private static SrmDocument InitWiffDocument(TestFilesDir testFilesDir)
{
const LabelAtoms labelAtoms = LabelAtoms.C13 | LabelAtoms.N15;
List <StaticMod> heavyMods = new List <StaticMod>
{
new StaticMod("Heavy K", "K", ModTerminus.C, null, labelAtoms, null, null),
new StaticMod("Heavy R", "R", ModTerminus.C, null, labelAtoms, null, null),
};
SrmSettings settings = SrmSettingsList.GetDefault();
settings = settings.ChangePeptideModifications(mods => mods.ChangeHeavyModifications(heavyMods));
SrmDocument doc = new SrmDocument(settings);
IdentityPath selectPath;
string path = testFilesDir.GetTestPath("051309_transition list.csv");
// Product m/z out of range
var docError = doc;
List <MeasuredRetentionTime> irtPeptides;
List <SpectrumMzInfo> librarySpectra;
List <TransitionImportErrorInfo> errorList;
var inputs = new MassListInputs(path)
{
FormatProvider = CultureInfo.InvariantCulture,
Separator = TextUtil.SEPARATOR_CSV
};
docError.ImportMassList(inputs, null, out selectPath, out irtPeptides, out librarySpectra, out errorList);
Assert.AreEqual(errorList.Count, 1);
AssertEx.AreComparableStrings(TextUtil.SpaceSeparate(Resources.MassListRowReader_CalcTransitionExplanations_The_product_m_z__0__is_out_of_range_for_the_instrument_settings__in_the_peptide_sequence__1_,
Resources.MassListRowReader_CalcPrecursorExplanations_Check_the_Instrument_tab_in_the_Transition_Settings),
errorList[0].ErrorMessage,
2);
Assert.AreEqual(errorList[0].Column, 1);
Assert.AreEqual(errorList[0].Row, 19);
doc = doc.ChangeSettings(settings.ChangeTransitionInstrument(inst => inst.ChangeMaxMz(1800)));
inputs = new MassListInputs(path)
{
FormatProvider = CultureInfo.InvariantCulture,
Separator = TextUtil.SEPARATOR_CSV
};
doc = doc.ImportMassList(inputs, null, out selectPath);
AssertEx.IsDocumentState(doc, 2, 9, 9, 18, 54);
return(doc);
}
private void UpdateMasses()
{
string formula = null;
LabelAtoms labelAtoms = LabelAtoms.None;
if (cbChemicalFormula.Checked)
{
formula = Formula;
}
else
{
labelAtoms = LabelAtoms;
string aaString = comboAA.Text;
if (!string.IsNullOrEmpty(aaString) && aaString.Length == 1 &&
AminoAcid.IsAA(aaString[0]) && labelAtoms != LabelAtoms.None)
{
formula = SequenceMassCalc.GetHeavyFormula(aaString[0], labelAtoms);
}
}
if (string.IsNullOrEmpty(formula))
{
// If the mass edit boxes are already enabled, don't clear what a user
// may have typed in them.
if (!_formulaBox.MassEnabled)
{
_formulaBox.MonoMass = null;
_formulaBox.AverageMass = null;
}
_formulaBox.MassEnabled = (labelAtoms == LabelAtoms.None);
}
else
{
_formulaBox.Formula = formula;
}
}
public void OkDialog()
{
var helper = new MessageBoxHelper(this);
string name;
if (!helper.ValidateNameTextBox(_editing ? (Control)textName : comboMod, out name))
{
return;
}
// Allow updating the original modification
if (!_editing || !Equals(name, Modification.Name))
{
if (!ModNameAvailable(name))
{
helper.ShowTextBoxError(_editing ? (Control)textName : comboMod,
Resources.EditStaticModDlg_OkDialog_The_modification__0__already_exists, name);
return;
}
}
string aas = comboAA.Text;
if (string.IsNullOrEmpty(aas))
{
aas = null;
}
else
{
// Use the cleanest possible format.
