFilter.Count,
_instrument.MinTime, _instrument.MaxTime, null, null, 0, _isHighAccMsFilter, _isHighAccProductFilter));
}
}
if (EnabledMsMs)
{
_isHighAccProductFilter = !Equals(_fullScan.ProductMassAnalyzer,
FullScanMassAnalyzerType.qit);
if (_fullScan.AcquisitionMethod == FullScanAcquisitionMethod.DIA &&
_fullScan.IsolationScheme.IsAllIons)
{
if (instrumentInfo != null)
{
_isWatersMse = _isWatersFile;
_isAgilentMse = instrumentInfo.IsAgilentFile;
}
_mseLevel = 1;
}
}
Func <double, double> calcWindowsQ1 = _fullScan.GetPrecursorFilterWindow;
Func <double, double> calcWindowsQ3 = _fullScan.GetProductFilterWindow;
_minTime = _instrument.MinTime;
_maxTime = _instrument.MaxTime;
bool canSchedule = CanSchedule(document, retentionTimePredictor);
// TODO: Figure out a way to turn off time sharing on first SIM scan so that
// times can be shared for MS1 without SIM scans
_isSharedTime = !canSchedule;
// If we're using bare measured drift times from spectral libraries, go get those now
var libraryIonMobilityInfo = document.Settings.PeptideSettings.Prediction.UseLibraryDriftTimes
? document.Settings.GetIonMobilities(msDataFileUri)
: null;
foreach (var nodePep in document.Molecules)
{
if (firstPass && !retentionTimePredictor.IsFirstPassPeptide(nodePep))
{
continue;
}
foreach (TransitionGroupDocNode nodeGroup in nodePep.Children)
{
if (nodeGroup.Children.Count == 0)
{
continue;
}
double? minTime = _minTime, maxTime = _maxTime;
double? startDriftTimeMsec = null, endDriftTimeMsec = null;
double windowDT;
double highEnergyDriftTimeOffsetMsec = 0;
DriftTimeInfo centerDriftTime = document.Settings.PeptideSettings.Prediction.GetDriftTime(
nodePep, nodeGroup, libraryIonMobilityInfo, out windowDT);
if (centerDriftTime.DriftTimeMsec(false).HasValue)
{
startDriftTimeMsec = centerDriftTime.DriftTimeMsec(false) - windowDT / 2; // Get the low energy drift time
endDriftTimeMsec = startDriftTimeMsec + windowDT;
highEnergyDriftTimeOffsetMsec = centerDriftTime.HighEnergyDriftTimeOffsetMsec;
}
if (canSchedule)
{
if (RetentionTimeFilterType.scheduling_windows == _fullScan.RetentionTimeFilterType)
{
double?centerTime = null;
double windowRT = 0;
if (retentionTimePredictor != null)
{
centerTime = retentionTimePredictor.GetPredictedRetentionTime(nodePep);
}
else
{
var prediction = document.Settings.PeptideSettings.Prediction;
if (prediction.RetentionTime == null || !prediction.RetentionTime.IsAutoCalculated)
{
centerTime = document.Settings.PeptideSettings.Prediction.PredictRetentionTimeForChromImport(
document, nodePep, nodeGroup, out windowRT);
}
}
// Force the center time to be at least zero
if (centerTime.HasValue && centerTime.Value < 0)
{
centerTime = 0;
}
if (_fullScan.RetentionTimeFilterLength != 0)
{
windowRT = _fullScan.RetentionTimeFilterLength * 2;
}
if (centerTime != null)
{
double startTime = centerTime.Value - windowRT / 2;
double endTime = startTime + windowRT;
minTime = Math.Max(minTime ?? 0, startTime);
maxTime = Math.Min(maxTime ?? double.MaxValue, endTime);
}
}
else if (RetentionTimeFilterType.ms2_ids == _fullScan.RetentionTimeFilterType)
{
var times = document.Settings.GetBestRetentionTimes(nodePep, msDataFileUri);
if (times.Length > 0)
{
minTime = Math.Max(minTime ?? 0, times.Min() - _fullScan.RetentionTimeFilterLength);
maxTime = Math.Min(maxTime ?? double.MaxValue, times.Max() + _fullScan.RetentionTimeFilterLength);
