protected override void DoTest()
{
// This test is quite specific to the input data set - needs results for all nodes to export the list. Shut off the special non-proteomic test mode, otherwise you get:
// To export a scheduled method, you must first choose a retention time predictor in Peptide Settings / Prediction, or import results for all peptides in the document.
TestSmallMolecules = false;
// For now, CSV files are produced with invariant culture because some manufacturers do not handle internationalized CSVs.
_cultureInfo = CultureInfo.InvariantCulture;
_fieldSeparator = TextUtil.GetCsvSeparator(_cultureInfo);
string isolationWidth = string.Format(_cultureInfo, "Narrow (~{0:0.0} m/z)", 1.3);
const double slens = 1.234;
// Load document which is already configured for DDA, and contains data for scheduling
string standardDocumentFile = TestFilesDir.GetTestPath("BSA_Protea_label_free_meth3.sky");
RunUI(() => { SkylineWindow.OpenFile(standardDocumentFile); });
WaitForDocumentLoaded();
if (SmallMoleculeTestMode != RefinementSettings.ConvertToSmallMoleculesMode.none)
{
ConvertDocumentToSmallMolecules(SmallMoleculeTestMode, AsSmallMoleculesNegativeMode);
WaitForDocumentLoaded();
}
var t46 = 46.790;
var t39 = 39.900;
var halfWin = 1.0;
if (AsExplicitRetentionTimes)
{
const double timeOffset = 10; // To verify that explicit retention times are in use
const double winOffset = .4;
RunUI(() => SkylineWindow.ModifyDocument("Convert to explicit retention times", document =>
{
var refine = new RefinementSettings();
return(refine.ConvertToExplicitRetentionTimes(document, timeOffset, winOffset));
}));
t46 += timeOffset;
t39 += timeOffset;
halfWin += winOffset * 0.5;
}
// Conversion to negative charge states shifts the masses
var mzFirst = AsSmallMoleculesNegative ? 580.304419 : 582.318971;
var mzLast = AsSmallMoleculesNegative ? 442.535468 : 444.55002;
var zFirst = AsSmallMoleculesNegative ? -2 : 2;
var zLast = AsSmallMoleculesNegative ? -3 : 3;
var ceFirst = AsSmallMoleculesNegative ? 20.3 : 20.4;
var ceLast = AsSmallMoleculesNegative ? 19.1 : 19.2;
double?slensA = null;
double?slensB = null;
if (WithSLens)
{
slensA = slens;
slensB = ThermoMassListExporter.DEFAULT_SLENS;
}
// Export Agilent unscheduled DDA list.
ExportIsolationList(
"AgilentUnscheduledDda.csv",
ExportInstrumentType.AGILENT_TOF, FullScanAcquisitionMethod.None, ExportMethodType.Standard,
AgilentIsolationListExporter.GetDdaHeader(_fieldSeparator),
FieldSeparate("True", mzFirst, 20, zFirst, "Preferred", 0, string.Empty, isolationWidth, ceFirst),
FieldSeparate("True", mzLast, 20, zLast, "Preferred", 0, string.Empty, isolationWidth, ceLast));
// Export Agilent scheduled DDA list.
if (!AsSmallMoleculesNegative) // .skyd file chromatograms are not useful in this conversion due to mass shift
{
ExportIsolationList(
"AgilentScheduledDda.csv",
ExportInstrumentType.AGILENT_TOF, FullScanAcquisitionMethod.None, ExportMethodType.Scheduled,
AgilentIsolationListExporter.GetDdaHeader(_fieldSeparator),
FieldSeparate("True", mzFirst, 20, zFirst, "Preferred", t46, 2 * halfWin, isolationWidth, ceFirst),
FieldSeparate("True", mzLast, 20, zLast, "Preferred", t39, 2 * halfWin, isolationWidth, ceLast));
}
// Export Thermo unscheduled DDA list.
const double nce = ThermoQExactiveIsolationListExporter.NARROW_NCE;
var conversionDecorator = SmallMoleculeTestMode == RefinementSettings.ConvertToSmallMoleculesMode.none ?
string.Empty :
RefinementSettings.TestingConvertedFromProteomicPeptideNameDecorator;
bool AsSmallMoleculeMasses = (SmallMoleculeTestMode == RefinementSettings.ConvertToSmallMoleculesMode.masses_only);
var peptideA = AsSmallMoleculeMasses ?
CustomMolecule.INVARIANT_NAME_DETAIL + " [1162.623390/1163.328090] (light)" :
conversionDecorator + "LVNELTEFAK (light)";
var peptideB = AsSmallMoleculeMasses ?
