protected override void DoTest()
{
// Create the modification and library spec used in this test
var phosphoLossMod = new StaticMod("Phospho Loss", "S, T", null, true, "HPO3",
LabelAtoms.None, RelativeRT.Matching, null, null, new[] { new FragmentLoss("H3PO4"), });
var multipleLossMod = new StaticMod("Multiple Loss-only", "D", null, false, null,
LabelAtoms.None, RelativeRT.Matching, null, null, new[]
{
new FragmentLoss("NH3"),
new FragmentLoss("H2O"),
new FragmentLoss(null, 20, 25)
});
var heavyKMod = new StaticMod("Heavy K", "K", ModTerminus.C, null, LabelAtoms.C13 | LabelAtoms.N15, null, null);
var librarySpec = new BiblioSpecLiteSpec("Phospho Library",
TestFilesDir.GetTestPath("phospho_30882_v2.blib"));
// Prepare settings for this test
Settings.Default.StaticModList.Clear();
Settings.Default.StaticModList.AddRange(StaticModList.GetDefaultsOn());
Settings.Default.StaticModList.Add(phosphoLossMod);
Settings.Default.HeavyModList.Clear();
Settings.Default.HeavyModList.Add(heavyKMod);
Settings.Default.SpectralLibraryList.Clear();
Settings.Default.SpectralLibraryList.Add(librarySpec);
// Prepare document settings for this test
const int countIons = 6;
var settings = SrmSettingsList.GetDefault()
.ChangePeptideModifications(mods => mods.ChangeStaticModifications(new List <StaticMod>(mods.StaticModifications)
{
phosphoLossMod
}))
.ChangePeptideLibraries(lib => lib.ChangeLibrarySpecs(new[] { librarySpec }))
.ChangeTransitionLibraries(tlib => tlib.ChangeIonCount(countIons));
RunUI(() => SkylineWindow.ModifyDocument("Set test settings",
doc => doc.ChangeSettings(settings)));
WaitForDocumentLoaded();
// Add FASTA sequence
RunUI(() => SkylineWindow.Paste(TEXT_FASTA_SPROT));
var docLibLoss = SkylineWindow.Document;
AssertEx.IsDocumentState(docLibLoss, null, 3, 4, 24);
Assert.AreEqual(7, GetLossCount(docLibLoss, 1));
string lossLabel = "-" + Math.Round(phosphoLossMod.Losses[0].MonoisotopicMass, 1);
for (int i = 0; i < docLibLoss.PeptideTransitionGroupCount; i++)
{
var pathTranGroup = docLibLoss.GetPathTo((int)SrmDocument.Level.TransitionGroups, i);
var nodeGroup = (TransitionGroupDocNode)docLibLoss.FindNode(pathTranGroup);
if (!nodeGroup.Children.Contains(child => ((TransitionDocNode)child).HasLoss))
{
continue;
}
// Select the transition groups that contain loss ions
SelectNode(SrmDocument.Level.TransitionGroups, i);
WaitForGraphs();
// Make sure the spectrum graph contains some -98 ions
RunUI(() => Assert.IsTrue(SkylineWindow.GraphSpectrum.IonLabels.Contains(label => label.Contains(lossLabel)),
string.Format("Missing loss labels in spectrum graph for {0}", nodeGroup.TransitionGroup.Peptide.Target)));
// Make sure the transition tree nodes contain -98 ions
RunUI(() => Assert.IsTrue(GetChildLabels(SkylineWindow.SelectedNode).Contains(label => label.Contains(lossLabel)),
string.Format("Missing loss labels in transition tree nodes for {0}", nodeGroup.TransitionGroup.Peptide.Target)));
}
// Make the settings significantly more complex
// - 2 neutral losses
// - a second modification with 3 potential neutral losses
// - a heavy labeling modification
// - only ions between precursor m/z and last ion
// - allow both y- and b- ions
// - no proline peaks
// - only use filtered ions to match library
RunUI(() => SkylineWindow.ModifyDocument("Set test settings", doc =>
doc.ChangeSettings(doc.Settings.ChangePeptideModifications(mod =>
mod.ChangeMaxNeutralLosses(2)
.ChangeStaticModifications(new List <StaticMod>(mod.StaticModifications)
{
multipleLossMod
})
.ChangeModifications(IsotopeLabelType.heavy, new[] { heavyKMod }))
.ChangeTransitionFilter(filter =>
filter.ChangeFragmentRangeFirstName("m/z > precursor")
.ChangeFragmentRangeLastName("last ion")
.ChangePeptideIonTypes(new[] { IonType.y, IonType.b })
.ChangeMeasuredIons(new MeasuredIon[0]))
.ChangeTransitionLibraries(lib =>
lib.ChangePick(TransitionLibraryPick.filter)))));
var docComplex = WaitForDocumentChange(docLibLoss);
// The document has 2 variable mod peptides at the protein terminus
Assert.AreEqual(docLibLoss.PeptideTransitionGroupCount * 2 - 2, docComplex.PeptideTransitionGroupCount);
Assert.AreEqual(4, GetLossCount(docComplex, 2));
Assert.AreEqual(16, GetLossCount(docComplex, 1));
foreach (var nodePep in docComplex.Peptides)
{
if (nodePep.Children.Count != 2)
{
continue;
}
var nodeGroup1 = (TransitionGroupDocNode)nodePep.Children[0];
var nodeGroup2 = (TransitionGroupDocNode)nodePep.Children[1];
Assert.IsTrue(nodeGroup1.EquivalentChildren(nodeGroup2));
}
// CONSIDER: Can't check cloned because of libraries. Maybe add a new method for this
// AssertEx.Serializable(docComplex, AssertEx.DocumentCloned);
SelectNode(SrmDocument.Level.Molecules, 1);
WaitForGraphs();
// Verify that the ion labels in the graph match those in the tree view
RunUI(() =>
{
var nodePepSelected = (PeptideDocNode)docComplex.FindNode(SkylineWindow.SelectedPath);
string[] ionLabels = SkylineWindow.GraphSpectrum.IonLabels.ToArray();
foreach (TransitionGroupDocNode nodeGroup in nodePepSelected.Children)
{
var setSeenRanks = new HashSet <int>();
foreach (TransitionDocNode nodeTran in nodeGroup.Children)
{
Assert.IsTrue(nodeTran.HasLibInfo);
// Make sure the rank has not been seen
int rankTran = nodeTran.LibInfo.Rank;
Assert.IsFalse(setSeenRanks.Contains(rankTran));
setSeenRanks.Add(rankTran);
// And it is within the expected range
Assert.IsTrue(1 <= rankTran && rankTran <= countIons);
// Make sure there is a matching label in the spectrum graph
var regexRank = nodeTran.HasLoss ?