}
}
}
SpectrumFilterPair filter;
string textId = nodePep.RawTextId; // Modified Sequence for peptides, or some other string for custom ions
var mz = new SignedMz(nodeGroup.PrecursorMz, nodeGroup.PrecursorCharge < 0);
var key = new PrecursorTextId(mz, textId, ChromExtractor.summed);
if (!dictPrecursorMzToFilter.TryGetValue(key, out filter))
{
filter = new SpectrumFilterPair(key, nodePep.Color, dictPrecursorMzToFilter.Count, minTime, maxTime,
startDriftTimeMsec, endDriftTimeMsec, highEnergyDriftTimeOffsetMsec,
_isHighAccMsFilter, _isHighAccProductFilter);
dictPrecursorMzToFilter.Add(key, filter);
}
if (!EnabledMs)
{
filter.AddQ3FilterValues(from TransitionDocNode nodeTran in nodeGroup.Children
select nodeTran.Mz, calcWindowsQ3);
}
else if (!EnabledMsMs)
{
filter.AddQ1FilterValues(GetMS1MzValues(nodeGroup), calcWindowsQ1);
}
else
{
filter.AddQ1FilterValues(GetMS1MzValues(nodeGroup), calcWindowsQ1);
filter.AddQ3FilterValues(from TransitionDocNode nodeTran in nodeGroup.Children
where !nodeTran.IsMs1
select nodeTran.Mz, calcWindowsQ3);
}
}
}
_filterMzValues = dictPrecursorMzToFilter.Values.ToArray();
var listChromKeyFilterIds = new List <ChromKey>();
foreach (var spectrumFilterPair in _filterMzValues)
{
spectrumFilterPair.AddChromKeys(listChromKeyFilterIds);
}
_productChromKeys = listChromKeyFilterIds.ToArray();
// Sort a copy of the filter pairs by maximum retention time so that we can detect when
// filters are no longer active.
_filterRTValues = new SpectrumFilterPair[_filterMzValues.Length];
Array.Copy(_filterMzValues, _filterRTValues, _filterMzValues.Length);
Array.Sort(_filterRTValues, CompareByRT);
}
InitRTLimits();
}
public void OkDialog()
{
var helper = new MessageBoxHelper(this);
// Validate and store prediction settings
string massType = comboPrecursorMass.SelectedItem.ToString();
MassType precursorMassType = MassTypeExtension.GetEnum(massType);
massType = comboIonMass.SelectedItem.ToString();
MassType fragmentMassType = MassTypeExtension.GetEnum(massType);
string nameCE = comboCollisionEnergy.SelectedItem.ToString();
CollisionEnergyRegression collisionEnergy =
Settings.Default.GetCollisionEnergyByName(nameCE);
string nameDP = comboDeclusterPotential.SelectedItem.ToString();
DeclusteringPotentialRegression declusteringPotential =
Settings.Default.GetDeclusterPotentialByName(nameDP);
string nameCoV = comboCompensationVoltage.SelectedItem.ToString();
CompensationVoltageParameters compensationVoltage =
Settings.Default.GetCompensationVoltageByName(nameCoV);
string nameOptLib = comboOptimizationLibrary.SelectedItem.ToString();
OptimizationLibrary optimizationLibrary =
Settings.Default.GetOptimizationLibraryByName(nameOptLib);
OptimizedMethodType optimizedMethodType = OptimizedMethodType.None;
if (cbUseOptimized.Checked)
{
optimizedMethodType = OptimizedMethodTypeExtension.GetEnum(comboOptimizeType.SelectedItem.ToString());
}
TransitionPrediction prediction = new TransitionPrediction(precursorMassType,
fragmentMassType, collisionEnergy,
declusteringPotential,
compensationVoltage,
optimizationLibrary,
optimizedMethodType);
Helpers.AssignIfEquals(ref prediction, Prediction);
// Validate and store filter settings
int[] precursorCharges;
int min = TransitionGroup.MIN_PRECURSOR_CHARGE;
int max = TransitionGroup.MAX_PRECURSOR_CHARGE;
