private void MainTest()
{
// Clean-up before running the test
RunUI(() => SkylineWindow.ModifyDocument("Set default settings",
doc => doc.ChangeSettings(SrmSettingsList.GetDefault())));
// Check using libkey with small molecules
var adduct = Adduct.FromStringAssumeProtonated("M+3Na");
var z = adduct.AdductCharge;
const string caffeineFormula = "C8H10N4O2";
const string caffeineInChiKey = "RYYVLZVUVIJVGH-UHFFFAOYSA-N";
const string caffeineHMDB = "HMDB01847";
const string caffeineInChi = "InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3";
const string caffeineCAS = "58-08-2";
const string caffeineSMILES = "Cn1cnc2n(C)c(=O)n(C)c(=O)c12";
const string caffeineKEGG = "C07481";
var mId = new MoleculeAccessionNumbers(string.Join("\t", MoleculeAccessionNumbers.TagHMDB + ":" + caffeineHMDB,
MoleculeAccessionNumbers.TagInChI + ":" + caffeineInChi, MoleculeAccessionNumbers.TagCAS + ":" + caffeineCAS, MoleculeAccessionNumbers.TagInChiKey + ":" + caffeineInChiKey,
MoleculeAccessionNumbers.TagSMILES + ":" + caffeineSMILES, MoleculeAccessionNumbers.TagKEGG + ":" + caffeineKEGG));
Assert.AreEqual(caffeineInChiKey, mId.GetInChiKey());
Assert.AreEqual(caffeineCAS, mId.GetCAS());
Assert.AreEqual(caffeineSMILES, mId.GetSMILES());
Assert.AreEqual(caffeineKEGG, mId.GetKEGG());
var moleculeName = "caffeine";
var smallMolAttributes = SmallMoleculeLibraryAttributes.Create(moleculeName, caffeineFormula, caffeineInChiKey,
string.Join("\t", MoleculeAccessionNumbers.TagHMDB + ":" + caffeineHMDB,
MoleculeAccessionNumbers.TagInChI + ":" + caffeineInChi, MoleculeAccessionNumbers.TagCAS + ":" + caffeineCAS,
MoleculeAccessionNumbers.TagSMILES + ":" + caffeineSMILES, MoleculeAccessionNumbers.TagKEGG + ":" + caffeineKEGG));
LibKey key;
for (var loop = 0; loop++ < 2;)
{
key = new LibKey(smallMolAttributes, adduct);
Assert.IsFalse(key.IsPrecursorKey);
Assert.IsFalse(key.IsProteomicKey);
Assert.IsTrue(key.IsSmallMoleculeKey);
Assert.IsFalse(key.IsModified);
Assert.AreEqual(0, key.ModificationCount);
Assert.AreEqual(z, key.Charge);
Assert.AreEqual(adduct, key.Adduct);
Assert.AreEqual(caffeineInChiKey, key.Target.ToString());
var viewLibPepInfo = new ViewLibraryPepInfo(key);
Assert.AreEqual(key, viewLibPepInfo.Key);
var smallMolInfo = viewLibPepInfo.GetSmallMoleculeLibraryAttributes();
Assert.AreEqual(moleculeName, smallMolInfo.MoleculeName);
Assert.AreEqual(caffeineInChiKey, smallMolInfo.InChiKey);
Assert.AreEqual(caffeineFormula, smallMolInfo.ChemicalFormula);
Assert.IsTrue(smallMolInfo.OtherKeys.Contains(caffeineCAS));
Assert.IsTrue(smallMolInfo.OtherKeys.Contains(caffeineInChi));
Assert.IsTrue(smallMolInfo.OtherKeys.Contains(caffeineHMDB));
Assert.IsTrue(smallMolInfo.OtherKeys.Contains(caffeineSMILES));
Assert.IsTrue(smallMolInfo.OtherKeys.Contains(caffeineKEGG));
adduct = Adduct.FromString("M+3Si", Adduct.ADDUCT_TYPE.non_proteomic, z = -17); // Not realistic, but let's see if it's handled consistently
}
// Check general libkey operation
var seq = "YTQSNSVC[+57.0]YAK";
key = new LibKey(seq, Adduct.DOUBLY_PROTONATED);
Assert.IsFalse(key.IsPrecursorKey);
Assert.IsTrue(key.IsProteomicKey);
Assert.IsFalse(key.IsSmallMoleculeKey);
Assert.IsTrue(key.IsModified);
Assert.AreEqual(2, key.Charge);
Assert.AreEqual(1, key.ModificationCount);
Assert.AreEqual(Adduct.DOUBLY_PROTONATED, key.Adduct);
Assert.AreEqual(seq, key.Target.ToString());
// Test error conditions
BuildLibraryError("missing_charge.pep.XML", TestFilesDir.FullPath);
BuildLibraryError("non_int_charge.pep.XML", null);
BuildLibraryError("zero_charge.pep.XML", null);
BuildLibraryError("truncated.pep.XML", null);
BuildLibraryError("no_such_file.pep.XML", null, "Failed to open");
BuildLibraryError("missing_mzxml.pep.XML", null, "Could not find spectrum file");
// Check for proper handling of labeled addducts in small molecule files