new Regex(string.Format(@"(\w)(\d+) -([^ +]+).* \({0}\)", string.Format(Resources.AbstractSpectrumGraphItem_GetLabel_rank__0__, rankTran))) :
new Regex(string.Format(@"(\w)(\d+).* \({0}\)", string.Format(Resources.AbstractSpectrumGraphItem_GetLabel_rank__0__, rankTran)));
int iLabel = ionLabels.IndexOf(regexRank.IsMatch);
Assert.IsTrue(iLabel != -1);
var match = regexRank.Match(ionLabels[iLabel]);
Assert.AreEqual(nodeTran.Transition.IonType.ToString(), match.Groups[1].Value);
Assert.AreEqual(nodeTran.Transition.Ordinal, int.Parse(match.Groups[2].Value));
if (nodeTran.HasLoss)
{
Assert.AreEqual(nodeTran.Losses.Mass, double.Parse(match.Groups[3].Value), 0.1);
}
}
}
});
// Make sure setting losses as included Never works
{
var docBeforeNever = SkylineWindow.Document;
var peptideSettingsUINever = ShowDialog <PeptideSettingsUI>(() =>
SkylineWindow.ShowPeptideSettingsUI(PeptideSettingsUI.TABS.Modifications));
var editModsDlgNever = ShowEditStaticModsDlg(peptideSettingsUINever);
RunUI(() => editModsDlgNever.SelectItem(phosphoLossMod.Name));
var editModDlgNever = ShowDialog <EditStaticModDlg>(editModsDlgNever.EditItem);
RunUI(() => editModDlgNever.LossSelectedIndex = 0);
RunDlg <EditFragmentLossDlg>(editModDlgNever.EditLoss, dlg =>
{
dlg.Inclusion = LossInclusion.Never;
dlg.OkDialog();
});
RunDlg <MultiButtonMsgDlg>(editModDlgNever.OkDialog, dlg => dlg.Btn1Click());
OkDialog(editModsDlgNever, editModsDlgNever.OkDialog);
OkDialog(peptideSettingsUINever, peptideSettingsUINever.OkDialog);
var docAfterNever = WaitForDocumentChange(docBeforeNever);
Assert.AreEqual(0, GetLossCount(docAfterNever, 1));
}
}
public void TestModificationMatcher()
{
InitSeqs();
var carbC = StaticModList.GetDefaultsOn()[0];
// Test exception thrown if unable to match - mass.
UpdateMatcherFail(STR_FAIL_MASS);
UpdateMatcherFail(STR_FAIL_NOT_A_NUMBER);
// Test exception thrown if unable to match - name.
UpdateMatcherFail(STR_FAIL_NAME);
// Can't match empty modifications.
UpdateMatcherFail(STR_FAIL_EMPTY_MOD);
UpdateMatcherFail(STR_FAIL_EMPTY_MOD2);
// Can't match double modifications.
UpdateMatcherFail(STR_FAIL_DOUBLE_MOD);
// Test exception thrown if unimod not specified correctly
UpdateMatcherFail(STR_FAIL_UNIMOD);
UpdateMatcherFail(STR_UNKNOWN_UNIMOD);
// Can't phosphorylate tryptophan
UpdateMatcherFail(STR_FAIL_WRONG_AA_UNIMOD);
// Can't put C-terminal modification in middle of peptide
UpdateMatcherFail(STR_FAIL_UNIMOD_TERMINUS);
// Test mods in UniMod match correctly.
UpdateMatcher(StaticModList.GetDefaultsOn(), HeavyModList.GetDefaultsOn(), null, null);
// A sequence with no modifications should not be explicitly modified.
Assert.IsFalse(MATCHER.GetModifiedNode(STR_NO_MODS).HasExplicitMods);
var nodeCysOxi = MATCHER.GetModifiedNode(STR_CYS_AND_OXI);
Assert.IsTrue(nodeCysOxi.HasExplicitMods);
Assert.IsFalse(nodeCysOxi.ExplicitMods.HasHeavyModifications);
// Modifications should match by name.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_MOD_BY_NAME).ExplicitMods.StaticModifications.Contains(mod =>
Equals(mod.Modification.Name, "Phospho (ST)")));
// Test can find terminal modification
Assert.IsTrue(MATCHER.GetModifiedNode(STR_TERM_ONLY).ExplicitMods.HeavyModifications.Contains(mod =>
mod.Modification.EquivalentAll(UniMod.GetModification("Label:13C(6) (C-term R)", false))));
// Test can find matches on terminus that are not terminal
Assert.IsTrue(MATCHER.GetModifiedNode(STR_MOD_BY_NAME).ExplicitMods.StaticModifications.Contains(mod =>
mod.Modification.Terminus == null));
// Test matching negative masses
Assert.IsTrue(MATCHER.GetModifiedNode(STR_AMMONIA_LOSS).ExplicitMods.StaticModifications.Contains(mod =>
mod.Modification.EquivalentAll(UniMod.GetModification("Ammonia-loss (N-term C)", true))));
// General and specific
// If all AAs modified, try for most general modification.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15)
.ExplicitMods.HeavyModifications.Contains(mod => mod.Modification.Equivalent(LABEL15_N)));
// Updating the settings.
// Peptide settings should change to include new mods.
var docNew = new SrmDocument(SrmSettingsList.GetDefault());
IdentityPath firstAdded;
IdentityPath nextAdded;
docNew = docNew.AddPeptideGroups(new[] { new PeptideGroupDocNode(new PeptideGroup(), "PepGroup1", "",
new[] { MATCHER.GetModifiedNode(STR_MOD_BY_NAME) }) }, true, null, out firstAdded, out nextAdded);
var pepSetNew = MATCHER.GetDocModifications(docNew);
Assert.IsTrue(pepSetNew.StaticModifications.Contains(UniMod.GetModification("Phospho (ST)", true).ChangeExplicit(true)));
// Update the document to the new settings.
var pepSetNew1 = pepSetNew;
var settingsNew2 = docNew.Settings.ChangePeptideModifications(mods => pepSetNew1);
var lightGlobalMods = new MappedList <string, StaticMod>();
lightGlobalMods.AddRange(settingsNew2.PeptideSettings.Modifications.StaticModifications);
var heavyGlobalMods = new MappedList <string, StaticMod>();
heavyGlobalMods.AddRange(settingsNew2.PeptideSettings.Modifications.AllHeavyModifications);
// Match again. Test FoundMatches string should now be empty.
MATCHER.CreateMatches(docNew.Settings.ChangePeptideModifications(mods => pepSetNew1),
new List <string> {
STR_MOD_BY_NAME
}, lightGlobalMods, heavyGlobalMods);
Assert.IsTrue(string.IsNullOrEmpty(MATCHER.FoundMatches));
// Adding 15N to the settings.
UpdateMatcher(new[] { carbC }, new[] { LABEL15_N }, null, null);
// Test sequences with only explicit heavy mods should not have explicit light mods
Assert.IsNull(MATCHER.GetModifiedNode(STR_HEAVY_ONLY).ExplicitMods.StaticModifications);
// Test sequences with only explicit light mods should not have explicit heavy mods
Assert.IsFalse(MATCHER.GetModifiedNode(STR_LIGHT_ONLY).ExplicitMods.HasHeavyModifications);
// Test global mods take precendence over UniMod
UpdateMatcher(new[] { carbC }, null, new[] { OXIDATION_M_GLOBAL }, new[] { LABEL15_N });
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).ExplicitMods.StaticModifications
.Contains(mod => Equals(mod.Modification, OXIDATION_M_GLOBAL)));
// Test document mods take precendence over UniMod
UpdateMatcher(new[] { carbC, METHIONINE_OXIDATION }, null, new[] { OXIDATION_M_GLOBAL }, new[] { LABEL15_N });
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).HasExplicitMods);
// Test exception thrown if match doesn't make sense - wrong AA.
UpdateMatcherFail(STR_FAIL_OX_ON_D);
// Test exception thrown if match doesn't make sense - wrong terminus.
_seqs.Add(STR_FAIL_OX_TERM);
AssertEx.ThrowsException <FormatException>(() => UpdateMatcher(new[] { OXIDATION_M_C_TERM }, null, null, null));
_seqs.Remove(STR_FAIL_OX_TERM);
// Heavy 15N - All AAs.
UpdateMatcher(new[] { carbC, METHIONINE_OXIDATION }, new[] { LABEL15_N }, null, null);
// Node should be created from document settings if possible.
