From 0c9a30c4b45f770b65effcf0564d5e99b63bab1f Mon Sep 17 00:00:00 2001 From: trishorts Date: Mon, 10 Feb 2025 15:32:12 -0600 Subject: [PATCH 1/2] use internal ions as default in top down search --- MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs | 1 + MetaMorpheus/GUI/Util/UpdateGUISettings.cs | 3 ++- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs b/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs index f4351efcf..e179053a8 100644 --- a/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs +++ b/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs @@ -902,6 +902,7 @@ private void ProteaseSpecificUpdate(object sender, SelectionChangedEventArgs e) CheckBoxNoQuant.IsChecked = true; MassDiffAccept3mm.IsChecked = true; maxModificationIsoformsTextBox.Text = "4096"; + MinInternalFragmentLengthTextBox.Text = "10"; //uncheck all variable mods foreach (var mod in VariableModTypeForTreeViewObservableCollection) { diff --git a/MetaMorpheus/GUI/Util/UpdateGUISettings.cs b/MetaMorpheus/GUI/Util/UpdateGUISettings.cs index 326829141..b24b451e3 100644 --- a/MetaMorpheus/GUI/Util/UpdateGUISettings.cs +++ b/MetaMorpheus/GUI/Util/UpdateGUISettings.cs @@ -83,9 +83,10 @@ public static bool UseTopDownRecommendedSettings() "\t-Use '60' for 'Deconvolution Max Assumed Charge State'\n" + "\t-Uncheck 'Trim MS2 Peaks'\n" + "\t-Uncheck all variable mods (Please use a GPTMD database instead)\n" + + "\t-GPTMD TASK ONLY: Search for only acetylation, phosphorylation, and oxidation of M\n\n" + "\t-SEARCH TASK ONLY: Check 'No Quantification'\n" + "\t-SEARCH TASK ONLY: Check '1, 2, or 3 Missed Monoisotopic Peaks'\n" + - "\t-GPTMD TASK ONLY: Search for only acetylation, phosphorylation, and oxidation of M\n\n" + + "\t-SEARCH TASK ONLY: Check 'Internal Ions - Min Internal Length 10'\n" + "Would you like to use these recommended settings?"); if (results.UseSettings) From 52b38d18bcf2036bc53bb74d9d5000cb99a8a5ff Mon Sep 17 00:00:00 2001 From: trishorts Date: Mon, 10 Feb 2025 15:38:10 -0600 Subject: [PATCH 2/2] update popup window sizze --- MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs | 1 + MetaMorpheus/GUI/Util/UpdateGUISettings.cs | 2 +- MetaMorpheus/GUI/Views/ProteaseSpecificParamsMsgBox.xaml | 4 ++-- 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs b/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs index e179053a8..1c41b1d58 100644 --- a/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs +++ b/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs @@ -902,6 +902,7 @@ private void ProteaseSpecificUpdate(object sender, SelectionChangedEventArgs e) CheckBoxNoQuant.IsChecked = true; MassDiffAccept3mm.IsChecked = true; maxModificationIsoformsTextBox.Text = "4096"; + InternalIonsCheckBox.IsChecked = true; MinInternalFragmentLengthTextBox.Text = "10"; //uncheck all variable mods foreach (var mod in VariableModTypeForTreeViewObservableCollection) diff --git a/MetaMorpheus/GUI/Util/UpdateGUISettings.cs b/MetaMorpheus/GUI/Util/UpdateGUISettings.cs index b24b451e3..e938456a5 100644 --- a/MetaMorpheus/GUI/Util/UpdateGUISettings.cs +++ b/MetaMorpheus/GUI/Util/UpdateGUISettings.cs @@ -83,7 +83,7 @@ public static bool UseTopDownRecommendedSettings() "\t-Use '60' for 'Deconvolution Max Assumed Charge State'\n" + "\t-Uncheck 'Trim MS2 Peaks'\n" + "\t-Uncheck all variable mods (Please use a GPTMD database instead)\n" + - "\t-GPTMD TASK ONLY: Search for only acetylation, phosphorylation, and oxidation of M\n\n" + + "\t-GPTMD TASK ONLY: Search for only acetylation, phosphorylation, and oxidation of M\n" + "\t-SEARCH TASK ONLY: Check 'No Quantification'\n" + "\t-SEARCH TASK ONLY: Check '1, 2, or 3 Missed Monoisotopic Peaks'\n" + "\t-SEARCH TASK ONLY: Check 'Internal Ions - Min Internal Length 10'\n" + diff --git a/MetaMorpheus/GUI/Views/ProteaseSpecificParamsMsgBox.xaml b/MetaMorpheus/GUI/Views/ProteaseSpecificParamsMsgBox.xaml index 731d0a1a6..ac6238fcc 100644 --- a/MetaMorpheus/GUI/Views/ProteaseSpecificParamsMsgBox.xaml +++ b/MetaMorpheus/GUI/Views/ProteaseSpecificParamsMsgBox.xaml @@ -5,12 +5,12 @@ xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" xmlns:local="clr-namespace:MetaMorpheusGUI" mc:Ignorable="d" - Height="253.921" Width="545.393" + Height="275" Width="545.393" WindowStartupLocation="CenterScreen" ResizeMode="NoResize"> -