diff --git a/pwiz_tools/Skyline/Model/AbstractDdaSearchEngine.cs b/pwiz_tools/Skyline/Model/AbstractDdaSearchEngine.cs index 2e6fe46b91..711363df00 100644 --- a/pwiz_tools/Skyline/Model/AbstractDdaSearchEngine.cs +++ b/pwiz_tools/Skyline/Model/AbstractDdaSearchEngine.cs @@ -53,7 +53,7 @@ public class Setting : IAuditLogObject public Setting(string name, int defaultValue, int minValue = int.MinValue, int maxValue = int.MaxValue) { Name = name; - _value = defaultValue; + _value = DefaultValue = defaultValue; MinValue = minValue; MaxValue = maxValue; } @@ -61,7 +61,7 @@ public Setting(string name, int defaultValue, int minValue = int.MinValue, int m public Setting(string name, double defaultValue, double minValue = double.MinValue, double maxValue = double.MaxValue) { Name = name; - _value = defaultValue; + _value = DefaultValue = defaultValue; MinValue = minValue; MaxValue = maxValue; } @@ -69,7 +69,7 @@ public Setting(string name, double defaultValue, double minValue = double.MinVal public Setting(string name, bool defaultValue) { Name = name; - _value = defaultValue; + _value = DefaultValue = defaultValue; MinValue = false; MaxValue = true; } @@ -78,16 +78,16 @@ public Setting(string name, string defaultValue = null, IEnumerable vali { Name = name; MinValue = string.Empty; - _value = defaultValue ?? string.Empty; + _value = DefaultValue = defaultValue ?? string.Empty; ValidValues = validValues; } - public Setting(Setting other) + public Setting(Setting other, object newValue = null) { Name = other.Name; MinValue = other.MinValue; MaxValue = other.MaxValue; - _value = other.Value; + _value = DefaultValue = newValue ?? other.Value; ValidValues = other.ValidValues; } @@ -104,6 +104,9 @@ public object Value set { _value = Validate(value); } } + public object DefaultValue { get; } + public bool IsDefault => Equals(DefaultValue, _value); + public object Validate(object value) { // incoming value must either be a string or value type must stay the same diff --git a/pwiz_tools/Skyline/Model/DdaSearch/MsFraggerSearchEngine.cs b/pwiz_tools/Skyline/Model/DdaSearch/MsFraggerSearchEngine.cs index ed2500405f..8183856d15 100644 --- a/pwiz_tools/Skyline/Model/DdaSearch/MsFraggerSearchEngine.cs +++ b/pwiz_tools/Skyline/Model/DdaSearch/MsFraggerSearchEngine.cs @@ -61,11 +61,14 @@ public enum DataType dia_gpf = 2 } - private bool DataIsDIA => (DataType) AdditionalSettings[@"data_type"].Value != DataType.dda; - private string PepXmlSuffix => DataIsDIA ? @"_rank1.pepXML" : @".pepXML"; + private readonly DataType _initialDataType; + private bool DataIsDIA => _initialDataType != DataType.dda; + private string PepXmlSuffix => (DataType) AdditionalSettings[@"data_type"].Value != DataType.dda ? @"_rank1.pepXML" : @".pepXML"; public MsFraggerSearchEngine(DataType dataType) { + _initialDataType = dataType; + AdditionalSettings = new Dictionary { {CHECK_SPECTRAL_FILES, new Setting(CHECK_SPECTRAL_FILES, 1, 0, 1)}, @@ -148,6 +151,23 @@ private void AddAdditionalSetting(List settingNameList, Setting setting) AdditionalSettings[setting.Name] = setting; } + private Dictionary _replacedAdditionalSettings = new Dictionary(); + private void ReplaceAdditionalSettingIfDefault(string settingName, object newValue) + { + if (!AdditionalSettings[settingName].IsDefault) + return; + _replacedAdditionalSettings[settingName] = AdditionalSettings[settingName]; + AdditionalSettings[settingName] = new Setting(AdditionalSettings[settingName], newValue); + } + + private void RestoreAdditionalSettingIfDefault(string settingName) + { + if (!AdditionalSettings[settingName].IsDefault) + return; + AdditionalSettings[settingName] = _replacedAdditionalSettings[settingName]; + _replacedAdditionalSettings.Remove(settingName); + } + private static readonly string[] FRAGMENTATION_METHODS = { @"b,y", @@ -465,7 +485,7 @@ private void GetPercolatorScores(string percolatorTsvFilepath, Dictionary qvalueByPsmId, IProgressMonitor monitor) { bool isBrukerSource = DataSourceUtil.GetSourceType(spectrumFilename.GetFilePath()) == DataSourceUtil.TYPE_BRUKER; - var lastPsmIdRegex = new Regex(@".* spectrum=""([^""]+?)"" .*",RegexOptions.Compiled); + var lastPsmIdRegex = new Regex(@".* assumed_charge=""(\d+)"" spectrum=""([^""]+?)\.\d+"" .*", RegexOptions.Compiled); // This looks for an ampersand that is NOT followed by: // - "amp;", "lt;", "gt;", "quot;", "apos;" (predefined XML entities) @@ -486,14 +506,17 @@ private void FixPercolatorPepXml(string cruxOutputFilepath, string finalOutputFi line = unescapedAmpersandRegex.Replace(line, @"&"); } if (line.Contains(@"", qvalueByPsmId[lastPsmId].ToString(CultureInfo.InvariantCulture)); // MCC: This happens when percolator's text tables drops a PSM that is in pepXML; I'm not sure why it happens though. - //else - // Console.WriteLine($"{lastPsmId} not found in percolator scores."); + else + { + fixedPepXmlFile.WriteLine(@""); + //Console.WriteLine($"{lastPsmId} not found in percolator scores."); + } } else if (line.Contains(@"")) { @@ -1000,9 +1023,57 @@ public override void SetMs2Analyzer(string ms2Analyzer) // not used by MSFragger } + private static bool IsLowRes(MzTolerance mzTolerance) + { + if (mzTolerance == null || mzTolerance.Value == 0) + return false; + return mzTolerance.Unit == MzTolerance.Units.ppm + ? mzTolerance.Value > 50 + : mzTolerance.Value > 0.05 /* Da */; + } + public override void SetPrecursorMassTolerance(MzTolerance mzTolerance) { + bool wasLowRes = IsLowRes(_precursorMzTolerance); + _precursorMzTolerance = mzTolerance; + + if (!DataIsDIA) + return; + + // Use DDA settings for DIA if precursor tolerance is not high resolution: + // From Alexey: running as DDA data, with +- 3 Da window, 0.2 Da, 100 peaks per spectrum, charge state 1 fragments for scoring only + bool nowLowRes = IsLowRes(mzTolerance); + bool lowResChanged = wasLowRes != nowLowRes; + if (!lowResChanged) + return; + + if (nowLowRes) + { + ReplaceAdditionalSettingIfDefault(@"data_type", (int) DataType.dda); + ReplaceAdditionalSettingIfDefault(@"calibrate_mass", 0); + ReplaceAdditionalSettingIfDefault(@"deisotope", 0); + ReplaceAdditionalSettingIfDefault(@"deneutralloss", 0); + ReplaceAdditionalSettingIfDefault(@"intensity_transform", 