Assert.IsNull(MATCHER.GetModifiedNode(STR_HEAVY_15).ExplicitMods);
// Heavy 15N - specific AA.
// If only a specific AA is modified, there must be an explicit mod.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15_F).HasExplicitMods);
// Test variable mods match correctly.
// Put variable mod in global mod and not on doc - make sure don't get variable mod,
// should get explicit mod in that case.
var variableMetOx = METHIONINE_OXIDATION.ChangeVariable(true);
UpdateMatcher(new[] { carbC }, null, new[] { variableMetOx }, null);
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).HasExplicitMods);
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_OXI_PHOS).ExplicitMods.IsVariableStaticMods);
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_OXI_PHOS_CAP).ExplicitMods.IsVariableStaticMods);
// Add variable mod to doc
UpdateMatcher(new[] { carbC, variableMetOx }, null, null, null);
// Mod can be created by the settings.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).HasExplicitMods);
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).ExplicitMods.IsVariableStaticMods);
// Mod cannot be created by the settings.
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_OXI_PHOS).ExplicitMods.IsVariableStaticMods);
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_OXI_PHOS_CAP).ExplicitMods.IsVariableStaticMods);
// Add Met Ox to global. Test: +16 finds it.
UpdateMatcher(new[] { carbC }, null, new[] { MET_OX_ROUNDED }, null);
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).
ExplicitMods.StaticModifications.Contains(mod => Equals(mod.Modification, MET_OX_ROUNDED)));
// Test: +15.99 finds UniMod.
Assert.IsFalse(MATCHER.GetModifiedNode(STR_HEAVY_15).
ExplicitMods.StaticModifications.Contains(mod => Equals(mod.Modification, MET_OX_ROUNDED)));
// Add Methionine Oxidation before Met Ox. Test: +16 finds it.
UpdateMatcher(new[] { carbC }, null, new[] { METHIONINE_OXIDATION, MET_OX_ROUNDED }, null);
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).
ExplicitMods.StaticModifications.Contains(mod => Equals(mod.Modification, MET_OX_ROUNDED)));
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).
ExplicitMods.StaticModifications.Contains(mod => Equals(mod.Modification, METHIONINE_OXIDATION)));
// Test long masses rounded.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_METOX_LONG_MASS).ExplicitMods.StaticModifications.Contains(mod =>
Equals(mod.Modification, METHIONINE_OXIDATION)));
// Test UniMod label types
var node = MATCHER.GetModifiedNode(STR_UNIMOD_LABEL);
Assert.IsNotNull(node);
Assert.IsNull(node.ExplicitMods.StaticModifications);
Assert.IsTrue(node.ExplicitMods.HeavyModifications.Contains(mod =>
Equals(mod.Modification, N_TERM_LABEL)));
UpdateMatcherWithNoSequences(new[] { carbC }, new[] { N_TERM_LABEL }, new[] { METHIONINE_OXIDATION, MET_OX_ROUNDED }, null);
var nodeNew = MATCHER.GetModifiedNode(STR_UNIMOD_LABEL);
Assert.IsNotNull(nodeNew);
Assert.IsTrue(nodeNew.TransitionGroups.Any(group => Equals(group.TransitionGroup.LabelType, IsotopeLabelType.heavy)));
UpdateMatcher(new[] { carbC }, null, new[] { METHIONINE_OXIDATION, MET_OX_ROUNDED }, null);
// Test case where there are lots of unimod labels
var nodeUniAll = MATCHER.GetModifiedNode(STR_UNIMOD_ALL);
Assert.AreEqual(nodeUniAll.ExplicitMods.HeavyModifications.Count, 10);
Assert.IsNull(nodeUniAll.ExplicitMods.StaticModifications);
foreach (var mod in nodeUniAll.ExplicitMods.HeavyModifications)
{
Assert.AreEqual(mod.Modification.ShortName, "+01");
Assert.AreEqual(mod.Modification.UnimodId, 994);
}
// Test unimod terminal label
var nodeUniTerm = MATCHER.GetModifiedNode(STR_UNIMOD_TERMINUS);
Assert.AreEqual(nodeUniTerm.ExplicitMods.HeavyModifications.Count, 1);
Assert.IsNull(nodeUniTerm.ExplicitMods.StaticModifications);
Assert.AreEqual(nodeUniTerm.ExplicitMods.HeavyModifications[0].Modification.Terminus, ModTerminus.C);
Assert.AreEqual(nodeUniTerm.ExplicitMods.HeavyModifications[0].Modification.UnimodId, 298);
// Basic multi-label test
var heavyLabelType2 = new IsotopeLabelType("Heavy2", 1);
var typedMod = new TypedModifications(heavyLabelType2, new List <StaticMod> {
LABEL15_N
});
var peptideMods = new PeptideModifications(new List <StaticMod>(), new List <TypedModifications> {
typedMod
});
var settingsMultiLabel = SrmSettingsList.GetDefault().ChangePeptideModifications(mods => peptideMods);
var defSetSetLight = new MappedList <string, StaticMod>();
defSetSetLight.AddRange(StaticModList.GetDefaultsOn());
var defSetHeavy = new MappedList <string, StaticMod>();
defSetHeavy.AddRange(HeavyModList.GetDefaultsOn());
defSetHeavy.Add(LABEL15_N);
MATCHER.CreateMatches(settingsMultiLabel, new List <string> {
STR_HEAVY_15_F
}, defSetSetLight, defSetHeavy);
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15_F).ExplicitMods.GetHeavyModifications().Contains(mod => Equals(mod.LabelType, heavyLabelType2)));
// Peptide settings should not change.
var docNew0 = new SrmDocument(settingsMultiLabel).AddPeptideGroups(new[] { new PeptideGroupDocNode(new PeptideGroup(),
"PepGroup1", "", new[] { MATCHER.GetModifiedNode(STR_HEAVY_15_F) }) }, true, null, out firstAdded, out nextAdded);
var settingsNew = MATCHER.GetDocModifications(docNew0);
Assert.AreEqual(settingsMultiLabel.PeptideSettings.Modifications.ChangeHasHeavyModifications(false),
settingsNew.ChangeHasHeavyModifications(false));
// Finding specific modifications.
// If only specific AA modified, try for most specific modification.
UpdateMatcher(null, null, null, null, new[] { STR_HEAVY_15_F });
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15_F)
.ExplicitMods.HeavyModifications.Contains(mod =>
mod.Modification.AminoAcids.Contains(c => c == 'F')));
// If only some AAs modified, try for most specific modifications.
UpdateMatcher(null, null, null, null, new[] { STR_HEAVY_15_NOT_ALL });
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15_NOT_ALL)
.ExplicitMods.HeavyModifications.Contains(mod =>
mod.Modification.AminoAcids.Contains(c => c == 'I')));
using (var testDir = new TestFilesDir(TestContext, ZIP_FILE))
using (var modMatchDocContainer = InitMatchDocContainer(testDir))
{
var libkeyModMatcher = new LibKeyModificationMatcher();
var anlLibSpec = new BiblioSpecLiteSpec("ANL_Combo", testDir.GetTestPath("ANL_Combined.blib"));
var yeastLibSpec = new BiblioSpecLiteSpec("Yeast", testDir.GetTestPath("Yeast_atlas_small.blib"));
modMatchDocContainer.ChangeLibSpecs(new[] { anlLibSpec, yeastLibSpec });
var docLibraries = modMatchDocContainer.Document.Settings.PeptideSettings.Libraries.Libraries;
int anlLibIndex = docLibraries.IndexOf(library => Equals(library.Name, anlLibSpec.Name));
int yeastLibIndex = docLibraries.IndexOf(library => Equals(library.Name, yeastLibSpec.Name));
libkeyModMatcher.CreateMatches(modMatchDocContainer.Document.Settings,
docLibraries[anlLibIndex].Keys, defSetSetLight, defSetHeavy);
// Test can match 15N
Assert.IsTrue(libkeyModMatcher.Matches.Values.Contains(match =>
match.HeavyMod != null && match.HeavyMod.Equivalent(LABEL15_N)));
var uniModMetOx = UniMod.GetModification("Oxidation (M)", true);
// Test can match Met Ox
Assert.IsTrue(libkeyModMatcher.Matches.Values.Contains(match =>
match.StructuralMod != null && match.StructuralMod.Equivalent(uniModMetOx)));
// Test can match 15N and Met ox!