// (formerly this would throw on a null object, fixed with the use of ExplicitMods.EMPTY)
BuildLibraryValid("heavy_adduct.ssl", true, false, false, 1);
// Make sure explorer handles this adduct type
var viewLibUI = ShowDialog <ViewLibraryDlg>(SkylineWindow.ViewSpectralLibraries);
RunUI(() => AssertEx.IsTrue(viewLibUI.GraphItem.IonLabels.Any()));
RunUI(viewLibUI.CancelDialog);
// Barbara added code to ProteoWizard to rebuild a missing or invalid mzXML index
// BuildLibraryError("bad_mzxml.pep.XML", "<index> not found");
BuildLibraryValid(TestFilesDir.GetTestPath("library_errors"), new[] { "bad_mzxml.pep.XML" }, false, false, false, 1);
string libraryBaseName = _libraryName;
// Test mascot parser
_libraryName = libraryBaseName + "mascot";
string libraryMascot = _libraryName + BiblioSpecLiteSpec.EXT;
BuildLibraryValid(TestFilesDir.GetTestPath("mascot"), new[] { "F027319.dat" },
true, false, false, 121, 4);
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryMascot)));
// Test successful builds
_libraryName = libraryBaseName + "a";
string libraryA = _libraryName + BiblioSpecLiteSpec.EXT;
string libraryARedundant = _libraryName + BiblioSpecLiteSpec.EXT_REDUNDANT;
BuildLibraryValid("CPTAC_Set4_725_091509.pep.XML", true, false, false, 1);
BuildLibraryValid("CPTAC_Set4_610_080509.pep.XML", true, false, true, 2);
_libraryName = libraryBaseName + "b";
string libraryB = _libraryName + BiblioSpecLiteSpec.EXT;
BuildLibraryValid("CPTAC_Set4_624_072409.pep.XML", false, false, false, 6);
_libraryName = libraryBaseName + "c";
string libraryC = _libraryName + BiblioSpecLiteSpec.EXT;
BuildLibraryValid(TestFilesDir.FullPath, new[] { libraryA, libraryB },
false, false, false, 8);
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryA)));
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryARedundant)));
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryB)));
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryC)));
// Test peptide filter
const string filterList = "ACARPIISVYSEK\n" +
// TODO: Having the modified sequence as the first line causes an error with European number formats
"ADRDESSPYAAM[+{0:F01}]IAAQDVAQR\n" +
"ADAIQAGASQFETSAAK";
PastePeptideList(string.Format(filterList, 16.0), true, 0, 3, true);
_libraryName = libraryBaseName + "filter";
string libraryFilter = _libraryName + BiblioSpecLiteSpec.EXT;
BuildLibraryValid(TestFilesDir.GetTestPath("maxquant"), new[] { "test.msms.txt" },
false, true, false, 2);
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryFilter)));
RunUI(SkylineWindow.Undo);
RunUI(SkylineWindow.Undo);
// Test AddPathsDlg (file not found)
EnsurePeptideSettings();
var buildLibraryDlg = ShowDialog <BuildLibraryDlg>(PeptideSettingsUI.ShowBuildLibraryDlg);
string[] invalidPaths =
{
Path.Combine(TestFilesDir.GetTestPath("maxquant"), "test.msms.xml"),
Path.Combine(TestFilesDir.GetTestPath("library_valid"), "CPTAC_Set4_624_072409.pep.XML")
};
TestAddPaths(buildLibraryDlg, invalidPaths, true);
// Test AddPathsDlg (file invalid type)
string[] invalidTypes =
{
Path.Combine(TestFilesDir.GetTestPath("maxquant"), "test.msms.txt"),
Path.Combine(TestFilesDir.GetTestPath("maxquant"), "mqpar.xml")
};
TestAddPaths(buildLibraryDlg, invalidTypes, true);
// Test AddPathsDlg (valid files)
string[] goodPaths =
{
Path.Combine(TestFilesDir.GetTestPath("maxquant"), "test.msms.txt"),
Path.Combine(TestFilesDir.GetTestPath("library_valid"), "CPTAC_Set4_624_072409.pep.XML")
};
TestAddPaths(buildLibraryDlg, goodPaths, false);
OkDialog(buildLibraryDlg, buildLibraryDlg.CancelDialog);
const string heavyRPeptide = "TPAQFDADELR";
const string oxidizedMPeptide = "LVGNMHGDETVSR";
const string peptideList = heavyRPeptide + "\n" +
oxidizedMPeptide + "\n" +
"ALSIGFETCR\n" +
"GNMHGDETVSR\n" +
"VGNMHGDETVSR";
PastePeptideList(peptideList, true, 0, 1);
// Set modifications on peptides to verify they connect with library spectra.