0); + //ReplaceAdditionalSettingIfDefault(@"output_report_topN", 1); + ReplaceAdditionalSettingIfDefault(@"precursor_charge", @"1 4"); + ReplaceAdditionalSettingIfDefault(@"max_fragment_charge", 1); + ReplaceAdditionalSettingIfDefault(@"use_topN_peaks", 100); + ReplaceAdditionalSettingIfDefault(@"minimum_ratio", 0.01); + } + else + { + RestoreAdditionalSettingIfDefault(@"data_type"); + RestoreAdditionalSettingIfDefault(@"calibrate_mass"); + RestoreAdditionalSettingIfDefault(@"deisotope"); + RestoreAdditionalSettingIfDefault(@"deneutralloss"); + RestoreAdditionalSettingIfDefault(@"intensity_transform"); + //RestoreAdditionalSettingIfDefault(@"output_report_topN"); + RestoreAdditionalSettingIfDefault(@"precursor_charge"); + RestoreAdditionalSettingIfDefault(@"max_fragment_charge"); + RestoreAdditionalSettingIfDefault(@"use_topN_peaks"); + RestoreAdditionalSettingIfDefault(@"minimum_ratio"); + } } public override void SetCutoffScore(double cutoffScore) diff --git a/pwiz_tools/Skyline/TestPerf/DiaSearchTutorialTest.cs b/pwiz_tools/Skyline/TestPerf/DiaSearchTutorialTest.cs index 89dd6d5fe2..a7a4685e5e 100644 --- a/pwiz_tools/Skyline/TestPerf/DiaSearchTutorialTest.cs +++ b/pwiz_tools/Skyline/TestPerf/DiaSearchTutorialTest.cs @@ -67,6 +67,8 @@ private class AnalysisValues public string ProteinToSelect; public string PeptideToSelect; + public MzTolerance PrecursorMzTolerance; + public MzTolerance FragmentMzTolerance; public Dictionary AdditionalSettings; } @@ -90,7 +92,7 @@ public void TestDiaSearchStellarTutorial() IsolationSchemeHasGaps = true, IsolationSchemeHasOverlaps = false, - FinalTargetCounts = new[] { 3801, 4730, 4730, 30353 }, + FinalTargetCounts = new[] { 107, 145, 145, 910 }, ZipPath = "https://skyline.ms/tutorials/DiaSearchTutorial.zip", DiaFiles = new[] { @@ -99,9 +101,11 @@ public void TestDiaSearchStellarTutorial() }, IsGpfData = true, - ProteinToSelect = "sp|P01591|IGJ_HUMAN", - PeptideToSelect = "ENISDPTSPLR", + ProteinToSelect = "sp|O15240|VGF_HUMAN", + PeptideToSelect = "LADLASDLLLQYLLQGGAR", + PrecursorMzTolerance = new MzTolerance(3.0), + FragmentMzTolerance = new MzTolerance(0.2), AdditionalSettings = new Dictionary { //{ "data_type", "2" } // set MSFragger to GPF mode @@ -157,6 +161,9 @@ public void TestDiaSearchQeTutorial() ProteinToSelect = "sp|P21333|FLNA_HUMAN", PeptideToSelect = "IANLQTDLSDGLR", + + PrecursorMzTolerance = new MzTolerance(10, MzTolerance.Units.ppm), + FragmentMzTolerance = new MzTolerance(10, MzTolerance.Units.ppm), }; TestFilesZipPaths = new[] @@ -391,8 +398,8 @@ private void TestMsFraggerSearch() RunUI(() => { - importPeptideSearchDlg.SearchSettingsControl.PrecursorTolerance = new MzTolerance(10, MzTolerance.Units.ppm); - importPeptideSearchDlg.SearchSettingsControl.FragmentTolerance = new MzTolerance(10, MzTolerance.Units.ppm); + importPeptideSearchDlg.SearchSettingsControl.PrecursorTolerance = _analysisValues.PrecursorMzTolerance; + importPeptideSearchDlg.SearchSettingsControl.FragmentTolerance = _analysisValues.FragmentMzTolerance; // Using the default q value of 0.01 (FDR 1%) is best for teaching and requires