Assert.IsTrue(libkeyModMatcher.Matches.Contains(match => match.Key.Mass == 17 &&
match.Value.StructuralMod != null && match.Value.StructuralMod.Equivalent(uniModMetOx) &&
match.Value.HeavyMod != null && match.Value.HeavyMod.Equivalent(LABEL15_N)));
// Test can match Cysteine (Implicit) and Met Ox (variable)
libkeyModMatcher.CreateMatches(modMatchDocContainer.Document.Settings,
docLibraries[yeastLibIndex].Keys, defSetSetLight, defSetHeavy);
Assert.IsTrue(libkeyModMatcher.MatcherPepMods.StaticModifications.Contains(mod =>
mod.Formula.Equals(UniMod.GetModification(StaticModList.DEFAULT_NAME, true).Formula) && !mod.IsVariable));
Assert.IsTrue(libkeyModMatcher.MatcherPepMods.StaticModifications.Contains(mod =>
mod.Formula.Equals("O") && mod.IsVariable));
}
}
protected override void DoTest()
{
// Create modifications used in this test
var aquaMod = new StaticMod("Aqua 13C", "K, R", ModTerminus.C, null, LabelAtoms.C13 | LabelAtoms.N15, null, null);
var phosphoLossMod = new StaticMod("Phospho Loss", "S, T, Y", null, false, "HPO3",
LabelAtoms.None, RelativeRT.Matching, null, null, new[] { new FragmentLoss("H3PO4"), });
var multipleLossMod = new StaticMod("Multiple Loss-only", "A", null, false, null,
LabelAtoms.None, RelativeRT.Matching, null, null, new[] { new FragmentLoss("NH3"), new FragmentLoss("H2O") });
var explicitMassesLossMod = new StaticMod("Explicit Mass Loss", "N", null, false, null,
LabelAtoms.None, RelativeRT.Matching, null, null, new[] { new FragmentLoss(null, 5, 10) });
var variableLossMod = new StaticMod("Methionine Oxidized Loss", "M", null, true, "O",
LabelAtoms.None, RelativeRT.Matching, null, null, new[] { new FragmentLoss("CH3O") });
Settings.Default.HeavyModList.Clear();
Settings.Default.HeavyModList.Add(aquaMod);
Settings.Default.StaticModList.Clear();
Settings.Default.StaticModList.AddRange(StaticModList.GetDefaultsOn());
Settings.Default.StaticModList.Add(variableLossMod);
// Bump up the max mz a bit
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Instrument;
transitionSettingsUI.MaxMz = 1510;
});
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
// Bring up add modification dialog
var peptideSettingsUI = ShowDialog <PeptideSettingsUI>(() =>
SkylineWindow.ShowPeptideSettingsUI(PeptideSettingsUI.TABS.Modifications));
var editModsDlg = ShowEditStaticModsDlg(peptideSettingsUI);
var addModDlg = ShowAddModDlg(editModsDlg);
// Try a few things with new loss UI on the phospho loss modification
RunUI(() =>
{
addModDlg.Modification = phosphoLossMod;
Assert.IsTrue(addModDlg.GetLossText(0).EndsWith(phosphoLossMod.Losses[0].Formula));
addModDlg.LossSelectedIndex = 0;
addModDlg.DeleteLoss();
});
// Add back the original loss with the new loss editor dialog
RunDlg <EditFragmentLossDlg>(addModDlg.AddLoss, dlg =>
{
dlg.Loss = phosphoLossMod.Losses[0];
dlg.OkDialog();
});
// Add a smaller formula loss with the new loss editor dialog
var fragmentLossWater = new FragmentLoss("H2O");
RunDlg <EditFragmentLossDlg>(addModDlg.AddLoss, dlg =>
{
dlg.Loss = fragmentLossWater;
dlg.OkDialog();
});
// Add an explicit mass loss with the new loss editor dialog
var fragmentLossConstants = new FragmentLoss(null, 20, 25);
RunDlg <EditFragmentLossDlg>(addModDlg.AddLoss, dlg =>
{
dlg.Loss = fragmentLossConstants;
dlg.OkDialog();
});
// Check the added losses, and remove all but the original loss
RunUI(() =>
{
VerifyLossText(addModDlg.GetLossText(0), fragmentLossWater);
VerifyLossText(addModDlg.GetLossText(1), fragmentLossConstants);
VerifyLossText(addModDlg.GetLossText(2), phosphoLossMod.Losses[0]);
addModDlg.LossSelectedIndex = 0;
addModDlg.DeleteLoss();
addModDlg.DeleteLoss();
});
OkDialog(addModDlg, addModDlg.OkDialog);
// Add a loss modification with 2 losses and no formula
RunDlg <EditStaticModDlg>(editModsDlg.AddItem, dlg =>
{
dlg.Modification = multipleLossMod;
VerifyLossText(dlg.GetLossText(0), multipleLossMod.Losses[0]);
VerifyLossText(dlg.GetLossText(1), multipleLossMod.Losses[1]);
dlg.OkDialog();
});
// Add a loss modification with explicit numeric losses and no formula
// starting with no losses
var addExplicitLossDlg = ShowAddModDlg(editModsDlg);
RunUI(() =>
{
addExplicitLossDlg.Modification = explicitMassesLossMod;
addExplicitLossDlg.ShowLoss = true;
VerifyLossText(addExplicitLossDlg.GetLossText(0), explicitMassesLossMod.Losses[0]);
addExplicitLossDlg.LossSelectedIndex = 0;
addExplicitLossDlg.DeleteLoss();
});
// Add the explicit numeric loss
RunDlg <EditFragmentLossDlg>(addExplicitLossDlg.AddLoss, dlg =>
{
dlg.Loss = fragmentLossConstants;
dlg.OkDialog();
});
OkDialog(addExplicitLossDlg, addExplicitLossDlg.OkDialog);
OkDialog(editModsDlg, editModsDlg.OkDialog);
// Check the phospho loss modification
RunUI(() => peptideSettingsUI.PickedStaticMods =
new List <string>(peptideSettingsUI.PickedStaticMods)
{
phosphoLossMod.Name
}.ToArray());
WaitForOpenForm <PeptideSettingsUI>(); // Show Modifications tab for form testing
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
// Add FASTA sequence
RunUI(() => SkylineWindow.Paste(TEXT_FASTA_YEAST_7));
// Losses not added by default without a library
Assert.AreEqual(0, GetLossCount(SkylineWindow.Document, 1));
// Make sure setting losses as included Always works
{
var docBeforeAlways = SkylineWindow.Document;
var peptideSettingsUIAlways = ShowDialog <PeptideSettingsUI>(() =>