if (!helper.ValidateNumberListTextBox(tabControl1, (int)TABS.Filter, textPrecursorCharges,
min, max, out precursorCharges))
{
return;
}
precursorCharges = precursorCharges.Distinct().ToArray();
int[] productCharges;
min = Transition.MIN_PRODUCT_CHARGE;
max = Transition.MAX_PRODUCT_CHARGE;
if (!helper.ValidateNumberListTextBox(tabControl1, (int)TABS.Filter, textIonCharges,
min, max, out productCharges))
{
return;
}
productCharges = productCharges.Distinct().ToArray();
IonType[] types = TransitionFilter.ParseTypes(textIonTypes.Text, new IonType[0]);
if (types.Length == 0)
{
helper.ShowTextBoxError(tabControl1, (int)TABS.Filter, textIonTypes,
Resources.TransitionSettingsUI_OkDialog_Ion_types_must_contain_a_comma_separated_list_of_ion_types_a_b_c_x_y_z_and_p_for_precursor);
return;
}
types = types.Distinct().ToArray();
double exclusionWindow = 0;
if (!string.IsNullOrEmpty(textExclusionWindow.Text) &&
!Equals(textExclusionWindow.Text, exclusionWindow.ToString(LocalizationHelper.CurrentCulture)))
{
if (!helper.ValidateDecimalTextBox(tabControl1, (int)TABS.Filter, textExclusionWindow,
TransitionFilter.MIN_EXCLUSION_WINDOW, TransitionFilter.MAX_EXCLUSION_WINDOW, out exclusionWindow))
{
return;
}
}
string fragmentRangeFirst = TransitionFilter.GetStartFragmentNameFromLabel(comboRangeFrom.SelectedItem.ToString());
string fragmentRangeLast = TransitionFilter.GetEndFragmentNameFromLabel(comboRangeTo.SelectedItem.ToString());
var measuredIons = _driverIons.Chosen;
bool autoSelect = cbAutoSelect.Checked;
bool exclusionUseDIAWindow = FullScanSettingsControl.IsDIA() && cbExclusionUseDIAWindow.Checked;
var filter = new TransitionFilter(precursorCharges, productCharges, types,
fragmentRangeFirst, fragmentRangeLast, measuredIons,
exclusionWindow, exclusionUseDIAWindow, autoSelect);
Helpers.AssignIfEquals(ref filter, Filter);
// Validate and store library settings
TransitionLibraryPick pick = TransitionLibraryPick.none;
if (cbLibraryPick.Checked)
{
if (radioAll.Checked)
{
pick = TransitionLibraryPick.all;
}
else if (radioAllAndFiltered.Checked)
{
pick = TransitionLibraryPick.all_plus;
}
else
{
pick = TransitionLibraryPick.filter;
}
}
double ionMatchTolerance;
double minTol = TransitionLibraries.MIN_MATCH_TOLERANCE;
double maxTol = TransitionLibraries.MAX_MATCH_TOLERANCE;
if (!helper.ValidateDecimalTextBox(tabControl1, (int)TABS.Library, textTolerance,
minTol, maxTol, out ionMatchTolerance))
{
return;
}
int ionCount = Libraries.IonCount;
if (pick != TransitionLibraryPick.none)
{
min = TransitionLibraries.MIN_ION_COUNT;
max = TransitionLibraries.MAX_ION_COUNT;
if (!helper.ValidateNumberTextBox(tabControl1, (int)TABS.Library, textIonCount,
min, max, out ionCount))
{
return;
}
}
TransitionLibraries libraries = new TransitionLibraries(ionMatchTolerance, ionCount, pick);
Helpers.AssignIfEquals(ref libraries, Libraries);
// This dialog does not yet change integration settings
TransitionIntegration integration = _transitionSettings.Integration;
// Validate and store instrument settings
int minMz;
min = TransitionInstrument.MIN_MEASUREABLE_MZ;
max = TransitionInstrument.MAX_MEASURABLE_MZ - TransitionInstrument.MIN_MZ_RANGE;
if (!helper.ValidateNumberTextBox(tabControl1, (int)TABS.Instrument, textMinMz, min, max, out minMz))
{
return;
}
int maxMz;
min = minMz + TransitionInstrument.MIN_MZ_RANGE;
max = TransitionInstrument.MAX_MEASURABLE_MZ;