less explaining // importPeptideSearchDlg.SearchSettingsControl.CutoffScore = 0.05; importPeptideSearchDlg.SearchSettingsControl.SetAdditionalSetting("check_spectral_files", "0"); @@ -406,7 +413,7 @@ private void TestMsFraggerSearch() }); PauseForScreenShot("Import Peptide Search - Search Settings page", tutorialPage++); - WaitForConditionUI(() => MzTolerance.Units.ppm == importPeptideSearchDlg.SearchSettingsControl.FragmentTolerance.Unit); + WaitForConditionUI(() => _analysisValues.FragmentMzTolerance.Unit == importPeptideSearchDlg.SearchSettingsControl.FragmentTolerance.Unit); // Run the search SkylineWindow.BeginInvoke(new Action(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()))); diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaSearchStellarTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaSearchStellarTutorial.log index 0f90210513..2f6cc7f1f6 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaSearchStellarTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/en/TestDiaSearchStellarTutorial.log @@ -52,14 +52,14 @@ Import Peptide Search > Associate Proteins > Find minimal protein list is False Import Peptide Search > Associate Proteins > Remove subset proteins is False Import Peptide Search > Associate Proteins > Shared peptides option is "Assigned to first protein" Import Peptide Search > Associate Proteins > Min peptides per protein is "1" -Import Peptide Search > Associate Proteins > Proteins mapped is "3988" -Import Peptide Search > Associate Proteins > Peptides mapped is "4720" -Import Peptide Search > Associate Proteins > Proteins unmapped is "16383" -Import Peptide Search > Associate Proteins > Protein targets is "3801" -Import Peptide Search > Associate Proteins > Peptide targets is "4730" +Import Peptide Search > Associate Proteins > Proteins mapped is "136" +Import Peptide Search > Associate Proteins > Peptides mapped is "143" +Import Peptide Search > Associate Proteins > Proteins unmapped is "20235" +Import Peptide Search > Associate Proteins > Protein targets is "107" +Import Peptide Search > Associate Proteins > Peptide targets is "145" Import Peptide Search > DDA search settings > Search Engine is "MSFragger" -Import Peptide Search > DDA search settings > Precursor tolerance is "10" ppm -Import Peptide Search > DDA search settings > Fragment tolerance is "10" ppm +Import Peptide Search > DDA search settings > Precursor tolerance is "3" m/z +Import Peptide Search > DDA search settings > Fragment tolerance is "0.2" m/z Import Peptide Search > DDA search settings > Max variable mods per peptide is "3" Import Peptide Search > DDA search settings > Fragment ion types is "b,y" Import Peptide Search > DDA search settings > Score type is "Max q-value" @@ -95,17 +95,17 @@ Associate Proteins = Remove subset proteins = False, Shared peptides option = "Assigned to first protein", Min peptides per protein = "1", - Proteins mapped = "3988", - Peptides mapped = "4720", - Proteins unmapped = "16383", - Protein targets = "3801", - Peptide targets = "4730" + Proteins mapped = "136", + Peptides mapped = "143", + Proteins