SkylineWindow.ShowPeptideSettingsUI(PeptideSettingsUI.TABS.Modifications));
var editModsDlgAlways = ShowEditStaticModsDlg(peptideSettingsUIAlways);
RunUI(() => editModsDlgAlways.SelectItem(phosphoLossMod.Name));
var editModDlgAlways = ShowDialog <EditStaticModDlg>(editModsDlgAlways.EditItem);
RunUI(() => editModDlgAlways.LossSelectedIndex = 0);
RunDlg <EditFragmentLossDlg>(editModDlgAlways.EditLoss, dlg =>
{
dlg.Inclusion = LossInclusion.Always;
dlg.OkDialog();
});
OkDialog(editModDlgAlways, editModDlgAlways.OkDialog);
OkDialog(editModsDlgAlways, editModsDlgAlways.OkDialog);
OkDialog(peptideSettingsUIAlways, peptideSettingsUIAlways.OkDialog);
var docAfterAlways = WaitForDocumentChange(docBeforeAlways);
Assert.AreEqual(5, GetLossCount(docAfterAlways, 1));
AssertEx.Serializable(docAfterAlways);
// Undo and revert to original phospo loss modification definition
RunUI(SkylineWindow.Undo);
Settings.Default.StaticModList.SetValue(phosphoLossMod);
}
// Show losses in the pick list
var docFasta = WaitForProteinMetadataBackgroundLoaderCompletedUI();
SelectNode(SrmDocument.Level.TransitionGroups, 0);
RunDlg <PopupPickList>(SkylineWindow.ShowPickChildrenInTest, dlg =>
{
dlg.ApplyFilter(false);
var losses = GetLossGroups(dlg.ItemNames).ToArray();
Assert.AreEqual(1, losses.Length);
VerifyLossGroup(losses, 0, 98, 124);
dlg.ToggleFind();
dlg.SearchString = "-98";
dlg.ToggleItem(0);
dlg.ToggleItem(1);
dlg.OnOk();
});
var docLoss = WaitForDocumentChange(docFasta);
// Make sure two losses were added
Assert.AreEqual(2, GetLossCount(docLoss, 1));
// Allow 2 neutral losses per fragment
RunDlg <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI, dlg =>
{
dlg.MaxNeutralLosses = 2;
dlg.OkDialog();
});
var docLoss2 = WaitForDocumentChange(docLoss);
// Make sure 2 phospho losses are now possible
IGrouping <double, string>[] losses1 = null;
RunDlg <PopupPickList>(SkylineWindow.ShowPickChildrenInTest, dlg =>
{
dlg.ApplyFilter(false);
losses1 = GetLossGroups(dlg.ItemNames).ToArray();
Assert.AreEqual(2, losses1.Length);
VerifyLossGroup(losses1, 0, 98, 124);
VerifyLossGroup(losses1, 1, 196, 109);
dlg.OnCancel();
});
// Add a modification with multiple possible losses
RunDlg <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI, dlg =>
{
dlg.PickedStaticMods = new List <string>(dlg.PickedStaticMods)
{
multipleLossMod.Name
}.ToArray();
dlg.OkDialog();
});
var docLossMulti = WaitForDocumentChange(docLoss2);
// Make sure all combinations of 2 except 2 of the multiple
// losses are possible, since only one amino acid A exists in this
// peptide.
RunDlg <PopupPickList>(SkylineWindow.ShowPickChildrenInTest, dlg =>
{
dlg.ApplyFilter(false);
var losses = GetLossGroups(dlg.ItemNames).ToArray();
Assert.AreEqual(6, losses.Length);
VerifyLossGroup(losses, 0, 17, 66);
VerifyLossGroup(losses, 1, 18, 66);
VerifyLossGroup(losses, 2, 98, 124);
VerifyLossGroup(losses, 3, 115, 61);
VerifyLossGroup(losses, 4, 116, 61);
VerifyLossGroup(losses, 5, 196, 109);
AssertEx.NoDiff(TextUtil.LineSeparate(losses1[0].ToArray()), TextUtil.LineSeparate(losses[2].ToArray()));
AssertEx.NoDiff(TextUtil.LineSeparate(losses1[1].ToArray()), TextUtil.LineSeparate(losses[5].ToArray()));
// Add new neutral loss transitions to the document
dlg.ToggleFind();
dlg.SearchString = "-17]";
dlg.ToggleItem(0);
dlg.SearchString = "-115]";
dlg.ToggleItem(0);
dlg.OnOk();
});
var docLossMultiAdded = WaitForDocumentChange(docLossMulti);
Assert.AreEqual(1, GetLossCount(docLossMultiAdded, 2));
// Add heavy modifications and make sure transition group is added with losses
RunDlg <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI, dlg =>
{
dlg.PickedHeavyMods = new[] { aquaMod.Name };
dlg.OkDialog();
});
var docLossMultiHeavy = WaitForDocumentChange(docLossMultiAdded);
Assert.AreEqual(4, docLossMultiHeavy.PeptideTransitionGroupCount);
Assert.AreEqual(8, GetLossCount(docLossMultiHeavy, 1));
Assert.AreEqual(2, GetLossCount(docLossMultiHeavy, 2));
// Make sure this document is serializable
AssertEx.Serializable(docLossMultiHeavy, AssertEx.DocumentCloned);
// Reset to just 1 neutral loss per fragment, and turn off heavy mod
RunDlg <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI, dlg =>
{
dlg.PickedHeavyMods = new string[0];
dlg.MaxNeutralLosses = 1;
dlg.OkDialog();
});
var docLossMulti1 = WaitForDocumentChange(docLossMultiHeavy);
Assert.AreEqual(3, GetLossCount(docLossMulti1, 1));
Assert.AreEqual(0, GetLossCount(docLossMulti1, 2));
// Remove all neutral loss modifications currently on the document
// and add the constant numeric loss
RunDlg <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI, dlg =>
{
dlg.PickedStaticMods = new[] { explicitMassesLossMod.Name };
dlg.OkDialog();
});
var docNoLoss2 = WaitForDocumentChange(docLossMulti1);
Assert.AreEqual(0, GetLossCount(docNoLoss2, 1));
// Add a neutral loss transition with constant numeric loss
RunDlg <PopupPickList>(SkylineWindow.ShowPickChildrenInTest, dlg =>
{
dlg.ApplyFilter(false);
var losses = GetLossGroups(dlg.ItemNames).ToArray();
Assert.AreEqual(1, losses.Length);
VerifyLossGroup(losses, 0, 20, 85);
// Add new neutral loss transitions to the document
dlg.ToggleFind();
dlg.SearchString = "-20";
dlg.ToggleItem(0);
dlg.OnOk();
});
// Verify that the expected loss was added to the document