const LabelAtoms labelAtoms = LabelAtoms.C13 | LabelAtoms.N15;
const string heavyR = "Heavy R";
Settings.Default.HeavyModList.Add(new StaticMod(heavyR, "R", ModTerminus.C, null, labelAtoms, null, null));
const string oMeth = "Oxidized Methionine";
Settings.Default.StaticModList.Add(new StaticMod(oMeth, "M", null, "O"));
var sequenceTree = SkylineWindow.SequenceTree;
var docCurrent = SkylineWindow.Document;
// Select the heavyR peptide
PeptideTreeNode nodePepTree = null;
IdentityPath pathPep = docCurrent.GetPathTo((int)SrmDocument.Level.Molecules, 0);
RunUI(() =>
{
sequenceTree.SelectedPath = pathPep;
nodePepTree = sequenceTree.SelectedNode as PeptideTreeNode;
});
Assert.IsNotNull(nodePepTree);
Assert.AreEqual(heavyRPeptide, nodePepTree.DocNode.Peptide.Sequence);
// Set the Heavy R modification explicitly
var editPepModsDlg = ShowDialog <EditPepModsDlg>(SkylineWindow.ModifyPeptide);
RunUI(() =>
{
editPepModsDlg.SetModification(heavyRPeptide.Length - 1, IsotopeLabelType.heavy, heavyR);
editPepModsDlg.OkDialog();
});
WaitForCondition(() => (SkylineWindow.Document.Molecules.First().TransitionGroupCount == 2));
// The peptide should now match the spectrum in the library, and have
// both heavy and light precursors, with ranked transitions
PeptideDocNode nodePep = null;
RunUI(() => nodePep = nodePepTree.DocNode);
Assert.IsNotNull(nodePep);
Debug.Assert(nodePep != null);
Assert.AreEqual(2, nodePep.Children.Count, "Missing precursor for heavy R peptide.");
docCurrent = SkylineWindow.Document;
foreach (TransitionGroupDocNode nodeGroup in nodePep.Children)
{
AssertLibInfo(docCurrent, nodeGroup);
}
// Which means all transition groups should now have spectrum info
foreach (var nodeGroup in docCurrent.PeptideTransitionGroups)
{
AssertLibInfo(docCurrent, nodeGroup);
}
// New document
var docNew = new SrmDocument(SrmSettingsList.GetDefault());
var docNewCopy = docNew;
RunUI(() => SkylineWindow.SwitchDocument(docNewCopy, null));
const string idpList3 = "FHYKTDQGIK\n" +
"WCAIGHQER\n" +
"WCTISTHEANK";
int idpCount3 = idpList3.Split('\n').Length;
const string idpList = "ADVTLGGGAK\n" +
"AGFAGDDAPR\n" +
"ALEFAKK\n" +
"CCTESLVNR\n" +
"DSYVGDEAQSK\n" +
"YICDNQDTISSK\n" +
// charge 3 peptides all have 2 also
idpList3;
int idpCount = idpList.Split('\n').Length;
_libraryName = libraryBaseName + "_idp";
string libraryIdp = _libraryName + BiblioSpecLiteSpec.EXT;
BuildLibraryValid(TestFilesDir.GetTestPath("idp_xml"), new[] { "orbi-small-eg.idpXML" },
false, false, false, idpCount + idpCount3);
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryIdp)));
// Add peptides expected to have charge 2 spectra in the library
PastePeptideList(idpList, true, 0, 0);
// Undo the paste
RunUI(SkylineWindow.Undo);
// Try filtering for only charge 3 spectra
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(
SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettingsUI.PrecursorCharges = "3";
transitionSettingsUI.OkDialog();
});
PastePeptideList(idpList, false, idpCount - idpCount3 + 1 /* missing cleavage*/, 0);
// New document
var docNewCopy2 = docNew;
RunUI(() => SkylineWindow.SwitchDocument(docNewCopy2, null));
_libraryName = libraryBaseName + "_cpas1";
string libraryCpas1 = _libraryName + BiblioSpecLiteSpec.EXT;
BuildLibraryValid(TestFilesDir.GetTestPath("cpas"), null,
false, false, false, 3);
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryCpas1)));
// These are very poor searches, so repeat with no filter
Settings.Default.LibraryResultCutOff = 0;
_libraryName = libraryBaseName + "_cpas2";
BuildLibraryValid(TestFilesDir.GetTestPath("cpas"), null,
false, false, false, 100, 100);
// And, since the spectra are really poor, allow lots of
// possibilities for fragment ions.
var transitionSettingsCpas = ShowDialog <TransitionSettingsUI>(
SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettingsCpas.PrecursorCharges =
transitionSettingsCpas.ProductCharges = "1,2,3";
transitionSettingsCpas.FragmentTypes = "y,b";
transitionSettingsCpas.InstrumentMaxMz = 2000;
transitionSettingsCpas.OkDialog();
});
EnsurePeptideSettings();
RunUI(() =>
{
// Turn off carbamidomethyl cys, since not in these searches
PeptideSettingsUI.PickedStaticMods = new string[0];
PeptideSettingsUI.OkDialog();
});
// Get the set of peptides to paste from the library, since there
// are a lot.