if (!helper.ValidateNumberTextBox(tabControl1, (int)TABS.Instrument, textMaxMz, min, max, out maxMz))
{
return;
}
bool isDynamicMin = cbDynamicMinimum.Checked;
double mzMatchTolerance;
minTol = TransitionInstrument.MIN_MZ_MATCH_TOLERANCE;
maxTol = TransitionInstrument.MAX_MZ_MATCH_TOLERANCE;
if (!helper.ValidateDecimalTextBox(tabControl1, (int)TABS.Instrument, textMzMatchTolerance,
minTol, maxTol, out mzMatchTolerance))
{
return;
}
int?maxTrans = null;
if (!string.IsNullOrEmpty(textMaxTrans.Text))
{
int maxTransTemp;
min = TransitionInstrument.MIN_TRANSITION_MAX;
max = TransitionInstrument.MAX_TRANSITION_MAX;
if (!helper.ValidateNumberTextBox(tabControl1, (int)TABS.Instrument, textMaxTrans,
min, max, out maxTransTemp))
{
return;
}
maxTrans = maxTransTemp;
}
int?maxInclusions = null;
if (!string.IsNullOrEmpty(textMaxInclusions.Text))
{
int maxInclusionsTemp;
min = TransitionInstrument.MIN_INCLUSION_MAX;
max = TransitionInstrument.MAX_INCLUSION_MAX;
if (!helper.ValidateNumberTextBox(tabControl1, (int)TABS.Instrument, textMaxInclusions,
min, max, out maxInclusionsTemp))
{
return;
}
maxInclusions = maxInclusionsTemp;
}
int?minTime = null, maxTime = null;
min = TransitionInstrument.MIN_TIME;
max = TransitionInstrument.MAX_TIME;
if (!string.IsNullOrEmpty(textMinTime.Text))
{
int minTimeTemp;
if (!helper.ValidateNumberTextBox(tabControl1, (int)TABS.Instrument, textMinTime,
min, max, out minTimeTemp))
{
return;
}
minTime = minTimeTemp;
}
if (!string.IsNullOrEmpty(textMaxTime.Text))
{
int maxTimeTemp;
if (!helper.ValidateNumberTextBox(tabControl1, (int)TABS.Instrument, textMaxTime,
min, max, out maxTimeTemp))
{
return;
}
maxTime = maxTimeTemp;
}
if (minTime.HasValue && maxTime.HasValue && maxTime.Value - minTime.Value < TransitionInstrument.MIN_TIME_RANGE)
{
helper.ShowTextBoxError(tabControl1, (int)TABS.Instrument, textMaxTime,
string.Format(Resources.TransitionSettingsUI_OkDialog_The_allowable_retention_time_range__0__to__1__must_be_at_least__2__minutes_apart,
minTime, maxTime, TransitionInstrument.MIN_TIME_RANGE));
return;
}
TransitionInstrument instrument = new TransitionInstrument(minMz,
maxMz, isDynamicMin, mzMatchTolerance, maxTrans, maxInclusions, minTime, maxTime);
Helpers.AssignIfEquals(ref instrument, Instrument);
// Validate and store full-scan settings
// If high resolution MS1 filtering is enabled, make sure precursor m/z type
// is monoisotopic and isotope enrichments are set
FullScanPrecursorIsotopes precursorIsotopes = PrecursorIsotopesCurrent;
FullScanMassAnalyzerType precursorAnalyzerType = PrecursorMassAnalyzer;
if (precursorIsotopes != FullScanPrecursorIsotopes.None &&
precursorAnalyzerType != FullScanMassAnalyzerType.qit)
{
if (precursorMassType != MassType.Monoisotopic)
{
MessageDlg.Show(this, Resources.TransitionSettingsUI_OkDialog_High_resolution_MS1_filtering_requires_use_of_monoisotopic_precursor_masses);
tabControl1.SelectedIndex = (int)TABS.Prediction;
comboPrecursorMass.Focus();
return;
}
if (FullScanSettingsControl.Enrichments == null)
{
tabControl1.SelectedIndex = (int)TABS.FullScan;
MessageDlg.Show(GetParentForm(this), Resources.TransitionSettingsUI_OkDialog_Isotope_enrichment_settings_are_required_for_MS1_filtering_on_high_resolution_mass_spectrometers);
FullScanSettingsControl.ComboEnrichmentsSetFocus();
return;
}
}
IsolationScheme isolationScheme = FullScanSettingsControl.IsolationScheme;
