/// <summary>
/// Serializes the contents of a single <see cref="TransitionDocNode"/>
/// to XML.
/// </summary>
/// <param name="writer">The XML writer</param>
/// <param name="nodePep">The transition group's parent peptide node</param>
/// <param name="nodeGroup">The transition node's parent group node</param>
/// <param name="nodeTransition">The transition document node</param>
private void WriteTransitionXml(XmlWriter writer, PeptideDocNode nodePep, TransitionGroupDocNode nodeGroup,
TransitionDocNode nodeTransition)
{
Transition transition = nodeTransition.Transition;
writer.WriteAttribute(ATTR.fragment_type, transition.IonType);
writer.WriteAttribute(ATTR.quantitative, nodeTransition.ExplicitQuantitative, true);
if (transition.IsCustom())
{
if (!(transition.CustomIon is SettingsCustomIon))
{
transition.CustomIon.WriteXml(writer, transition.Adduct);
}
else
{
writer.WriteAttributeString(ATTR.measured_ion_name, transition.CustomIon.Name);
}
}
writer.WriteAttributeNullable(ATTR.decoy_mass_shift, transition.DecoyMassShift);
// NOTE: MassIndex is the peak index in the isotopic distribution of the precursor.
// 0 for monoisotopic peaks and for non "precursor" ion types.
if (transition.MassIndex != 0)
{
writer.WriteAttribute(ATTR.mass_index, transition.MassIndex);
}
if (nodeTransition.HasDistInfo)
{
writer.WriteAttribute(ATTR.isotope_dist_rank, nodeTransition.IsotopeDistInfo.Rank);
writer.WriteAttribute(ATTR.isotope_dist_proportion, nodeTransition.IsotopeDistInfo.Proportion);
}
if (!transition.IsPrecursor())
{
if (!transition.IsCustom())
{
writer.WriteAttribute(ATTR.fragment_ordinal, transition.Ordinal);
writer.WriteAttribute(ATTR.calc_neutral_mass, nodeTransition.GetMoleculePersistentNeutralMass());
}
writer.WriteAttribute(ATTR.product_charge, transition.Charge);
if (!transition.IsCustom())
{
writer.WriteAttribute(ATTR.cleavage_aa, transition.AA.ToString(CultureInfo.InvariantCulture));
writer.WriteAttribute(ATTR.loss_neutral_mass, nodeTransition.LostMass); //po
}
}
// Order of elements matters for XSD validation
WriteAnnotations(writer, nodeTransition.Annotations);
writer.WriteElementString(EL.precursor_mz, SequenceMassCalc.PersistentMZ(nodeGroup.PrecursorMz));
writer.WriteElementString(EL.product_mz, SequenceMassCalc.PersistentMZ(nodeTransition.Mz));
TransitionPrediction predict = Settings.TransitionSettings.Prediction;
var optimizationMethod = predict.OptimizedMethodType;
double?ce = null;
double?dp = null;
var lib = predict.OptimizedLibrary;
if (lib != null && !lib.IsNone)
{
var optimization = lib.GetOptimization(OptimizationType.collision_energy,
Settings.GetSourceTarget(nodePep), nodeGroup.PrecursorAdduct,
nodeTransition.FragmentIonName, nodeTransition.Transition.Adduct);
if (optimization != null)
{
ce = optimization.Value;
}
}
double regressionMz = Settings.GetRegressionMz(nodePep, nodeGroup);
var ceRegression = predict.CollisionEnergy;
var dpRegression = predict.DeclusteringPotential;
if (optimizationMethod == OptimizedMethodType.None)
{
if (ceRegression != null && !ce.HasValue)
{
ce = ceRegression.GetCollisionEnergy(nodeGroup.PrecursorAdduct, regressionMz);
}
if (dpRegression != null)
{
dp = dpRegression.GetDeclustringPotential(regressionMz);
}
}
else
{
if (!ce.HasValue)
{
ce = OptimizationStep <CollisionEnergyRegression> .FindOptimizedValue(Settings,
nodePep, nodeGroup, nodeTransition, optimizationMethod, ceRegression,
SrmDocument.GetCollisionEnergy);
}
dp = OptimizationStep <DeclusteringPotentialRegression> .FindOptimizedValue(Settings,
nodePep, nodeGroup, nodeTransition, optimizationMethod, dpRegression,