var sb = new StringBuilder();
foreach (string aaPart in aas.Split(SEPARATOR_AA))
{
string aa = aaPart.Trim();
if (aa.Length == 0)
{
continue;
}
if (sb.Length > 0)
{
sb.Append(", "); // Not L10N
}
sb.Append(aa);
}
}
string termString = comboTerm.SelectedItem.ToString();
ModTerminus?term = null;
if (!string.IsNullOrEmpty(termString))
{
term = (ModTerminus)Enum.Parse(typeof(ModTerminus), termString);
}
if (cbVariableMod.Checked && aas == null && term == null)
{
MessageDlg.Show(this, Resources.EditStaticModDlg_OkDialog_Variable_modifications_must_specify_amino_acid_or_terminus);
comboAA.Focus();
return;
}
string formula = null;
double? monoMass = null;
double? avgMass = null;
LabelAtoms labelAtoms = LabelAtoms.None;
if (cbChemicalFormula.Checked)
{
formula = Formula;
}
else
{
labelAtoms = LabelAtoms;
}
// Get the losses to know whether any exist below
IList <FragmentLoss> losses = null;
if (listNeutralLosses.Items.Count > 0)
{
losses = Losses.ToArray();
}
if (!string.IsNullOrEmpty(formula))
{
try
{
SequenceMassCalc.FormulaMass(BioMassCalc.MONOISOTOPIC, formula, SequenceMassCalc.MassPrecision);
}
catch (ArgumentException x)
{
_formulaBox.ShowTextBoxErrorFormula(helper, x.Message);
return;
}
}
else if (labelAtoms == LabelAtoms.None)
{
formula = null;
// Allow formula and both masses to be empty, if losses are present
if (NotZero(_formulaBox.MonoMass) || NotZero(_formulaBox.AverageMass) || losses == null)
{
// TODO: Maximum and minimum masses should be formalized and applied everywhere
double mass;
if (!_formulaBox.ValidateMonoText(helper, -1500, 5000, out mass))
{
return;
}
monoMass = mass;
if (!_formulaBox.ValidateAverageText(helper, -1500, 5000, out mass))
{
return;
}
avgMass = mass;
}
// Loss-only modifications may not be variable
else if (cbVariableMod.Checked)
{
MessageDlg.Show(this, Resources.EditStaticModDlg_OkDialog_The_variable_checkbox_only_applies_to_precursor_modification_Product_ion_losses_are_inherently_variable);
cbVariableMod.Focus();
return;
}
}
else if (aas == null && term.HasValue)
{
MessageDlg.Show(this, Resources.EditStaticModDlg_OkDialog_Labeled_atoms_on_terminal_modification_are_not_valid);
return;
}
RelativeRT relativeRT = RelativeRT.Matching;
if (comboRelativeRT.Visible && comboRelativeRT.SelectedItem != null)
{
relativeRT = RelativeRTExtension.GetEnum(comboRelativeRT.SelectedItem.ToString());
}
// Store state of the chemical formula checkbox for next use.
if (cbChemicalFormula.Visible)
{
Settings.Default.ShowHeavyFormula = _formulaBox.FormulaVisible;
}
var newMod = new StaticMod(name,
aas,
term,
cbVariableMod.Checked,
formula,
labelAtoms,
relativeRT,
monoMass,
avgMass,
losses);
foreach (StaticMod mod in _existing)
{
if (newMod.Equivalent(mod) && !(_editing && mod.Equals(_originalModification)))
{
if (DialogResult.OK == MultiButtonMsgDlg.Show(
this,
TextUtil.LineSeparate(Resources.EditStaticModDlg_OkDialog_There_is_an_existing_modification_with_the_same_settings,
string.Format("'{0}'.", mod.Name), // Not L10N
string.Empty,
Resources.EditStaticModDlg_OkDialog_Continue),
MultiButtonMsgDlg.BUTTON_OK))
{
Modification = newMod;
DialogResult = DialogResult.OK;
}
return;
}
}
var uniMod = UniMod.GetModification(name, IsStructural);
// If the modification name is not found in Unimod, check if there exists a modification in Unimod that matches
// the dialog modification, and prompt the user to to use the Unimod modification instead.
if (uniMod == null)
{
var matchingMod = UniMod.FindMatchingStaticMod(newMod, IsStructural);
if (matchingMod != null &&
(ModNameAvailable(matchingMod.Name) ||
(_editing && Equals(matchingMod.Name, Modification.Name))))
{
var result = MultiButtonMsgDlg.Show(
this,
TextUtil.LineSeparate(Resources.EditStaticModDlg_OkDialog_There_is_a_Unimod_modification_with_the_same_settings,
string.Empty,
string.Format(Resources.EditStaticModDlg_OkDialog_Click__Unimod__to_use_the_name___0___, matchingMod.Name),
string.Format(Resources.EditStaticModDlg_OkDialog_Click__Custom__to_use_the_name___0___, name)),
Resources.EditStaticModDlg_OkDialog_Unimod,
Resources.EditStaticModDlg_OkDialog_Custom,
true);
if (result == DialogResult.Yes)
{
newMod = matchingMod.MatchVariableAndLossInclusion(newMod); // Unimod
}
if (result == DialogResult.Cancel)
{
return;
}
}
}
else
{
// If the dialog modification matches the modification of the same name in Unimod,
// use the UnimodId.