var setPeptides = new HashSet <Target>();
var library = SkylineWindow.Document.Settings.PeptideSettings.Libraries.Libraries[0];
foreach (var libKey in library.Keys)
{
if (!libKey.IsModified)
{
setPeptides.Add(libKey.Target);
}
}
string cpasPeptides = string.Join("\n", setPeptides.Select(p => p.ToString()).ToArray());
var pasteFilteredPeptideDlg = ShowDialog <PasteFilteredPeptidesDlg>(
() => SkylineWindow.Paste(cpasPeptides));
RunUI(pasteFilteredPeptideDlg.NoDialog);
Assert.IsTrue(WaitForCondition(() => SkylineWindow.Document.PeptideCount == setPeptides.Count),
string.Format("Expecting {0} peptides, found {1}.", setPeptides.Count, SkylineWindow.Document.PeptideCount));
Assert.AreEqual(setPeptides.Count, SkylineWindow.Document.PeptideTransitionGroupCount,
"Expecting precursors for peptides matched to library spectrum.");
// New document
docNew = new SrmDocument(SrmSettingsList.GetDefault());
RunUI(() => SkylineWindow.SwitchDocument(docNew, null));
// Tests for adding iRTs to spectral library after building
// 1. ask to recalibrate iRTs
// 2. ask to add iRTs
// 3. if added iRTs, ask to add RT predictor
// no recalibrate, add iRTs, no add predictor
_libraryName = libraryBaseName + "_irt1"; // library_test_irt1
BuildLibraryIrt(true, false, false);
RunUI(() => Assert.IsTrue(PeptideSettingsUI.Prediction.RetentionTime == null));
// no recalibrate, add iRTs, add predictor
_libraryName = libraryBaseName + "_irt2"; // library_test_irt2
BuildLibraryIrt(true, false, true);
RunUI(() => Assert.IsTrue(PeptideSettingsUI.Prediction.RetentionTime.Name.Equals(_libraryName)));
var editIrtDlg2 = ShowDialog <EditIrtCalcDlg>(PeptideSettingsUI.EditCalculator);
RunUI(() => Assert.IsTrue(ReferenceEquals(editIrtDlg2.IrtStandards, IrtStandard.BIOGNOSYS_10)));
OkDialog(editIrtDlg2, editIrtDlg2.CancelDialog);
// recalibrate, add iRTs, no add predictor
_libraryName = libraryBaseName + "_irt3"; // library_test_irt3
BuildLibraryIrt(true, true, false);
RunUI(() => Assert.IsTrue(PeptideSettingsUI.Prediction.RetentionTime.Name.Equals(libraryBaseName + "_irt2")));
// recalibrate, add iRTs, add predictor
_libraryName = libraryBaseName + "_irt4"; // library_test_irt4
BuildLibraryIrt(true, true, true);
RunUI(() => Assert.IsTrue(PeptideSettingsUI.Prediction.RetentionTime.Name.Equals(_libraryName)));
var editIrtDlg4 = ShowDialog <EditIrtCalcDlg>(PeptideSettingsUI.EditCalculator);
RunUI(() => Assert.IsTrue(ReferenceEquals(editIrtDlg4.IrtStandards, IrtStandard.EMPTY)));
OkDialog(editIrtDlg4, editIrtDlg4.CancelDialog);
OkDialog(PeptideSettingsUI, PeptideSettingsUI.CancelDialog);
}
private void TestBasicFunctionality()
{
// Launch the Library Explorer dialog
_viewLibUI = ShowDialog <ViewLibraryDlg>(SkylineWindow.ViewSpectralLibraries);
// Ensure the appropriate default library is selected
ComboBox libComboBox = null;
ListBox pepList = null;
string libSelected = null;
RunUI(() =>
{
libComboBox = (ComboBox)_viewLibUI.Controls.Find("comboLibrary", true)[0];
Assert.IsNotNull(libComboBox);
libSelected = libComboBox.SelectedItem.ToString();
// Find the peptides list control
pepList = (ListBox)_viewLibUI.Controls.Find("listPeptide", true)[0];
Assert.IsNotNull(pepList);
});
Assert.AreEqual(_testLibs[0].Name, libSelected);
// Initially, peptide with index 0 should be selected
WaitForConditionUI(() => pepList.SelectedIndex != -1);
var modDlg = WaitForOpenForm <MultiButtonMsgDlg>();
RunUI(modDlg.Btn1Click);
ViewLibraryPepInfo previousPeptide = new ViewLibraryPepInfo();
int peptideIndex = -1;
RunUI(() =>
{
previousPeptide = (ViewLibraryPepInfo)pepList.SelectedItem;
peptideIndex = pepList.SelectedIndex;
});
Assert.IsNotNull(previousPeptide);
Assert.AreEqual(0, peptideIndex);
Assert.AreEqual(3, previousPeptide.Charge, "Expected charge 3 on " + previousPeptide.DisplayString);
// Now try to select a different peptide and check to see if the
// selection changes
const int selectPeptideIndex = 1;
RunUI(() =>
{
pepList.SelectedIndex = selectPeptideIndex;
});
ViewLibraryPepInfo selPeptide = new ViewLibraryPepInfo();
RunUI(() =>
{
Assert.AreEqual(selectPeptideIndex, pepList.SelectedIndex); // Did selection change work?