FullScanAcquisitionMethod acquisitionMethod = AcquisitionMethod;
if (isolationScheme == null && acquisitionMethod == FullScanAcquisitionMethod.DIA)
{
tabControl1.SelectedIndex = (int)TABS.FullScan;
MessageDlg.Show(this, Resources.TransitionSettingsUI_OkDialog_An_isolation_scheme_is_required_to_match_multiple_precursors);
FullScanSettingsControl.ComboIsolationSchemeSetFocus();
return;
}
if (isolationScheme != null && isolationScheme.WindowsPerScan.HasValue && !maxInclusions.HasValue)
{
MessageDlg.Show(this, Resources.TransitionSettingsUI_OkDialog_Before_performing_a_multiplexed_DIA_scan_the_instrument_s_firmware_inclusion_limit_must_be_specified);
tabControl1.SelectedIndex = (int)TABS.Instrument;
textMaxInclusions.Focus();
return;
}
if (FullScanSettingsControl.IsDIA() && cbExclusionUseDIAWindow.Checked)
{
if (FullScanSettingsControl.IsolationScheme.IsAllIons)
{
MessageDlg.Show(this, Resources.TransitionSettingsUI_OkDialog_Cannot_use_DIA_window_for_precusor_exclusion_when__All_Ions__is_selected_as_the_isolation_scheme___To_use_the_DIA_window_for_precusor_exclusion__change_the_isolation_scheme_in_the_Full_Scan_settings_);
tabControl1.SelectedIndex = (int)TABS.Filter;
cbExclusionUseDIAWindow.Focus();
return;
}
if (FullScanSettingsControl.IsolationScheme.FromResults)
{
MessageDlg.Show(this, Resources.TransitionSettingsUI_OkDialog_Cannot_use_DIA_window_for_precursor_exclusion_when_isolation_scheme_does_not_contain_prespecified_windows___Please_select_an_isolation_scheme_with_prespecified_windows_);
tabControl1.SelectedIndex = (int)TABS.Filter;
cbExclusionUseDIAWindow.Focus();
return;
}
}
TransitionFullScan fullScan;
if (!FullScanSettingsControl.ValidateFullScanSettings(helper, out fullScan, tabControl1, (int)TABS.FullScan))
{
return;
}
Helpers.AssignIfEquals(ref fullScan, FullScan);
TransitionSettings settings = new TransitionSettings(prediction,
filter, libraries, integration, instrument, fullScan);
// Only update, if anything changed
if (!Equals(settings, _transitionSettings))
{
if (!_parent.ChangeSettingsMonitored(this, Resources.TransitionSettingsUI_OkDialog_Changing_transition_settings,
s => s.ChangeTransitionSettings(settings)))
{
return;
}
_transitionSettings = settings;
}
DialogResult = DialogResult.OK;
}
private void ExportIsolationList(
string csvFilename, string instrumentType, FullScanAcquisitionMethod acquisitionMethod,
ExportMethodType methodType, params string[] checkStrings)
{
// Set acquisition method, mass analyzer type, resolution, etc.
if (Equals(instrumentType, ExportInstrumentType.AGILENT_TOF))
{
RunUI(() => SkylineWindow.ModifyDocument("Set TOF full-scan settings", doc => doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs => fs
.ChangePrecursorResolution(FullScanMassAnalyzerType.tof, 10000, null)
.ChangeProductResolution(FullScanMassAnalyzerType.tof, 10000, null)
.ChangeAcquisitionMethod(acquisitionMethod, null)))));
}
else
{
RunUI(() => SkylineWindow.ModifyDocument("Set Orbitrap full-scan settings", doc => doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs => fs
.ChangePrecursorResolution(FullScanMassAnalyzerType.orbitrap, 60000, 400)
.ChangeProductResolution(FullScanMassAnalyzerType.orbitrap, 60000, 400)
.ChangeAcquisitionMethod(acquisitionMethod, null)))));
}
// Open Export Method dialog, and set method to scheduled or standard.