CustomMolecule.INVARIANT_NAME_DETAIL + " [1330.628231/1331.376801] (light)" :
SmallMoleculeTestMode == RefinementSettings.ConvertToSmallMoleculesMode.none ?
conversionDecorator + "IKNLQS[+79.966331]LDPSH (light)" :
conversionDecorator + "IKNLQS[+80.0]LDPSH (light)";
var polarity = AsSmallMoleculesNegative ? "Negative" : "Positive";
var thermoQExactiveIsolationListExporter = new ThermoQExactiveIsolationListExporter(SkylineWindow.Document)
{
UseSlens = WithSLens
};
ExportIsolationList(
"ThermoUnscheduledDda.csv",
ExportInstrumentType.THERMO_Q_EXACTIVE, FullScanAcquisitionMethod.None, ExportMethodType.Standard,
thermoQExactiveIsolationListExporter.GetHeader(_fieldSeparator),
FieldSeparate(mzFirst, string.Empty, string.Empty, Math.Abs(zFirst), polarity, string.Empty, string.Empty, nce, slensA, peptideA),
FieldSeparate(mzLast, string.Empty, string.Empty, Math.Abs(zLast), polarity, string.Empty, string.Empty, nce, slensB, peptideB));
// Export Thermo scheduled DDA list.
if (!AsSmallMoleculesNegative) // .skyd file chromatograms are not useful in this conversion due to mass shift
{
ExportIsolationList(
"ThermoScheduledDda.csv",
ExportInstrumentType.THERMO_Q_EXACTIVE, FullScanAcquisitionMethod.None, ExportMethodType.Scheduled,
thermoQExactiveIsolationListExporter.GetHeader(_fieldSeparator),
FieldSeparate(mzFirst, string.Empty, string.Empty, Math.Abs(zFirst), polarity, t46 - halfWin, t46 + halfWin, nce, slensA, peptideA),
FieldSeparate(mzLast, string.Empty, string.Empty, Math.Abs(zLast), polarity, t39 - halfWin, t39 + halfWin, nce, slensB, peptideB));
}
// Export Agilent unscheduled Targeted list.
ExportIsolationList(
"AgilentUnscheduledTargeted.csv",
ExportInstrumentType.AGILENT_TOF, FullScanAcquisitionMethod.Targeted, ExportMethodType.Standard,
AgilentIsolationListExporter.GetTargetedHeader(_fieldSeparator),
FieldSeparate("True", mzFirst, zFirst, 0, string.Empty, isolationWidth, ceFirst, string.Empty),
FieldSeparate("True", mzLast, zLast, 0, string.Empty, isolationWidth, ceLast, string.Empty));
// Export Agilent scheduled Targeted list.
if (!AsSmallMoleculesNegative) // .skyd file chromatograms are not useful in this conversion due to mass shift
{
ExportIsolationList(
"AgilentScheduledTargeted.csv",
ExportInstrumentType.AGILENT_TOF, FullScanAcquisitionMethod.Targeted, ExportMethodType.Scheduled,
AgilentIsolationListExporter.GetTargetedHeader(_fieldSeparator),
FieldSeparate("True", mzFirst, zFirst, t46, 2 * halfWin, isolationWidth, ceFirst, string.Empty),
FieldSeparate("True", mzLast, zLast, t39, 2 * halfWin, isolationWidth, ceLast, string.Empty));
}
// Export Thermo unscheduled Targeted list.
ExportIsolationList(
"ThermoUnscheduledTargeted.csv",
ExportInstrumentType.THERMO_Q_EXACTIVE, FullScanAcquisitionMethod.Targeted, ExportMethodType.Standard,
thermoQExactiveIsolationListExporter.GetHeader(_fieldSeparator),
FieldSeparate(mzFirst, string.Empty, string.Empty, Math.Abs(zFirst), polarity, string.Empty, string.Empty, nce, slensA, peptideA),
FieldSeparate(mzLast, string.Empty, string.Empty, Math.Abs(zLast), polarity, string.Empty, string.Empty, nce, slensB, peptideB));
// Export Thermo scheduled Targeted list.