selPeptide = (ViewLibraryPepInfo)pepList.SelectedItem;
});
Assert.IsNotNull(selPeptide);
if (Equals(previousPeptide, selPeptide))
{
Assert.AreNotEqual(previousPeptide.DisplayString, selPeptide.DisplayString);
}
Assert.AreEqual(2, selPeptide.Charge, "Expected charge 2 on " + selPeptide.DisplayString);
// Click the "Next" link
RunUI(() =>
{
var nextLink = (IButtonControl)_viewLibUI.Controls.Find("NextLink", true)[0];
Assert.IsNotNull(nextLink);
nextLink.PerformClick();
});
RunUI(() =>
{
previousPeptide = (ViewLibraryPepInfo)pepList.SelectedItem;
});
// Click "Previous" link and ensure the peptide selected changes
RunUI(() =>
{
var previousLink = (IButtonControl)_viewLibUI.Controls.Find("PreviousLink", true)[0];
Assert.IsNotNull(previousLink);
previousLink.PerformClick();
});
RunUI(() =>
{
selPeptide = (ViewLibraryPepInfo)pepList.SelectedItem;
});
Assert.AreNotEqual(previousPeptide, selPeptide);
// Test valid peptide search
TextBox pepTextBox = null;
RunUI(() =>
{
pepTextBox = (TextBox)_viewLibUI.Controls.Find("textPeptide", true)[0];
Assert.IsNotNull(pepTextBox);
pepTextBox.Focus();
pepTextBox.Text = _testLibs[0].UniquePeptide;
});
int pepsCount = 0;
RunUI(() =>
{
selPeptide = (ViewLibraryPepInfo)pepList.SelectedItem;
pepsCount = pepList.Items.Count;
});
Assert.AreEqual(_testLibs[0].UniquePeptide, selPeptide.DisplayString);
Assert.AreEqual(1, pepsCount);
// Test invalid peptide search
RunUI(() =>
{
pepTextBox.Focus();
pepTextBox.Text = INVALID_SEARCH;
});
RunUI(() =>
{
pepsCount = pepList.Items.Count;
});
Assert.AreEqual(0, pepsCount);
// Test clearing invalid peptide search
RunUI(() =>
{
pepTextBox.Focus();
pepTextBox.Text = "";
});
selPeptide = new ViewLibraryPepInfo();
RunUI(() =>
{
selPeptide = (ViewLibraryPepInfo)pepList.SelectedItem;
pepsCount = pepList.Items.Count;
});
Assert.IsNotNull(selPeptide);
Assert.AreNotEqual(0, pepsCount);
// Test selecting a different library
previousPeptide = selPeptide;
RunDlg <MultiButtonMsgDlg>(() => libComboBox.SelectedIndex = 1, dlg => dlg.Btn1Click());
RunUI(() =>
{
libComboBox.SelectedIndex = 1;
});
RunUI(() =>
{
libSelected = libComboBox.SelectedItem.ToString();
});
Assert.AreEqual(libSelected, _testLibs[1].Name);
RunUI(() =>
{
selPeptide = (ViewLibraryPepInfo)pepList.SelectedItem;
});
Assert.IsNotNull(selPeptide);
Assert.AreNotEqual(previousPeptide, selPeptide);
// If the library is not in the document settings, offer to add the library to the settings.
// If the user declines, add the peptides anyways, but strip them so they do not appear to be
// connected to any library.
RunDlg <MultiButtonMsgDlg>(_viewLibUI.AddPeptide, msgDlg => msgDlg.Btn1Click());
Assert.AreEqual(1, SkylineWindow.Document.PeptideCount);
Assert.IsFalse(SkylineWindow.Document.Peptides.Contains(nodePep => nodePep.HasLibInfo));
RunUI(() =>
{
SkylineWindow.SelectAll();
SkylineWindow.EditDelete();
});
// Test adding peptides offers to add library if not already in settings.
// Test add single peptide.
using (new CheckDocumentStateWithPossibleProteinMetadataBackgroundUpdate(1, 1, 1, 3))
{
RunDlg <MultiButtonMsgDlg>(_viewLibUI.AddPeptide, msgDlg => msgDlg.Btn0Click());
}
RunUI(SkylineWindow.EditDelete);
// Test unmatched peptides are correct.
// One unmatched because its precursor m/z is outside the instrument measurement range
AddAllPeptides(1, 4, 3);
// Verify that everything matches, given a wide enough mass range
RunUI(() => SkylineWindow.ModifyDocument("Change m/z range",
doc => doc.ChangeSettings(doc.Settings.ChangeTransitionInstrument(inst =>
inst.ChangeMaxMz(TransitionInstrument.MAX_MEASURABLE_MZ)))));
WaitForConditionUI(() => !_viewLibUI.HasUnmatchedPeptides);
RunUI(() => SkylineWindow.ModifyDocument("Change m/z range",
doc => doc.ChangeSettings(doc.Settings.ChangeTransitionInstrument(inst =>
inst.ChangeMaxMz(1500)))));
WaitForConditionUI(() => _viewLibUI.HasUnmatchedPeptides);
// Test library peptides are merged without duplicates.