unmapped = "20235", + Protein targets = "107", + Peptide targets = "145" }, DDA search settings = { Search Engine = "MSFragger", - Precursor tolerance = "10" ppm, - Fragment tolerance = "10" ppm, + Precursor tolerance = "3" m/z, + Fragment tolerance = "0.2" m/z, Max variable mods per peptide = "3", Fragment ion types = "b,y", Score type = "Max q-value", diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaSearchStellarTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaSearchStellarTutorial.log index 4379639d9f..cf09f12dbb 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaSearchStellarTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/fr/TestDiaSearchStellarTutorial.log @@ -52,14 +52,14 @@ Import Peptide Search > Associate Proteins > Find minimal protein list is False Import Peptide Search > Associate Proteins > Remove subset proteins is False Import Peptide Search > Associate Proteins > Shared peptides option is "Assigned to first protein" Import Peptide Search > Associate Proteins > Min peptides per protein is "1" -Import Peptide Search > Associate Proteins > Proteins mapped is "3988" -Import Peptide Search > Associate Proteins > Peptides mapped is "4720" -Import Peptide Search > Associate Proteins > Proteins unmapped is "16383" -Import Peptide Search > Associate Proteins > Protein targets is "3801" -Import Peptide Search > Associate Proteins > Peptide targets is "4730" +Import Peptide Search > Associate Proteins > Proteins mapped is "136" +Import Peptide Search > Associate Proteins > Peptides mapped is "143" +Import Peptide Search > Associate Proteins > Proteins unmapped is "20235" +Import Peptide Search > Associate Proteins > Protein targets is "107" +Import Peptide Search > Associate Proteins > Peptide targets is "145" Import Peptide Search > DDA search settings > Search Engine is "MSFragger" -Import Peptide Search > DDA search settings > Precursor tolerance is "10" ppm -Import Peptide Search > DDA search settings > Fragment tolerance is "10" ppm +Import Peptide Search > DDA search settings > Precursor tolerance is "3" m/z +Import Peptide Search > DDA search settings > Fragment tolerance is "0,2" m/z Import Peptide Search > DDA search settings > Max variable mods per peptide is "3" Import Peptide Search > DDA search settings > Fragment ion types is "b,y" Import Peptide Search > DDA search settings > Score type is "Max q-value" @@ -95,17 +95,17 @@ Associate Proteins = Remove subset proteins = False, Shared peptides option = "Assigned to first protein", Min peptides per protein = "1", - Proteins mapped = "3988", - Peptides mapped = "4720", - Proteins unmapped = "16383", - Protein targets = "3801", - Peptide targets = "4730" + Proteins mapped = "136", + Peptides mapped = "143", + Proteins unmapped = "20235", + Protein targets = "107", + Peptide targets = "145" }, DDA search settings = { Search Engine = "MSFragger", - Precursor tolerance = "10" ppm, - Fragment tolerance = "10" ppm, + Precursor tolerance = "3" m/z, + Fragment tolerance = "0,2" m/z, Max variable mods per peptide = "3", Fragment ion types = "b,y", Score type = "Max