string csvPath = TestContext.GetTestPath(csvFilename);
var exportMethodDlg = ShowDialog<ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.IsolationList));
RunUI(() =>
{
exportMethodDlg.InstrumentType = instrumentType;
exportMethodDlg.MethodType = methodType;
exportMethodDlg.UseSlens = WithSLens;
Assert.IsFalse(exportMethodDlg.IsOptimizeTypeEnabled);
Assert.IsTrue(exportMethodDlg.IsTargetTypeEnabled);
Assert.IsFalse(exportMethodDlg.IsDwellTimeVisible);
Assert.IsFalse(exportMethodDlg.IsMaxTransitionsEnabled);
});
if (methodType == ExportMethodType.Standard)
{
// Simply close the dialog.
OkDialog(exportMethodDlg, ()=> exportMethodDlg.OkDialog(csvPath));
}
else
{
// Close the SchedulingOptionsDlg, then wait for export dialog to close.
RunDlg<SchedulingOptionsDlg>(() => exportMethodDlg.OkDialog(csvPath), schedulingOptionsDlg => schedulingOptionsDlg.OkDialog());
WaitForClosedForm(exportMethodDlg);
}
// Check for expected output.
string csvOut = File.ReadAllText(csvPath);
AssertEx.Contains(csvOut, checkStrings);
}
public SpectrumFilter(SrmDocument document, MsDataFileUri msDataFileUri, IFilterInstrumentInfo instrumentInfo,
IRetentionTimePredictor retentionTimePredictor = null, bool firstPass = false)
{
_fullScan = document.Settings.TransitionSettings.FullScan;
_instrument = document.Settings.TransitionSettings.Instrument;
_acquisitionMethod = _fullScan.AcquisitionMethod;
if (instrumentInfo != null)
_isWatersFile = instrumentInfo.IsWatersFile;
IsFirstPass = firstPass;
var comparer = PrecursorTextId.PrecursorTextIdComparerInstance;
var dictPrecursorMzToFilter = new SortedDictionary<PrecursorTextId, SpectrumFilterPair>(comparer);
if (EnabledMs || EnabledMsMs)
{
if (EnabledMs)
{
_isHighAccMsFilter = !Equals(_fullScan.PrecursorMassAnalyzer,
FullScanMassAnalyzerType.qit);
if (!firstPass)
{
var key = new PrecursorTextId(0, null, ChromExtractor.summed); // TIC
dictPrecursorMzToFilter.Add(key, new SpectrumFilterPair(key, PeptideDocNode.UNKNOWN_COLOR, dictPrecursorMzToFilter.Count,
_instrument.MinTime, _instrument.MaxTime, null, null, 0, _isHighAccMsFilter, _isHighAccProductFilter));
key = new PrecursorTextId(0, null, ChromExtractor.base_peak); // BPC
dictPrecursorMzToFilter.Add(key, new SpectrumFilterPair(key, PeptideDocNode.UNKNOWN_COLOR, dictPrecursorMzToFilter.Count,
_instrument.MinTime, _instrument.MaxTime, null, null, 0, _isHighAccMsFilter, _isHighAccProductFilter));
}
}
if (EnabledMsMs)
{
_isHighAccProductFilter = !Equals(_fullScan.ProductMassAnalyzer,
FullScanMassAnalyzerType.qit);
if (_fullScan.AcquisitionMethod == FullScanAcquisitionMethod.DIA &&
_fullScan.IsolationScheme.IsAllIons)
{
if (instrumentInfo != null)
{
_isWatersMse = _isWatersFile;
_isAgilentMse = instrumentInfo.IsAgilentFile;
}
_mseLevel = 1;
}
}
Func<double, double> calcWindowsQ1 = _fullScan.GetPrecursorFilterWindow;
Func<double, double> calcWindowsQ3 = _fullScan.GetProductFilterWindow;
_minTime = _instrument.MinTime;
_maxTime = _instrument.MaxTime;
bool canSchedule = CanSchedule(document, retentionTimePredictor);
// TODO: Figure out a way to turn off time sharing on first SIM scan so that
// times can be shared for MS1 without SIM scans
_isSharedTime = !canSchedule;
// If we're using bare measured drift times from spectral libraries, go get those now
var libraryIonMobilityInfo = document.Settings.PeptideSettings.Prediction.UseLibraryDriftTimes
? document.Settings.GetIonMobilities(msDataFileUri)
: null;
foreach (var nodePep in document.Molecules)
{
if (firstPass && !retentionTimePredictor.IsFirstPassPeptide(nodePep))