if (newMod.Equivalent(uniMod))
{
newMod = uniMod.MatchVariableAndLossInclusion(newMod);
}
else
{
// Finally, if the modification name is found in Unimod, but the modification in Unimod does not
// match the dialog modification, prompt the user to use the Unimod modification definition instead.
if (DialogResult.OK != MultiButtonMsgDlg.Show(
this,
TextUtil.LineSeparate(string.Format(Resources.EditStaticModDlg_OkDialog_This_modification_does_not_match_the_Unimod_specifications_for___0___, name),
string.Empty,
Resources.EditStaticModDlg_OkDialog_Use_non_standard_settings_for_this_name),
MultiButtonMsgDlg.BUTTON_OK))
{
return;
}
}
}
_modification = newMod;
DialogResult = DialogResult.OK;
}
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);
}
public StaticMod ChangeLabelAtoms(LabelAtoms prop)
{
return ChangeProp(ImClone(this), im => im.LabelAtoms = prop);
}
public static string GetHeavyFormula(char aa, LabelAtoms labelAtoms)
{
string formulaAA = AMINO_FORMULAS[aa];
if (string.IsNullOrEmpty(formulaAA))
throw new ArgumentOutOfRangeException(string.Format(Resources.SequenceMassCalc_GetHeavyFormula_No_formula_found_for_the_amino_acid___0__, aa));
string formulaHeavy = formulaAA;
if ((labelAtoms & LabelAtoms.C13) != 0)
formulaHeavy = formulaHeavy.Replace(BioMassCalc.C, BioMassCalc.C13);
if ((labelAtoms & LabelAtoms.N15) != 0)
formulaHeavy = formulaHeavy.Replace(BioMassCalc.N, BioMassCalc.N15);
if ((labelAtoms & LabelAtoms.O18) != 0)
formulaHeavy = formulaHeavy.Replace(BioMassCalc.O, BioMassCalc.O18);
if ((labelAtoms & LabelAtoms.H2) != 0)
formulaHeavy = formulaHeavy.Replace(BioMassCalc.H, BioMassCalc.H2);
return formulaHeavy + " - " + formulaAA; // Not L10N
}
public StaticMod(string name,
string aas,
ModTerminus? term,
bool isVariable,
string formula,
LabelAtoms labelAtoms,
RelativeRT relativeRT,
double? monoMass,
double? avgMass,
IList<FragmentLoss> losses,
int? uniModId,
string shortName)
: base(name)
{
AAs = aas;
Terminus = term;
IsVariable = IsExplicit = isVariable; // All variable mods are explicit
Formula = formula;
LabelAtoms = labelAtoms;
RelativeRT = relativeRT;
MonoisotopicMass = monoMass;
AverageMass = avgMass;
Losses = losses;
UnimodId = uniModId;
ShortName = shortName;
Validate();
}
public StaticMod(string name, string aas, ModTerminus? term, bool isVariable, string formula,
LabelAtoms labelAtoms, RelativeRT relativeRT, double? monoMass, double? avgMass, IList<FragmentLoss> losses)
: this(name, aas, term, isVariable, formula, labelAtoms, relativeRT, monoMass, avgMass, losses, null, null)
{
}
public StaticMod(string name, string aas, ModTerminus? term,
string formula, LabelAtoms labelAtoms, double? monoMass, double? avgMass)
: this(name, aas, term, false, formula, labelAtoms, RelativeRT.Matching, monoMass, avgMass, null, null, null)
{
}
public StaticMod(string name, string aas, ModTerminus? term, LabelAtoms labelAtoms)
: this(name, aas, term, null, labelAtoms, null, null)
{
}
protected override void DoTest()
{
// Clean-up before running the test
RunUI(() => SkylineWindow.ModifyDocument("Set default settings",
doc => doc.ChangeSettings(SrmSettingsList.GetDefault())));
// Test error conditions
BuildLibraryError("missing_charge.pep.XML", TestFilesDir.FullPath, "uw.edu");
BuildLibraryError("non_int_charge.pep.XML");
BuildLibraryError("zero_charge.pep.XML");
BuildLibraryError("truncated.pep.XML");
BuildLibraryError("no_such_file.pep.XML", "Failed to open");
BuildLibraryError("missing_mzxml.pep.XML", "Could not find spectrum file");
// 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());
RunUI(() => SkylineWindow.SwitchDocument(docNew, 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
RunUI(() => SkylineWindow.SwitchDocument(docNew, 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.
HashSet <string> setPeptides = new HashSet <string>();
var library = SkylineWindow.Document.Settings.PeptideSettings.Libraries.Libraries[0];
foreach (var libKey in library.Keys)
{
if (!libKey.IsModified)
{
setPeptides.Add(libKey.Sequence);
}
}
string cpasPeptides = string.Join("\n", setPeptides.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.");
}