q-value", diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaSearchStellarTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaSearchStellarTutorial.log index 08b753805d..4cfba4b79c 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaSearchStellarTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/ja/TestDiaSearchStellarTutorial.log @@ -52,14 +52,14 @@ All Info : ペプチド検索のインポート>タンパク質の関連付け>サブセットのタンパク質を削除は偽です ペプチド検索のインポート>タンパク質の関連付け>共有ペプチドオプションは"最初のタンパク質に割当て"です ペプチド検索のインポート>タンパク質の関連付け>タンパク質あたりの最小ペプチドは"1"です -ペプチド検索のインポート>タンパク質の関連付け>マップ済みタンパク質は"3988"です -ペプチド検索のインポート>タンパク質の関連付け>マップ済みペプチドは"4720"です -ペプチド検索のインポート>タンパク質の関連付け>マップ解除されたタンパク質は"16383"です -ペプチド検索のインポート>タンパク質の関連付け>タンパク質のターゲットは"3801"です -ペプチド検索のインポート>タンパク質の関連付け>ペプチドのターゲットは"4730"です +ペプチド検索のインポート>タンパク質の関連付け>マップ済みタンパク質は"136"です +ペプチド検索のインポート>タンパク質の関連付け>マップ済みペプチドは"143"です +ペプチド検索のインポート>タンパク質の関連付け>マップ解除されたタンパク質は"20235"です +ペプチド検索のインポート>タンパク質の関連付け>タンパク質のターゲットは"107"です +ペプチド検索のインポート>タンパク質の関連付け>ペプチドのターゲットは"145"です ペプチド検索のインポート>DDA検索設定>検索エンジンは"MSFragger"です -ペプチド検索のインポート>DDA検索設定>プリカーサー許容範囲は"10" ppmです -ペプチド検索のインポート>DDA検索設定>フラグメント許容範囲は"10" ppmです +ペプチド検索のインポート>DDA検索設定>プリカーサー許容範囲は"3" m/zです +ペプチド検索のインポート>DDA検索設定>フラグメント許容範囲は"0.2" m/zです ペプチド検索のインポート>DDA検索設定>ペプチド当たりの最大可変修飾数は"3"です ペプチド検索のインポート>DDA検索設定>フラグメントイオンタイプは"b,y"です ペプチド検索のインポート>DDA検索設定>スコアタイプは"最大q値"です @@ -95,17 +95,17 @@ FASTAをインポート = サブセットのタンパク質を削除 = 偽, 共有ペプチドオプション = "最初のタンパク質に割当て", タンパク質あたりの最小ペプチド = "1", - マップ済みタンパク質 = "3988", - マップ済みペプチド = "4720", - マップ解除されたタンパク質 = "16383", - タンパク質のターゲット = "3801", - ペプチドのターゲット = "4730" + マップ済みタンパク質 = "136", + マップ済みペプチド = "143", + マップ解除されたタンパク質 = "20235", + タンパク質のターゲット = "107", + ペプチドのターゲット = "145" }, DDA検索設定 = { 検索エンジン = "MSFragger", - プリカーサー許容範囲 = "10" ppm, - フラグメント許容範囲 = "10" ppm, + プリカーサー許容範囲 = "3" m/z, + フラグメント許容範囲 = "0.2" m/z, ペプチド当たりの最大可変修飾数 = "3", フラグメントイオンタイプ = "b,y", スコアタイプ = "最大q値", diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaSearchStellarTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaSearchStellarTutorial.log index 4379639d9f..cf09f12dbb 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaSearchStellarTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/tr/TestDiaSearchStellarTutorial.log @@ -52,14 +52,14 @@ Import Peptide Search > Associate Proteins > Find minimal protein list is False Import Peptide Search > Associate Proteins > Remove subset proteins is False Import Peptide Search > Associate Proteins > Shared peptides option is "Assigned to first protein" Import Peptide Search > Associate Proteins > Min peptides per protein is "1" -Import Peptide Search > Associate Proteins > Proteins mapped is "3988" -Import Peptide Search > Associate Proteins > Peptides mapped is "4720" -Import Peptide Search > Associate Proteins > Proteins unmapped is "16383" -Import Peptide Search > Associate Proteins > Protein targets is "3801" -Import Peptide Search > Associate Proteins > Peptide targets is "4730" +Import Peptide Search > Associate Proteins > Proteins mapped is "136" +Import Peptide Search > Associate Proteins > Peptides mapped is "143" +Import Peptide Search > Associate Proteins > Proteins unmapped