var docConstantMono = WaitForDocumentChange(docNoLoss2);
Assert.AreEqual(1, GetLossCount(docConstantMono, 1));
var pathTranLoss = docConstantMono.GetPathTo((int)SrmDocument.Level.Transitions, 0);
var nodeTranLos = (TransitionDocNode)docConstantMono.FindNode(pathTranLoss);
Assert.AreEqual(IonType.precursor.GetLocalizedString() + " -20", nodeTranLos.FragmentIonName);
// Switch mass type to average
RunDlg <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI, dlg =>
{
dlg.FragmentMassType = MassType.Average;
dlg.OkDialog();
});
// Make sure neutral loss changes as expected
var docConstantAverage = WaitForDocumentChange(docConstantMono);
Assert.AreEqual(1, GetLossCount(docConstantAverage, 1));
nodeTranLos = (TransitionDocNode)docConstantAverage.FindNode(pathTranLoss);
Assert.AreEqual(IonType.precursor.GetLocalizedString() + " -25", nodeTranLos.FragmentIonName);
// Make sure the resulting document is serializable
AssertEx.Serializable(docConstantAverage, AssertEx.DocumentCloned);
}
protected override void DoTest()
{
// Clean-up before running the test
RunUI(() => SkylineWindow.ModifyDocument("Set default settings",
doc => doc.ChangeSettings(SrmSettingsList.GetDefault())));
Settings.Default.HeavyModList.Clear();
Settings.Default.StaticModList.Clear();
Settings.Default.StaticModList.AddRange(StaticModList.GetDefaultsOn());
// Show dialog asking user if text is FASTA or peptide list
RunDlg <PasteTypeDlg>(() => SkylineWindow.Paste(TextUtil.LineSeparate("QFVLSCVILQFVLSCVILQFVLSCVILQFVLSCVILR",
"DIEVYCDGAITTKDIEVYCDGAITTKDIEVYCDGAITTK")),
dlg => dlg.CancelDialog());
// Add two peptides
const string pepSequence1 = "QFVLSCVILR";
const string pepSequence2 = "DIEVYCDGAITTK";
RunUI(() => SkylineWindow.Paste(string.Join("\n", new[] { pepSequence1, pepSequence2 })));
// Check and save original document information
var docOrig = WaitForProteinMetadataBackgroundLoaderCompletedUI();
var pathPeptide = docOrig.GetPathTo((int)SrmDocument.Level.Molecules, 1);
var peptideImplicit = (PeptideDocNode)docOrig.FindNode(pathPeptide);
Assert.AreEqual(1, peptideImplicit.Children.Count);
Assert.IsNull(peptideImplicit.ExplicitMods);
// Add a new static modification on cysteine
var peptideSettingsUI = ShowPeptideSettings();
var modStatic = new StaticMod("Another Cysteine", "C", null, "CO8N2");
AddStaticMod(modStatic, peptideSettingsUI);
RunUI(peptideSettingsUI.OkDialog);
WaitForClosedForm(peptideSettingsUI);
// Select the peptide of interest
RunUI(() => SkylineWindow.SequenceTree.SelectedPath = pathPeptide);
Assert.AreSame(docOrig, SkylineWindow.Document);
// Explicitly add the new modification
var modifyPeptideDlg = ShowModifyPeptide();
RunUI(() =>
{
modifyPeptideDlg.SelectModification(IsotopeLabelType.light,
pepSequence2.IndexOf('C'), modStatic.Name);
modifyPeptideDlg.OkDialog();
});
// Check for correct response to modification
var docExplicit = WaitForDocumentChange(docOrig);
var peptideExplicit = (PeptideDocNode)docExplicit.FindNode(pathPeptide);
Assert.AreEqual(1, peptideExplicit.Children.Count);
// Precursor m/z value should have increased
Assert.IsTrue(((TransitionGroupDocNode)peptideExplicit.Children[0]).PrecursorMz >
((TransitionGroupDocNode)peptideImplicit.Children[0]).PrecursorMz);
var mods = peptideExplicit.ExplicitMods;
Assert.IsNotNull(mods);
Assert.IsTrue(mods.IsModified(IsotopeLabelType.light));
// Heavy should not be explicitly modified
Assert.IsFalse(mods.IsModified(IsotopeLabelType.heavy));
// Add new label types
peptideSettingsUI = ShowPeptideSettings();
string[] heavyLabelNames = { "heavy AA", "heavy All" };
SetHeavyLabelNames(peptideSettingsUI, heavyLabelNames);
// Make sure label type list edit worked
IsotopeLabelType[] heavyLabelTypes = peptideSettingsUI.LabelTypes.ToArray();
Assert.AreEqual(2, heavyLabelTypes.Length);
var labelTypeAa = heavyLabelTypes[0];
var labelTypeAll = heavyLabelTypes[1];
Assert.AreEqual(heavyLabelNames.Length, heavyLabelTypes.Length);
for (int i = 0; i < heavyLabelTypes.Length; i++)
{
Assert.AreEqual(heavyLabelNames[i], heavyLabelTypes[i].Name);
}
// Add new heavy modifications
var mod15N = new StaticMod("Label:15N", null, null, null, LabelAtoms.N15, null, null);
AddHeavyMod(mod15N, peptideSettingsUI);
// var mod13C = new StaticMod("All 13C", null, null, null, LabelAtoms.C13, null, null);
// AddHeavyMod(mod13C, peptideSettingsUI);
var modK13C = new StaticMod("Label:13C(6) (C-term K)", "K", ModTerminus.C, null, LabelAtoms.C13, null, null);
AddHeavyMod(modK13C, peptideSettingsUI);
var modR13C = new StaticMod("Label:13C(6) (C-term R)", "R", ModTerminus.C, null, LabelAtoms.C13, null, null);
AddHeavyMod(modR13C, peptideSettingsUI);
var modV13C = new StaticMod("Label:13C(5)15N(1) (V)", "V", null, null, LabelAtoms.C13 | LabelAtoms.N15, null, null);
AddHeavyMod(modV13C, peptideSettingsUI);
// Set heavy modification for the peptides
RunUI(() =>
{
peptideSettingsUI.SelectedLabelTypeName = heavyLabelNames[1];
peptideSettingsUI.PickedHeavyMods = new[] { mod15N.Name };
peptideSettingsUI.SelectedLabelTypeName = heavyLabelNames[0];
peptideSettingsUI.PickedHeavyMods = new[] { modK13C.Name, modR13C.Name };
peptideSettingsUI.OkDialog();
});
// Make sure the document was updated as expected. Explicit modification
// should not keep new types from adding precursors to both peptides.