TestForDuplicatePeptides();
// Test library peptides only get added to the document once.
var docOriginal = SkylineWindow.Document;
RunDlg <MessageDlg>(_viewLibUI.AddPeptide, msgDlg => msgDlg.OkDialog());
var filterMatchedPeptidesDlg5 = ShowDialog <FilterMatchedPeptidesDlg>(_viewLibUI.AddAllPeptides);
RunDlg <MessageDlg>(filterMatchedPeptidesDlg5.OkDialog, msgDlg => msgDlg.OkDialog());
Assert.AreSame(docOriginal, SkylineWindow.Document);
// Test missing peptides added.
RunUI(() =>
{
var sequenceTree = SkylineWindow.SequenceTree;
var nodePeps = sequenceTree.Nodes[0].Nodes;
sequenceTree.SelectedNode = nodePeps[0];
sequenceTree.KeysOverride = Keys.Control;
for (int i = 2; i < 10; i += 2)
{
sequenceTree.SelectedNode = nodePeps[i];
}
sequenceTree.KeysOverride = Keys.None;
SkylineWindow.EditDelete();
});
AddAllPeptides();
var docAddBack = SkylineWindow.Document;
// Peptides will be added back in a different order
AssertEx.IsDocumentState(docAddBack, null,
docOriginal.PeptideGroupCount, docOriginal.PeptideCount,
docOriginal.PeptideTransitionGroupCount, docOriginal.PeptideTransitionCount);
TestSamePeptides(docOriginal.Peptides);
// Test missing transition groups added correctly.
RunUI(() =>
{
var sequenceTree = SkylineWindow.SequenceTree;
sequenceTree.SelectedNode = sequenceTree.Nodes[0].Nodes[0].Nodes[0];
sequenceTree.KeysOverride = Keys.Control;
for (int x = 0; x < 5; x++)
{
var nodePep = sequenceTree.Nodes[0].Nodes[x];
var nodeGroups = nodePep.Nodes;
for (int i = 0; i < nodeGroups.Count; i += 2)
{
sequenceTree.SelectedNode = nodeGroups[i];
}
}
SkylineWindow.EditDelete();
});
AddAllPeptides();
var docAddBackGroups = SkylineWindow.Document;
// Check all precursor charges present.
foreach (PeptideDocNode nodePep in docOriginal.Peptides)
{
var key = nodePep.Key;
foreach (TransitionGroupDocNode nodeGroup in nodePep.Children)
{
var charge = nodeGroup.TransitionGroup.PrecursorCharge;
Assert.IsTrue(docAddBackGroups.Peptides.Contains(nodePepDoc => Equals(key, nodePepDoc.Key) &&
nodePepDoc.HasChildCharge(charge)));
}
}
// Check no duplicate TransitionGroups added.
TestForDuplicateTransitionGroups();
// Test peptides get heavy label modifications.
List <StaticMod> heavyMods15N =
new List <StaticMod> {
new StaticMod("15N", null, null, null, LabelAtoms.N15, null, null)
};
RunUI(() =>
{
SkylineWindow.SelectAll();
SkylineWindow.EditDelete();
var settings = SkylineWindow.Document.Settings.ChangePeptideModifications(mods => new PeptideModifications(mods.StaticModifications,
new[] { new TypedModifications(IsotopeLabelType.heavy, heavyMods15N) }));
SkylineWindow.ModifyDocument("Change heavy modifications", doc => doc.ChangeSettings(settings));
});
AddAllPeptides();
// All peptides should have a heavy label transition group.
// There should be no peptide whose children do not contain a transition group with heavy label type.
Assert.IsFalse(SkylineWindow.Document.Peptides.Contains(nodePep =>
!nodePep.Children.Contains(nodeGroup =>
((TransitionGroupDocNode)nodeGroup).TransitionGroup.LabelType.Equals(IsotopeLabelType.heavy))));
// Test peptide setting changes update the library explorer.
RunUI(() => SkylineWindow.ModifyDocument("Change static modifications",
doc => doc.ChangeSettings(SkylineWindow.Document.Settings.ChangePeptideModifications(mods =>
mods.ChangeStaticModifications(new List <StaticMod>())))));
AddAllPeptides(1, 8, 3);
// Along with Heavy 15N added earlier in the test, adding this modification means that all library peptides
// will match to the document settings.
StaticMod varMetOxidized = new StaticMod("Methionine Oxidized", "M", null, true, "O",
LabelAtoms.None, RelativeRT.Matching, null, null, null);
var metOxidizedSettings = SkylineWindow.Document.Settings.ChangePeptideModifications(mods =>
mods.ChangeStaticModifications(new[] { varMetOxidized }));
RunUI(() =>
{
SkylineWindow.SelectAll();
SkylineWindow.EditDelete();
SkylineWindow.ModifyDocument("Change static mods",
doc => doc.ChangeSettings(metOxidizedSettings));
});
// Switch to ANL_Combined library
RunDlg <MultiButtonMsgDlg>(() => { libComboBox.SelectedIndex = 2; }, msgDlg => msgDlg.BtnCancelClick());
// User prompted to add library since not in current settings.