if (!AsSmallMoleculesNegative) // .skyd file chromatograms are not useful in this conversion due to mass shift
{
ExportIsolationList(
"ThermoScheduledTargeted.csv",
ExportInstrumentType.THERMO_Q_EXACTIVE, FullScanAcquisitionMethod.Targeted, ExportMethodType.Scheduled,
thermoQExactiveIsolationListExporter.GetHeader(_fieldSeparator),
FieldSeparate(mzFirst, string.Empty, string.Empty, Math.Abs(zFirst), polarity, t46 - halfWin, t46 + halfWin, nce, slensA, peptideA),
FieldSeparate(mzLast, string.Empty, string.Empty, Math.Abs(zLast), polarity, t39 - halfWin, t39 + halfWin, nce, slensB, peptideB));
}
// Export Thermo Fusion unscheduled Targeted list.
var thermoFusionMassListExporter = new ThermoFusionMassListExporter(SkylineWindow.Document)
{
UseSlens = WithSLens
};
ExportIsolationList(
"FusionUnscheduledTargeted.csv",
ExportInstrumentType.THERMO_FUSION, FullScanAcquisitionMethod.Targeted, ExportMethodType.Standard,
thermoFusionMassListExporter.GetHeader(_fieldSeparator),
FieldSeparate(mzFirst, zFirst, string.Empty, string.Empty, nce),
FieldSeparate(mzLast, zLast, string.Empty, string.Empty, nce));
// Export Thermo Fusion scheduled Targeted list.
if (!AsSmallMoleculesNegative) // .skyd file chromatograms are not useful in this conversion due to mass shift
{
ExportIsolationList(
"FusionScheduledTargeted.csv",
ExportInstrumentType.THERMO_FUSION, FullScanAcquisitionMethod.Targeted, ExportMethodType.Scheduled,
thermoFusionMassListExporter.GetHeader(_fieldSeparator),
FieldSeparate(mzFirst, zFirst, t46 - halfWin, t46 + halfWin, nce, slensA),
FieldSeparate(mzLast, zLast, t39 - halfWin, t39 + halfWin, nce, slensB));
}
string fragmentsFirst;
if (!AsSmallMoleculesNegative)
{
fragmentsFirst = FieldSeparate("582.3190", "951.4782", "595.3086", "708.3927", "837.4353", "1017.5251");
}
else
{
fragmentsFirst = FieldSeparate("580.3044", "595.3097", "708.3938", "837.4364", "951.4793", "1017.5262");
}
string fragmentsLast;
if (!AsSmallMoleculesNegative)
{
fragmentsLast = FieldSeparate("444.5500", "496.7443", "340.1615", "406.8553", "609.7794", "545.7319");
}
else
{
fragmentsLast = FieldSeparate("340.1626", "406.8564", "442.5355", "455.1896", "488.7115", "496.7454");
}
var rtFirst = !AsExplicitRetentionTimes
? FieldSeparate("45.8", "47.8")
: FieldSeparate("55.6", "58.0");
var rtLast = !AsExplicitRetentionTimes
? FieldSeparate("38.9", "40.9")
: FieldSeparate("48.7", "51.1");
var trapCeFirstTrap = !AsSmallMoleculesNegative
? FieldSeparate("21.2", "27.9")
: FieldSeparate("21.2", "27.8");
var trapCeLastTrap = !AsSmallMoleculesNegative
? FieldSeparate("17.3", "23.0")
: FieldSeparate("17.2", "23.0");
var trapCeFirstTransfer = !AsSmallMoleculesNegative
? FieldSeparate("26.2", "32.9")
: FieldSeparate("26.2", "32.8");
var trapCeLastTransfer = !AsSmallMoleculesNegative
? FieldSeparate("22.3", "28.0")
: FieldSeparate("22.2", "28.0");
// Export Waters Synapt (trap region) unscheduled Targeted list
ExportIsolationList(
"WatersTrapUnscheduledTargeted.mrm",
ExportInstrumentType.WATERS_SYNAPT_TRAP, FullScanAcquisitionMethod.Targeted, ExportMethodType.Standard,
WatersIsolationListExporter.GetHeader(_fieldSeparator),
FieldSeparate(0, "0.0", "30.0", mzFirst.ToString("0.0000", CultureInfo.InvariantCulture), fragmentsFirst, trapCeFirstTrap, "2.0", "2.0", 30, "0.0000", 0, 199),
FieldSeparate(0, "0.0", "30.0", mzLast.ToString("0.0000", CultureInfo.InvariantCulture), fragmentsLast, trapCeLastTrap, "2.0", "2.0", 30, "0.0000", 0, 199));
// Export Waters Synapt (trap region) scheduled Targeted list