var docMultiType = WaitForDocumentChange(docExplicit);
foreach (var nodePep in docMultiType.Peptides)
{
Assert.AreEqual(3, nodePep.Children.Count);
TransitionGroupDocNode nodeGroupLast = null;
foreach (TransitionGroupDocNode nodeGroup in nodePep.Children)
{
if (nodeGroupLast != null)
{
Assert.IsTrue(nodeGroup.PrecursorMz > nodeGroupLast.PrecursorMz);
}
nodeGroupLast = nodeGroup;
var labelType = nodeGroup.TransitionGroup.LabelType;
if (!labelType.IsLight)
{
Assert.IsTrue(heavyLabelTypes.Contains(labelType));
}
}
}
// Get the modified peptide in the new document
peptideExplicit = (PeptideDocNode)docMultiType.FindNode(pathPeptide);
// Explicitly set the heavy All modification to match the heavy AA modification
var modifyPeptideMultiDlg = ShowModifyPeptide();
RunUI(() =>
{
for (int i = 0; i < pepSequence2.Length - 1; i++)
{
modifyPeptideMultiDlg.SelectModification(labelTypeAll, i, "");
}
modifyPeptideMultiDlg.SelectModification(labelTypeAll, pepSequence2.Length - 1, modK13C.Name);
modifyPeptideMultiDlg.OkDialog();
});
// Make sure both heavy types have precursor m/z value that match the original
var docModMatch = WaitForDocumentChange(docMultiType);
var peptideMatch = (PeptideDocNode)docModMatch.FindNode(pathPeptide);
AssertPrecursorMzAreEqaul(peptideExplicit, 1, peptideMatch, 1);
AssertPrecursorMzAreEqaul(peptideExplicit, 1, peptideMatch, 2);
// Remove the modification on K for heavyAA, and make sure this gets rid of the precursor
var modifyPeptideEmptyDlg = ShowModifyPeptide();
RunUI(() =>
{
modifyPeptideEmptyDlg.SelectModification(labelTypeAa, pepSequence2.Length - 1, "");
modifyPeptideEmptyDlg.OkDialog();
});
var docModRemoved = WaitForDocumentChange(docModMatch);
var peptideRemoved = (PeptideDocNode)docModRemoved.FindNode(pathPeptide);
Assert.AreEqual(2, peptideRemoved.Children.Count);
// Reset the modifications
var modifyPeptideResetDlg = ShowModifyPeptide();
RunUI(() =>
{
modifyPeptideResetDlg.ResetMods();
modifyPeptideResetDlg.OkDialog();
});
// Make sure this removes the explicit modification and adds back the removed precursor
var docModReset = WaitForDocumentChange(docModRemoved);
peptideImplicit = (PeptideDocNode)docModReset.FindNode(pathPeptide);
Assert.IsNull(peptideImplicit.ExplicitMods);
Assert.AreEqual(3, peptideImplicit.Children.Count);
// Explicitly set the heavy All modification to match the heavy AA modification
var modifyPeptideMatchDlg = ShowModifyPeptide();
RunUI(() =>
{
for (int i = 0; i < pepSequence2.Length - 1; i++)
{
modifyPeptideMatchDlg.SelectModification(labelTypeAll, i, "");
}
modifyPeptideMatchDlg.SelectModification(labelTypeAll, pepSequence2.Length - 1, modK13C.Name);
modifyPeptideMatchDlg.OkDialog();
});
var docModAA = WaitForDocumentChange(docModReset);
// Change implicit static modification and heavy AA
var peptideSettingsUIChange = ShowPeptideSettings();
RunUI(() =>
{
peptideSettingsUIChange.PickedStaticMods = new[] { modStatic.Name };
peptideSettingsUIChange.PickedHeavyMods = new[] { modV13C.Name };
peptideSettingsUIChange.OkDialog();
});
var docModImplicitStatic = WaitForDocumentChange(docModAA);
var peptideMatch2 = (PeptideDocNode)docModImplicitStatic.FindNode(pathPeptide);
Assert.IsNotNull(peptideMatch2.ExplicitMods);
Assert.IsFalse(peptideMatch2.ExplicitMods.IsModified(heavyLabelTypes[0]));
Assert.IsTrue(peptideMatch2.ExplicitMods.IsModified(heavyLabelTypes[1]));
AssertPrecursorMzAreEqaul(peptideMatch, 0, peptideMatch2, 0);
AssertPrecursorMzAreNotEqaul(peptideMatch, 1, peptideMatch2, 1);
AssertPrecursorMzAreEqaul(peptideMatch, 2, peptideMatch2, 2);
// Remove the heavy All type, which should remove the only explicit modification
var peptideSettingsUIRemove = ShowPeptideSettings();
SetHeavyLabelNames(peptideSettingsUIRemove, new[] { heavyLabelNames[0] });
RunUI(peptideSettingsUIRemove.OkDialog);
var docModRemoveType = WaitForDocumentChange(docModImplicitStatic);
foreach (var nodePep in docModRemoveType.Peptides)
{
Assert.IsNull(nodePep.ExplicitMods);
Assert.AreEqual(2, nodePep.Children.Count);
}
// Undo, and add an explicit modification to the heavy AA type
RunUI(SkylineWindow.Undo);
Assert.AreSame(docModImplicitStatic, SkylineWindow.Document);
var modifyPeptideAADlg = ShowModifyPeptide();
RunUI(() =>
{
modifyPeptideAADlg.SelectModification(labelTypeAa, pepSequence2.IndexOf('V'), "");
modifyPeptideAADlg.SelectModification(labelTypeAa, pepSequence2.Length - 1, modK13C.Name);
modifyPeptideAADlg.OkDialog();
});
var docModExplicitStatic = WaitForDocumentChange(docModImplicitStatic);
// Remove the heavy All label type again
peptideSettingsUIRemove = ShowPeptideSettings();
SetHeavyLabelNames(peptideSettingsUIRemove, new[] { heavyLabelNames[0] });
OkDialog(peptideSettingsUIRemove, peptideSettingsUIRemove.OkDialog);
var docMultiExplicit = WaitForDocumentChange(docModExplicitStatic);
var peptideStillExplicit = (PeptideDocNode)docMultiExplicit.FindNode(pathPeptide);
Assert.IsNotNull(peptideStillExplicit.ExplicitMods);
Assert.IsTrue(peptideStillExplicit.ExplicitMods.IsModified(labelTypeAa));
Assert.IsFalse(peptideStillExplicit.ExplicitMods.IsModified(labelTypeAll));
AssertPrecursorMzAreEqaul(peptideMatch, 1, peptideStillExplicit, 1);
}
protected override void DoTest()
{
// Create modifications used in this test
var aquaMods = new[]
{
new StaticMod("Heavy K", "K", ModTerminus.C, null, LabelAtoms.C13 | LabelAtoms.N15, null, null),
new StaticMod("Heavy R", "R", ModTerminus.C, null, LabelAtoms.C13 | LabelAtoms.N15, null, null)
};
var explicitMod = new StaticMod("13C L", "L", null, null, LabelAtoms.C13, null, null);
var variableMod = new StaticMod("Methionine Oxidized", "M", null, true, "O",
LabelAtoms.None, RelativeRT.Matching, null, null, null);
Settings.Default.HeavyModList.Clear();
Settings.Default.HeavyModList.AddRange(aquaMods);
Settings.Default.HeavyModList.Add(explicitMod);
Settings.Default.StaticModList.Clear();
Settings.Default.StaticModList.AddRange(StaticModList.GetDefaultsOn());
var carbMod = Settings.Default.StaticModList[0];
Settings.Default.StaticModList.Add(variableMod);
// Clean-up before running the test
var settings = SrmSettingsList.GetDefault().ChangePeptideModifications(mod =>
mod.ChangeHeavyModifications(aquaMods));
RunUI(() => SkylineWindow.ModifyDocument("Set test settings",
doc => doc.ChangeSettings(settings)));
// Add FASTA sequence
RunUI(() => SkylineWindow.Paste(TEXT_FASTA_YEAST_39));
// Check and save original document information
var docOrig = WaitForProteinMetadataBackgroundLoaderCompletedUI();
var pathPeptide = docOrig.GetPathTo((int)SrmDocument.Level.Molecules, docOrig.PeptideCount - 3);
var peptideOrig = (PeptideDocNode)docOrig.FindNode(pathPeptide);
Assert.AreEqual(2, peptideOrig.Children.Count);
Assert.IsNull(peptideOrig.ExplicitMods);
// Add methionine oxidation variable modification
SetStaticModifications(names => new List <string>(names)
{
variableMod.Name
});
var docVarMod = WaitForDocumentChange(docOrig);
// Check that variable modification worked, and that the peptide of
// interest is variably modified.