SrmDocument.GetDeclusteringPotential);
}
if (nodeGroup.ExplicitValues.CollisionEnergy.HasValue)
{
ce = nodeGroup.ExplicitValues.CollisionEnergy; // Explicitly imported, overrides any calculation
}
if (ce.HasValue)
{
writer.WriteElementString(EL.collision_energy, ce.Value);
}
if (dp.HasValue)
{
writer.WriteElementString(EL.declustering_potential, dp.Value);
}
WriteTransitionLosses(writer, nodeTransition.Losses);
if (nodeTransition.HasLibInfo)
{
writer.WriteStartElement(EL.transition_lib_info);
writer.WriteAttribute(ATTR.rank, nodeTransition.LibInfo.Rank);
writer.WriteAttribute(ATTR.intensity, nodeTransition.LibInfo.Intensity);
writer.WriteEndElement();
}
if (nodeTransition.HasResults)
{
if (nodeTransition.HasResults)
{
if (UseCompactFormat())
{
var protoResults = new SkylineDocumentProto.Types.TransitionResults();
protoResults.Peaks.AddRange(nodeTransition.GetTransitionPeakProtos(Settings.MeasuredResults));
byte[] bytes = protoResults.ToByteArray();
writer.WriteStartElement(EL.results_data);
writer.WriteBase64(bytes, 0, bytes.Length);
writer.WriteEndElement();
}
else
{
WriteResults(writer, Settings, nodeTransition.Results,
EL.transition_results, EL.transition_peak, WriteTransitionChromInfo);
}
}
}
if (WroteTransitions != null)
{
WroteTransitions(1);
}
}
/// <summary>
/// Serializes the contents of a single <see cref="TransitionGroupDocNode"/>
/// to XML.
/// </summary>
/// <param name="writer">The XML writer</param>
/// <param name="nodePep">The parent peptide document node</param>
/// <param name="node">The transition group document node</param>
private void WriteTransitionGroupXml(XmlWriter writer, PeptideDocNode nodePep, TransitionGroupDocNode node)
{
TransitionGroup group = node.TransitionGroup;
var isCustomIon = nodePep.Peptide.IsCustomMolecule;
writer.WriteAttribute(ATTR.charge, group.PrecursorAdduct.AdductCharge);
if (!group.LabelType.IsLight)
{
writer.WriteAttribute(ATTR.isotope_label, group.LabelType);
}
if (!isCustomIon)
{
writer.WriteAttribute(ATTR.calc_neutral_mass, node.GetPrecursorIonPersistentNeutralMass());
}
writer.WriteAttribute(ATTR.precursor_mz, SequenceMassCalc.PersistentMZ(node.PrecursorMz));
WriteExplicitTransitionGroupValuesAttributes(writer, node.ExplicitValues);
writer.WriteAttribute(ATTR.auto_manage_children, node.AutoManageChildren, true);
writer.WriteAttributeNullable(ATTR.decoy_mass_shift, group.DecoyMassShift);
writer.WriteAttributeNullable(ATTR.precursor_concentration, node.PrecursorConcentration);
TransitionPrediction predict = Settings.TransitionSettings.Prediction;
double regressionMz = Settings.GetRegressionMz(nodePep, node);
var ce = predict.CollisionEnergy.GetCollisionEnergy(node.TransitionGroup.PrecursorAdduct, regressionMz);
writer.WriteAttribute(ATTR.collision_energy, ce);
var dpRegression = predict.DeclusteringPotential;
if (dpRegression != null)
{
var dp = dpRegression.GetDeclustringPotential(regressionMz);
writer.WriteAttribute(ATTR.declustering_potential, dp);
}
if (!isCustomIon)
{
// modified sequence
var calcPre = Settings.GetPrecursorCalc(node.TransitionGroup.LabelType, nodePep.ExplicitMods);
var seq = node.TransitionGroup.Peptide.Target;
writer.WriteAttribute(ATTR.modified_sequence, calcPre.GetModifiedSequence(seq,
false)); // formatNarrow = false; We want InvariantCulture, not the local format
Assume.IsTrue(group.PrecursorAdduct.IsProteomic);
}
else
{
// Custom ion
node.CustomMolecule.WriteXml(writer, group.PrecursorAdduct);
}
// Write child elements
WriteAnnotations(writer, node.Annotations);
if (node.HasLibInfo)
{
var helpers = PeptideLibraries.SpectrumHeaderXmlHelpers;