continue;
foreach (TransitionGroupDocNode nodeGroup in nodePep.Children)
{
if (nodeGroup.Children.Count == 0)
continue;
double? minTime = _minTime, maxTime = _maxTime;
double? startDriftTimeMsec = null, endDriftTimeMsec = null;
double windowDT;
double highEnergyDriftTimeOffsetMsec = 0;
DriftTimeInfo centerDriftTime = document.Settings.PeptideSettings.Prediction.GetDriftTime(
nodePep, nodeGroup, libraryIonMobilityInfo, out windowDT);
if (centerDriftTime.DriftTimeMsec(false).HasValue)
{
startDriftTimeMsec = centerDriftTime.DriftTimeMsec(false) - windowDT / 2; // Get the low energy drift time
endDriftTimeMsec = startDriftTimeMsec + windowDT;
highEnergyDriftTimeOffsetMsec = centerDriftTime.HighEnergyDriftTimeOffsetMsec;
}
if (canSchedule)
{
if (RetentionTimeFilterType.scheduling_windows == _fullScan.RetentionTimeFilterType)
{
double? centerTime = null;
double windowRT = 0;
if (retentionTimePredictor != null)
{
centerTime = retentionTimePredictor.GetPredictedRetentionTime(nodePep);
}
else
{
var prediction = document.Settings.PeptideSettings.Prediction;
if (prediction.RetentionTime == null || !prediction.RetentionTime.IsAutoCalculated)
{
centerTime = document.Settings.PeptideSettings.Prediction.PredictRetentionTimeForChromImport(
document, nodePep, nodeGroup, out windowRT);
}
}
// Force the center time to be at least zero
if (centerTime.HasValue && centerTime.Value < 0)
centerTime = 0;
if (_fullScan.RetentionTimeFilterLength != 0)
{
windowRT = _fullScan.RetentionTimeFilterLength * 2;
}
if (centerTime != null)
{
double startTime = centerTime.Value - windowRT / 2;
double endTime = startTime + windowRT;
minTime = Math.Max(minTime ?? 0, startTime);
maxTime = Math.Min(maxTime ?? double.MaxValue, endTime);
}
}
else if (RetentionTimeFilterType.ms2_ids == _fullScan.RetentionTimeFilterType)
{
var times = document.Settings.GetBestRetentionTimes(nodePep, msDataFileUri);
if (times.Length > 0)
{
minTime = Math.Max(minTime ?? 0, times.Min() - _fullScan.RetentionTimeFilterLength);
maxTime = Math.Min(maxTime ?? double.MaxValue, times.Max() + _fullScan.RetentionTimeFilterLength);
}
}
}
SpectrumFilterPair filter;
string textId = nodePep.RawTextId; // Modified Sequence for peptides, or some other string for custom ions
double mz = nodeGroup.PrecursorMz;
var key = new PrecursorTextId(mz, textId, ChromExtractor.summed);
if (!dictPrecursorMzToFilter.TryGetValue(key, out filter))
{
filter = new SpectrumFilterPair(key, nodePep.Color, dictPrecursorMzToFilter.Count, minTime, maxTime,
startDriftTimeMsec, endDriftTimeMsec, highEnergyDriftTimeOffsetMsec,
_isHighAccMsFilter, _isHighAccProductFilter);
dictPrecursorMzToFilter.Add(key, filter);
}
if (!EnabledMs)
{
filter.AddQ3FilterValues(from TransitionDocNode nodeTran in nodeGroup.Children
select nodeTran.Mz, calcWindowsQ3);
}
else if (!EnabledMsMs)
{
filter.AddQ1FilterValues(GetMS1MzValues(nodeGroup), calcWindowsQ1);
}
else
{
filter.AddQ1FilterValues(GetMS1MzValues(nodeGroup), calcWindowsQ1);
filter.AddQ3FilterValues(from TransitionDocNode nodeTran in nodeGroup.Children
where !nodeTran.IsMs1
select nodeTran.Mz, calcWindowsQ3);
}
}
}
_filterMzValues = dictPrecursorMzToFilter.Values.ToArray();
var listChromKeyFilterIds = new List<ChromKey>();
foreach (var spectrumFilterPair in _filterMzValues)
{
spectrumFilterPair.AddChromKeys(listChromKeyFilterIds);
}
_productChromKeys = listChromKeyFilterIds.ToArray();
// Sort a copy of the filter pairs by maximum retention time so that we can detect when
// filters are no longer active.