Assert.IsTrue(docOrig.PeptideCount < docVarMod.PeptideCount);
pathPeptide = docVarMod.GetPathTo((int)SrmDocument.Level.Molecules, docVarMod.PeptideCount - 4);
var peptideVarMod = (PeptideDocNode)docVarMod.FindNode(pathPeptide);
Assert.AreEqual(2, peptideVarMod.Children.Count);
Assert.IsTrue(peptideVarMod.HasVariableMods,
string.Format("No variable modifications found on the peptide {0}", peptideVarMod.Peptide.Sequence));
Assert.IsFalse(peptideVarMod.ExplicitMods.IsModified(IsotopeLabelType.heavy));
AssertPrecursorMzIsModified(peptideVarMod, 0, peptideVarMod, 1, -5, 0.2);
// Select the peptide of interest
RunUI(() => SkylineWindow.SequenceTree.SelectedPath = pathPeptide);
// Make sure the explicit modifications dialog does not modify the
// peptide when nothing is changed.
string sequence = peptideVarMod.Peptide.Sequence;
RunDlg <EditPepModsDlg>(SkylineWindow.ModifyPeptide, dlg =>
{
for (int i = 0; i < sequence.Length; i++)
{
dlg.SelectModification(IsotopeLabelType.light, i, "");
dlg.SelectModification(IsotopeLabelType.heavy, i, "");
}
dlg.ResetMods();
dlg.OkDialog();
});
Assert.AreSame(docVarMod, SkylineWindow.Document);
// Explicitly change the heavy modification
RunDlg <EditPepModsDlg>(SkylineWindow.ModifyPeptide, dlg =>
{
dlg.SelectModification(IsotopeLabelType.heavy, sequence.Length - 1, "");
dlg.SelectModification(IsotopeLabelType.heavy, sequence.LastIndexOf('L'),
explicitMod.Name);
dlg.OkDialog();
});
// Check for correct response to modification
var docExplicit = WaitForDocumentChange(docOrig);
var peptideExplicit = (PeptideDocNode)docExplicit.FindNode(pathPeptide);
Assert.AreEqual(2, peptideExplicit.Children.Count);
// Precursor m/z for light should be same
AssertPrecursorMzAreEqaul(peptideVarMod, 0, peptideExplicit, 0);
// Heavy should have changed
AssertPrecursorMzIsModified(peptideExplicit, 0, peptideExplicit, 1, -3, 0.2);
// Heavy should now be explicitly modified
Assert.IsTrue(peptideExplicit.ExplicitMods.IsModified(IsotopeLabelType.heavy));
// Remove carbamidomethyl cysteine implicit modification
SetStaticModifications(names => new[] { variableMod.Name });
var docNoImplicit = WaitForDocumentChange(docExplicit);
var peptideNoImplicit = (PeptideDocNode)docNoImplicit.FindNode(pathPeptide);
// Light should have gotten 57.0 lighter
const double modCarbMz = 57.0 / 2;
AssertPrecursorMzIsModified(peptideExplicit, 0, peptideNoImplicit, 0, modCarbMz, 0.1);
// Heavy delta should not have changed
AssertPrecursorMzIsModified(peptideNoImplicit, 0, peptideNoImplicit, 1, -3, 0.2);
// Reset should still return to implicit heavy mods without removing
// variable mods.
RunDlg <EditPepModsDlg>(SkylineWindow.ModifyPeptide, dlg =>
{
dlg.ResetMods();
dlg.OkDialog();
});
var docReset = WaitForDocumentChange(docNoImplicit);
var peptideReset = (PeptideDocNode)docReset.FindNode(pathPeptide);
Assert.IsTrue(peptideReset.HasExplicitMods);
Assert.IsFalse(peptideReset.ExplicitMods.IsModified(IsotopeLabelType.heavy));
AssertPrecursorMzIsModified(peptideReset, 0, peptideReset, 1, -5, 0.2);
// Explicitly add back the Carbamidomethyl Cysteine
// Reset should still return to implicit heavy mods
RunDlg <EditPepModsDlg>(SkylineWindow.ModifyPeptide, dlg =>
{
dlg.SelectModification(IsotopeLabelType.light, sequence.IndexOf('C'), carbMod.Name);
dlg.OkDialog();
});
var docExCarb = WaitForDocumentChange(docReset);
var peptideExCarb = (PeptideDocNode)docExCarb.FindNode(pathPeptide);
Assert.IsTrue(peptideExCarb.HasExplicitMods);
Assert.IsFalse(peptideExCarb.HasVariableMods);
AssertPrecursorMzAreEqaul(peptideVarMod, 0, peptideExCarb, 0);
AssertPrecursorMzAreEqaul(peptideVarMod, 1, peptideExCarb, 1);
// Reset at this point should completely remove explicit modifications
// including oxidized M.
RunDlg <EditPepModsDlg>(SkylineWindow.ModifyPeptide, dlg =>
{
dlg.ResetMods();
dlg.OkDialog();
});
var docResetImplicit = WaitForDocumentChange(docExCarb);
var peptideResetImplicit = (PeptideDocNode)docResetImplicit.FindNode(pathPeptide);
Assert.IsFalse(peptideResetImplicit.HasExplicitMods);
AssertPrecursorMzIsModified(peptideOrig, 0, peptideResetImplicit, 0, modCarbMz, 0.1);
AssertPrecursorMzIsModified(peptideOrig, 1, peptideResetImplicit, 1, modCarbMz, 0.1);
// Turn off the variable modifications and explicitly modify using a variable mod
RunDlg <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI, dlg =>
{
dlg.PickedStaticMods = new string[0];
dlg.OkDialog();
});
var docNoStaticMods = WaitForDocumentChange(docResetImplicit);
// Explicitly modify the first peptide
var pathPeptideFirst = docNoStaticMods.GetPathTo((int)SrmDocument.Level.Molecules, 0);
var peptideUnmod = (PeptideDocNode)docNoStaticMods.FindNode(pathPeptideFirst);
RunUI(() => SkylineWindow.SelectedPath = pathPeptideFirst);
RunDlg <EditPepModsDlg>(SkylineWindow.ModifyPeptide, dlg =>
{
var sequenceUnmod = peptideUnmod.Peptide.Sequence;
dlg.SelectModification(IsotopeLabelType.light, sequenceUnmod.IndexOf('M'), variableMod.Name);
dlg.OkDialog();
});
var docExplicitVarMod = WaitForDocumentChange(docNoStaticMods);
var peptideExplicitVarMod = (PeptideDocNode)docExplicitVarMod.FindNode(pathPeptideFirst);
Assert.IsTrue(peptideExplicitVarMod.HasExplicitMods);
if (peptideExplicitVarMod.ExplicitMods.StaticModifications == null)
{
Assert.IsNotNull(peptideExplicitVarMod.ExplicitMods.StaticModifications);
return; // For ReSharper
}
var varModPeptide = peptideExplicitVarMod.ExplicitMods.StaticModifications[0].Modification;
Assert.AreEqual(variableMod.Name, varModPeptide.Name);
// The modification instance on the peptide should not be marked as variable
Assert.IsFalse(varModPeptide.IsVariable);
var varModSettings = docExplicitVarMod.Settings.PeptideSettings.Modifications.StaticModifications[0];
Assert.AreEqual(variableMod.Name, varModSettings.Name);
Assert.IsTrue(varModSettings.IsExplicit);
Assert.IsFalse(varModSettings.IsVariable);
// Make sure this did not turn on the variable modification in the settings UI
RunDlg <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI, dlg =>
{
Assert.AreEqual(0, dlg.PickedStaticMods.Length);
dlg.OkDialog();
});
Directory.CreateDirectory(TestContext.TestDir);
string saveFilePath = TestContext.GetTestPath("TestExplicitVariable.sky");
WaitForProteinMetadataBackgroundLoaderCompletedUI(); // make sure doc is complete before save
RunUI(() =>
{
Assert.IsTrue(SkylineWindow.SaveDocument(saveFilePath));
SkylineWindow.NewDocument();
Assert.IsTrue(SkylineWindow.OpenFile(saveFilePath));
});
WaitForProteinMetadataBackgroundLoaderCompletedUI();
var docRestored = SkylineWindow.Document;
var pathPeptideFirstNew = docRestored.GetPathTo((int)SrmDocument.Level.Molecules, 0);
var peptideExplicitVarModNew = docRestored.FindNode(pathPeptideFirstNew);
Assert.AreEqual(peptideExplicitVarMod, peptideExplicitVarModNew,
"Saved peptide with explicit variable modification was not restored correctly.");
Assert.IsTrue(Settings.Default.StaticModList.Contains(variableMod),
"Expected variable modification has been removed from the global list.");
}