writer.WriteElements(new[] { node.LibInfo }, helpers);
}
if (node.HasResults)
{
WriteResults(writer, Settings, node.Results,
EL.precursor_results, EL.precursor_peak, WriteTransitionGroupChromInfo);
}
if (UseCompactFormat())
{
writer.WriteStartElement(EL.transition_data);
var transitionData = new SkylineDocumentProto.Types.TransitionData();
transitionData.Transitions.AddRange(node.Transitions.Select(transition => transition.ToTransitionProto(Settings)));
byte[] bytes = transitionData.ToByteArray();
writer.WriteBase64(bytes, 0, bytes.Length);
writer.WriteEndElement();
if (WroteTransitions != null)
{
WroteTransitions(node.TransitionCount);
}
}
else
{
foreach (TransitionDocNode nodeTransition in node.Children)
{
writer.WriteStartElement(EL.transition);
WriteTransitionXml(writer, nodePep, node, nodeTransition);
writer.WriteEndElement();
}
}
}
/// <summary>
/// Makes sure settings loaded from XML are complete, and uses default
/// values where anything is missing.
/// </summary>
private void ValidateLoad()
{
SrmSettings defaults = SrmSettingsList.GetDefault();
PeptideSettings defPep = defaults.PeptideSettings;
if (PeptideSettings == null)
PeptideSettings = defPep;
else
{
PeptideSettings = PeptideSettings.MergeDefaults(defPep);
}
TransitionSettings defTran = defaults.TransitionSettings;
if (TransitionSettings == null)
TransitionSettings = defTran;
else
{
TransitionPrediction prediction = TransitionSettings.Prediction;
// Backward compatibility: handle the move of RetentionTime
// from TransitionSettings to PeptideSettings after v0.1.0.0
if (TransitionSettings.Prediction == null)
prediction = defTran.Prediction;
else if (prediction.RetentionTime != null)
{
if (PeptideSettings.Prediction != null && // Make Resharper happy
PeptideSettings.Prediction.RetentionTime == null)
{
PeptideSettings = PeptideSettings.ChangePrediction(
new PeptidePrediction(prediction.RetentionTime));
}
prediction = new TransitionPrediction(prediction);
}
TransitionFilter filter = TransitionSettings.Filter ?? defTran.Filter;
TransitionLibraries libraries = TransitionSettings.Libraries ?? defTran.Libraries;
TransitionIntegration integration = TransitionSettings.Integration ?? defTran.Integration;
TransitionInstrument instrument = TransitionSettings.Instrument ?? defTran.Instrument;
TransitionFullScan fullScan = TransitionSettings.FullScan ?? defTran.FullScan;
// Backward compatibility with v2.1, get a RT filter length from peptide prediction settings
if (fullScan.RetentionTimeFilterType == RetentionTimeFilterType.scheduling_windows &&
fullScan.RetentionTimeFilterLength == 0 &&
PeptideSettings.Prediction != null)
{
double rtFilterLen = 0;
if (PeptideSettings.Prediction.UseMeasuredRTs)
{
rtFilterLen = PeptideSettings.Prediction.MeasuredRTWindow.Value / 2;
}
else if (PeptideSettings.Prediction.RetentionTime != null)
{
rtFilterLen = PeptideSettings.Prediction.RetentionTime.TimeWindow / 2;
}
if (rtFilterLen > 0)
{
fullScan = fullScan.ChangeRetentionTimeFilter(fullScan.RetentionTimeFilterType, rtFilterLen);
}
}
TransitionSettings transitionSettings = new TransitionSettings(prediction,
filter,
libraries,
integration,
instrument,
fullScan);
// If the above null checks result in a changed PeptideSettings object,
// then use the changed version.
if (!Equals(TransitionSettings, transitionSettings))
TransitionSettings = transitionSettings;
}
// Initialize mass calculators
CreatePrecursorMassCalcs();
CreateFragmentMassCalcs();
}
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;
}
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());
}
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;
}