RunDlg <MultiButtonMsgDlg>(() => _viewLibUI.CheckLibraryInSettings(), msgDlg => msgDlg.Btn0Click());
// Add single peptide to the document.
RunUI(_viewLibUI.AddPeptide);
WaitForProteinMetadataBackgroundLoaderCompletedUI();
var nodePepAdded = SkylineWindow.SequenceTree.Nodes[0].Nodes[0];
// Because document settings match the library, no duplicates should be found.
AddAllPeptides(0);
// Even though there are two matches in the library for the the nodePep we just added
// to the document (one with light modifications and one with heavy), the two spectrum
// both have the same charge. In this case, both spectrum should be ignored when Add All
// is called.
Assert.AreEqual(nodePepAdded, SkylineWindow.SequenceTree.Nodes[0].Nodes[0]);
Assert.AreEqual(3, SkylineWindow.Document.PeptideCount);
// Switch to the Phospho Loss Library
RunDlg <MultiButtonMsgDlg>(() => libComboBox.SelectedIndex = 3, msgDlg => msgDlg.Btn1Click());
// Add modifications to the document matching the settings of the library.
var phosphoLossMod = new StaticMod("Phospho Loss", "S, T", null, true, "HPO3",
LabelAtoms.None, RelativeRT.Matching, null, null, new[] { new FragmentLoss("H3PO4"), });
var phosphoLossSettings =
SkylineWindow.Document.Settings.ChangePeptideModifications(mods => mods.ChangeStaticModifications(new[] { phosphoLossMod }));
RunUI(() =>
SkylineWindow.ModifyDocument("Change static mods", doc => doc.ChangeSettings(phosphoLossSettings)));
RunDlg <MultiButtonMsgDlg>(() => _viewLibUI.CheckLibraryInSettings(), msgDlg => msgDlg.Btn0Click());
// Again, we should be able to match all peptides since the document settings match use the peptides found
// in the library.
RunDlg <MultiButtonMsgDlg>(_viewLibUI.AddAllPeptides, msgDlg =>
{
Assert.AreEqual(0, (int)msgDlg.Tag);
msgDlg.Btn1Click();
});
// Test losses are being displayed in the graph, indicating that the spectrum have been matched correctly.
WaitForConditionUI(() => _viewLibUI.GraphItem.IonLabels.Contains(str => str.Contains("98")));
Assert.IsTrue(_viewLibUI.GraphItem.IonLabels.Contains(str => str.Contains("98")));
// Associate yeast background proteome
var peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunDlg <BuildBackgroundProteomeDlg>(peptideSettingsUI.ShowBuildBackgroundProteomeDlg,
buildBackgroundProteomeDlg =>
{
buildBackgroundProteomeDlg.BackgroundProteomePath = TestFilesDir.GetTestPath("yeast_mini.protdb");
buildBackgroundProteomeDlg.BackgroundProteomeName = "Yeast";
buildBackgroundProteomeDlg.OkDialog();
});
RunUI(peptideSettingsUI.OkDialog);
WaitForCondition(() =>
{
var peptideSettings = Program.ActiveDocument.Settings.PeptideSettings;
var backgroundProteome = peptideSettings.BackgroundProteome;
return(backgroundProteome.HasDigestion(peptideSettings));
});
WaitForDocumentLoaded(); // Give background loader a chance to get the protein metadata too
RunDlg <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI, transitionSettingsUI =>
{
transitionSettingsUI.PrecursorCharges = "1,2,3";
transitionSettingsUI.OkDialog();
});
// Test add all with the yeast background proteome connected.
RunUI(() =>
{
SkylineWindow.SelectAll();
SkylineWindow.EditDelete();
// Switch to yeast library.
libComboBox.SelectedIndex = 4;
_viewLibUI.AssociateMatchingProteins = true;
});
var addLibraryDlg = ShowDialog <MultiButtonMsgDlg>(_viewLibUI.AddAllPeptides);
// Add the library to the document.
var filterMatchedPeptidesDlg = ShowDialog <FilterMatchedPeptidesDlg>(addLibraryDlg.Btn0Click);
RunUI(() => filterMatchedPeptidesDlg.AddUnmatched = false);
using (new CheckDocumentStateWithPossibleProteinMetadataBackgroundUpdate(4, 10, 13, 39))
{
RunDlg <MultiButtonMsgDlg>(filterMatchedPeptidesDlg.OkDialog, messageDlg => messageDlg.Btn1Click());
}
Assert.IsFalse(SkylineWindow.Document.Peptides.Contains(nodePep => !nodePep.HasLibInfo));
// Test adding a single peptide that matches two different proteins using keep all.
RunUI(() =>
{
SkylineWindow.Undo();
_viewLibUI.ChangeSelectedPeptide("ADTGIAVEGATDAAR+");
});
using (new CheckDocumentStateWithPossibleProteinMetadataBackgroundUpdate(2, 2, 2, 6))
{
RunDlg <FilterMatchedPeptidesDlg>(_viewLibUI.AddPeptide,
filterMatchedPeptideDlg => filterMatchedPeptideDlg.OkDialog());
}
// Test adding a second charge state for that peptide.