if (!AsSmallMoleculesNegative || AsExplicitRetentionTimes) // Negative ions do not match results, so need explicit RTs for scheduling
{
ExportIsolationList(
"WatersTrapScheduledTargeted.mrm",
ExportInstrumentType.WATERS_SYNAPT_TRAP, FullScanAcquisitionMethod.Targeted, ExportMethodType.Scheduled,
WatersIsolationListExporter.GetHeader(_fieldSeparator),
FieldSeparate(0, rtFirst, mzFirst.ToString("0.0000", CultureInfo.InvariantCulture), fragmentsFirst, trapCeFirstTrap, "2.0", "2.0", 30, "0.0000", 0, 199),
FieldSeparate(0, rtLast, mzLast.ToString("0.0000", CultureInfo.InvariantCulture), fragmentsLast, trapCeLastTrap, "2.0", "2.0", 30, "0.0000", 0, 199));
}
// Export Waters Synapt (transfer region) unscheduled Targeted list
ExportIsolationList(
"WatersTransferUnscheduledTargeted.mrm",
ExportInstrumentType.WATERS_SYNAPT_TRANSFER, FullScanAcquisitionMethod.Targeted, ExportMethodType.Standard,
WatersIsolationListExporter.GetHeader(_fieldSeparator),
FieldSeparate(0, "0.0", "30.0", mzFirst.ToString("0.0000", CultureInfo.InvariantCulture), fragmentsFirst, "4.0", "4.0", trapCeFirstTransfer, 30, "0.0000", 0, 199),
FieldSeparate(0, "0.0", "30.0", mzLast.ToString("0.0000", CultureInfo.InvariantCulture), fragmentsLast, "4.0", "4.0", trapCeLastTransfer, 30, "0.0000", 0, 199));
// Export Waters Synapt (transfer region) scheduled Targeted list
if (!AsSmallMoleculesNegative || AsExplicitRetentionTimes) // Negative ions do not match results, so need explicit RTs for scheduling
{
ExportIsolationList(
"WatersTransferScheduledTargeted.mrm",
ExportInstrumentType.WATERS_SYNAPT_TRANSFER, FullScanAcquisitionMethod.Targeted, ExportMethodType.Scheduled,
WatersIsolationListExporter.GetHeader(_fieldSeparator),
FieldSeparate(0, rtFirst, mzFirst.ToString("0.0000", CultureInfo.InvariantCulture), fragmentsFirst, "4.0", "4.0", trapCeFirstTransfer, 30, "0.0000", 0, 199),
FieldSeparate(0, rtLast, mzLast.ToString("0.0000", CultureInfo.InvariantCulture), fragmentsLast, "4.0", "4.0", trapCeLastTransfer, 30, "0.0000", 0, 199));
}
// Export Waters Xevo unscheduled Targeted list
ExportIsolationList(
"WatersXevoUnscheduledTargeted.mrm",
ExportInstrumentType.WATERS_XEVO_QTOF, FullScanAcquisitionMethod.Targeted, ExportMethodType.Standard,
WatersIsolationListExporter.GetHeader(_fieldSeparator),
FieldSeparate(0, "0.0", "30.0", mzFirst.ToString("0.0000", CultureInfo.InvariantCulture), fragmentsFirst, trapCeFirstTrap, 30, "0.0000", 0, 199),
FieldSeparate(0, "0.0", "30.0", mzLast.ToString("0.0000", CultureInfo.InvariantCulture), fragmentsLast, trapCeLastTrap, 30, "0.0000", 0, 199));
// Export Waters Xevo scheduled Targeted list
if (!AsSmallMoleculesNegative || AsExplicitRetentionTimes) // Negative ions do not match results, so need explicit RTs for scheduling
{
ExportIsolationList(
"WatersXevoScheduledTargeted.mrm",
ExportInstrumentType.WATERS_XEVO_QTOF, FullScanAcquisitionMethod.Targeted, ExportMethodType.Scheduled,
WatersIsolationListExporter.GetHeader(_fieldSeparator),
FieldSeparate(0, rtFirst, mzFirst.ToString("0.0000", CultureInfo.InvariantCulture), fragmentsFirst, trapCeFirstTrap, 30, "0.0000", 0, 199),
FieldSeparate(0, rtLast, mzLast.ToString("0.0000", CultureInfo.InvariantCulture), fragmentsLast, trapCeLastTrap, 30, "0.0000", 0, 199));
}
// Check error if analyzer is not set correctly.
CheckMassAnalyzer(ExportInstrumentType.AGILENT_TOF, FullScanMassAnalyzerType.tof);
CheckMassAnalyzer(ExportInstrumentType.THERMO_Q_EXACTIVE, FullScanMassAnalyzerType.orbitrap);
}