_filterRTValues = new SpectrumFilterPair[_filterMzValues.Length];
Array.Copy(_filterMzValues, _filterRTValues, _filterMzValues.Length);
Array.Sort(_filterRTValues, CompareByRT);
}
InitRTLimits();
}
private IEnumerable<SpectrumFilterPair> FindFilterPairs(IsolationWindowFilter isoWin,
FullScanAcquisitionMethod acquisitionMethod, bool ignoreIsolationScheme = false)
{
if (!isoWin.IsolationMz.HasValue)
return new SpectrumFilterPair[0]; // empty
// Return cached value from dictionary if we've seen this target previously.
var isoWinKey = isoWin;
IList<SpectrumFilterPair> filterPairsCached;
if (_filterPairDictionary.TryGetValue(isoWinKey, out filterPairsCached))
{
return filterPairsCached;
}
var filterPairs = new List<SpectrumFilterPair>();
if (acquisitionMethod == FullScanAcquisitionMethod.DIA)
{
double isoTargMz = isoWin.IsolationMz.Value;
double? isoTargWidth = isoWin.IsolationWidth;
if (!ignoreIsolationScheme)
{
CalcDiaIsolationValues(ref isoTargMz, ref isoTargWidth);
}
if (isoTargWidth.HasValue)
{
// For multiple case, find the first possible value, and iterate until
// no longer matching or the end of the array is encountered
int iFilter = IndexOfFilter(isoTargMz, isoTargWidth.Value);
if (iFilter != -1)
{
while (iFilter < _filterMzValues.Length && CompareMz(isoTargMz,
_filterMzValues[iFilter].Q1, isoTargWidth.Value) == 0)
filterPairs.Add(_filterMzValues[iFilter++]);
}
}
}
else
{
// For single (Targeted) case, review all possible matches for the one closest to the
// desired precursor m/z value.
// per "Issue 263: Too strict about choosing only one precursor for every MS/MS scan in Targeted MS/MS",
// if more than one match at this m/z value return a list
double minMzDelta = double.MaxValue;
double mzDeltaEpsilon = Math.Min(_instrument.MzMatchTolerance, .0001);
// Isolation width for single is based on the instrument m/z match tolerance
double isoTargMz = isoWin.IsolationMz.Value;
var isoWinSingle = new IsolationWindowFilter(isoTargMz, _instrument.MzMatchTolerance * 2);
foreach (var filterPair in FindFilterPairs(isoWinSingle, FullScanAcquisitionMethod.DIA, true))
{
double mzDelta = Math.Abs(isoTargMz - filterPair.Q1);
if (mzDelta < minMzDelta) // new best match
{
minMzDelta = mzDelta;
// are any existing matches no longer within epsilion of new best match?
for (int n = filterPairs.Count; n-- > 0; )
{
if ((Math.Abs(isoTargMz - filterPairs[n].Q1) - minMzDelta) > mzDeltaEpsilon)
{
filterPairs.RemoveAt(n); // no longer a match by our new standard
}
}
filterPairs.Add(filterPair);
}
else if ((mzDelta - minMzDelta) <= mzDeltaEpsilon)
{
filterPairs.Add(filterPair); // not the best, but close to it
}
}
}
_filterPairDictionary[isoWinKey] = filterPairs;
return filterPairs;
}