RunUI(() => _viewLibUI.ChangeSelectedPeptide("ADTGIAVEGATDAAR++"));
using (new CheckDocumentStateWithPossibleProteinMetadataBackgroundUpdate(2, 2, 4, 12))
{
RunDlg <FilterMatchedPeptidesDlg>(_viewLibUI.AddPeptide,
filterMatchedPeptideDlg => filterMatchedPeptideDlg.OkDialog());
}
RunDlg <FilterMatchedPeptidesDlg>(_viewLibUI.AddPeptide,
filterMatchedPeptideDlg => filterMatchedPeptideDlg.OkDialog());
// Test adding a second charge state - No Duplicates.
RunUI(() => SkylineWindow.Undo());
var docPrev = WaitForDocumentLoaded();
RunDlg <FilterMatchedPeptidesDlg>(_viewLibUI.AddPeptide,
filterMatchedPeptideDlg =>
{
filterMatchedPeptideDlg.DuplicateProteinsFilter = BackgroundProteome.DuplicateProteinsFilter.NoDuplicates;
filterMatchedPeptideDlg.OkDialog();
});
Assert.AreEqual(docPrev, WaitForDocumentLoaded());
// Test adding a second charge state - First Only.
using (new CheckDocumentStateWithPossibleProteinMetadataBackgroundUpdate(2, 2, 3, 9))
{
RunDlg <FilterMatchedPeptidesDlg>(_viewLibUI.AddPeptide, filterMatchedPeptideDlg =>
{
filterMatchedPeptideDlg.DuplicateProteinsFilter =
BackgroundProteome.DuplicateProteinsFilter.FirstOccurence;
filterMatchedPeptideDlg.OkDialog();
});
}
RunUI(() =>
{
SkylineWindow.Undo();
SkylineWindow.Undo();
// Add doubly charged state, no protein association.
_viewLibUI.AssociateMatchingProteins = false;
_viewLibUI.AddPeptide();
_viewLibUI.AssociateMatchingProteins = true;
});
// Add doubly charged state with protein assocation.
RunDlg <FilterMatchedPeptidesDlg>(_viewLibUI.AddPeptide,
filterMatchedPeptideDlg => filterMatchedPeptideDlg.OkDialog()); // First only
// Select singly charged state
RunUI(() => _viewLibUI.ChangeSelectedPeptide("ADTGIAVEGATDAAR+"));
// Test adding peptide associated with the background proteome does not affect any matching peptides that are
// in peptide lists.
using (new CheckDocumentStateWithPossibleProteinMetadataBackgroundUpdate(2, 2, 3, 9))
{
RunDlg <FilterMatchedPeptidesDlg>(_viewLibUI.AddPeptide,
filterMatchedPeptideDlg => filterMatchedPeptideDlg.OkDialog()); // First only
}
var peptideGroups = SkylineWindow.Document.PeptideGroups.ToArray();
int index = peptideGroups.IndexOf(nodeGroup => nodeGroup.IsPeptideList);
Assert.IsTrue(peptideGroups[index].Children.Count == 1);
// Test selecting no duplicates prevents any peptide from appearing twice in the document.
RunUI(() => SkylineWindow.Undo());
RunUI(() => SkylineWindow.Undo());
var filterMatchedPeptidesDlg1 = ShowDialog <FilterMatchedPeptidesDlg>(_viewLibUI.AddAllPeptides);
RunUI(() => filterMatchedPeptidesDlg1.DuplicateProteinsFilter = BackgroundProteome.DuplicateProteinsFilter.NoDuplicates);
RunDlg <MultiButtonMsgDlg>(filterMatchedPeptidesDlg1.OkDialog, messageDlg => messageDlg.Btn1Click());
TestForDuplicatePeptides();
// Test selecting first occurence prevents any peptide from appearing twice in the document.
RunUI(() => SkylineWindow.Undo());
var filterMatchedPeptidesDlg2 = ShowDialog <FilterMatchedPeptidesDlg>(_viewLibUI.AddAllPeptides);
RunUI(() => filterMatchedPeptidesDlg2.DuplicateProteinsFilter = BackgroundProteome.DuplicateProteinsFilter.FirstOccurence);
RunDlg <MultiButtonMsgDlg>(filterMatchedPeptidesDlg2.OkDialog, messageDlg => messageDlg.Btn1Click());
TestForDuplicatePeptides();
// Test peptides are added to "Library Peptides" peptide list if this peptide group already exists.
using (new CheckDocumentStateWithPossibleProteinMetadataBackgroundUpdate(1, 2, 3, 9))
{
RunUI(() =>
{
SkylineWindow.Undo();
_viewLibUI.AssociateMatchingProteins = false;
_viewLibUI.AddPeptide();
_viewLibUI.ChangeSelectedPeptide("AAAP");
_viewLibUI.AddPeptide();
});
}
RunUI(() =>
{
SkylineWindow.SelectAll();
SkylineWindow.EditDelete();
});
// Close the Library Explorer dialog
OkDialog(_viewLibUI, _viewLibUI.CancelDialog);
}