is "20235" +Import Peptide Search > Associate Proteins > Protein targets is "107" +Import Peptide Search > Associate Proteins > Peptide targets is "145" Import Peptide Search > DDA search settings > Search Engine is "MSFragger" -Import Peptide Search > DDA search settings > Precursor tolerance is "10" ppm -Import Peptide Search > DDA search settings > Fragment tolerance is "10" ppm +Import Peptide Search > DDA search settings > Precursor tolerance is "3" m/z +Import Peptide Search > DDA search settings > Fragment tolerance is "0,2" m/z Import Peptide Search > DDA search settings > Max variable mods per peptide is "3" Import Peptide Search > DDA search settings > Fragment ion types is "b,y" Import Peptide Search > DDA search settings > Score type is "Max q-value" @@ -95,17 +95,17 @@ Associate Proteins = Remove subset proteins = False, Shared peptides option = "Assigned to first protein", Min peptides per protein = "1", - Proteins mapped = "3988", - Peptides mapped = "4720", - Proteins unmapped = "16383", - Protein targets = "3801", - Peptide targets = "4730" + Proteins mapped = "136", + Peptides mapped = "143", + Proteins unmapped = "20235", + Protein targets = "107", + Peptide targets = "145" }, DDA search settings = { Search Engine = "MSFragger", - Precursor tolerance = "10" ppm, - Fragment tolerance = "10" ppm, + Precursor tolerance = "3" m/z, + Fragment tolerance = "0,2" m/z, Max variable mods per peptide = "3", Fragment ion types = "b,y", Score type = "Max q-value", diff --git a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaSearchStellarTutorial.log b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaSearchStellarTutorial.log index f9b007f64b..2f256ad68e 100644 --- a/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaSearchStellarTutorial.log +++ b/pwiz_tools/Skyline/TestTutorial/TutorialAuditLogs/zh/TestDiaSearchStellarTutorial.log @@ -52,14 +52,14 @@ All Info : 导入肽段搜索 > 关联蛋白质 > 删除蛋白质子集 是 假 导入肽段搜索 > 关联蛋白质 > 共享的肽段选项 是 "已分配给第一个蛋白质" 导入肽段搜索 > 关联蛋白质 > 每个蛋白质的最少肽段数 是 "1" -导入肽段搜索 > 关联蛋白质 > 映射的蛋白质 是 "3988" -导入肽段搜索 > 关联蛋白质 > 映射的肽段 是 "4720" -导入肽段搜索 > 关联蛋白质 > 取消映射的蛋白质 是 "16383" -导入肽段搜索 > 关联蛋白质 > 蛋白质目标 是 "3801" -导入肽段搜索 > 关联蛋白质 > 肽段目标 是 "4730" +导入肽段搜索 > 关联蛋白质 > 映射的蛋白质 是 "136" +导入肽段搜索 > 关联蛋白质 > 映射的肽段 是 "143" +导入肽段搜索 > 关联蛋白质 > 取消映射的蛋白质 是 "20235" +导入肽段搜索 > 关联蛋白质 > 蛋白质目标 是 "107" +导入肽段搜索 > 关联蛋白质 > 肽段目标 是 "145" 导入肽段搜索 > DDA 搜索设置 > 搜索引擎 是 "MSFragger" -导入肽段搜索 > DDA 搜索设置 > 母离子耐受性 是 "10" ppm -导入肽段搜索 > DDA 搜索设置 > 片段耐受性 是 "10" ppm +导入肽段搜索 > DDA 搜索设置 > 母离子耐受性 是 "3" 质荷比 +导入肽段搜索 > DDA 搜索设置 > 片段耐受性 是 "0.2" 质荷比 导入肽段搜索 > DDA 搜索设置 > 每个肽段的最大可变修饰数 是 "3" 导入肽段搜索 > DDA 搜索设置 > 碎片离子类型 是 "b,y" 导入肽段搜索 > DDA 搜索设置 > 得分类型 是 "最大 Q 值" @@ -95,17 +95,17 @@ Extra Info: 提取色谱图 = 删除蛋白质子集 = 假, 共享的肽段选项 = "已分配给第一个蛋白质", 每个蛋白质的最少肽段数 = "1", - 映射的蛋白质 = "3988", - 映射的肽段 = "4720", - 取消映射的蛋白质 = "16383", - 蛋白质目标 = "3801", - 肽段目标 = "4730" + 映射的蛋白质 = "136", + 映射的肽段 = "143", + 取消映射的蛋白质 = "20235", + 蛋白质目标 = "107", + 肽段目标 = "145" }, DDA 搜索设置 = { 搜索引擎 = "MSFragger", - 母离子耐受性 = "10" ppm, - 片段耐受性 = "10" ppm, + 母离子耐受性 = "3" 质荷比, + 片段耐受性 = "0.2" 质荷比, 每个肽段的最大可变修饰数 = "3", 碎片离子类型 = "b,y", 得分类型 = "最大 Q 值",