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Top down default use internal ions #2469

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merged 2 commits into from
Feb 11, 2025
Merged

Top down default use internal ions #2469

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0c9a30c
use internal ions as default in top down search
trishorts Feb 10, 2025
52b38d1
update popup window sizze
trishorts Feb 10, 2025
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2 changes: 2 additions & 0 deletions MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -902,6 +902,8 @@ 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)
{
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3 changes: 2 additions & 1 deletion MetaMorpheus/GUI/Util/UpdateGUISettings.cs
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Expand Up @@ -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" +
"\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)
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4 changes: 2 additions & 2 deletions MetaMorpheus/GUI/Views/ProteaseSpecificParamsMsgBox.xaml
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Expand Up @@ -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">
<Grid Margin="5,5,5,5">
<StackPanel>
<Label Name="Label" Margin="5" Height="150" Width="500"/>
<Label Name="Label" Margin="5" Width="600"/>
<CheckBox Name="DoNotAskAgainCheckBox" Content="Remember my decision and don't ask me again." HorizontalAlignment="Center">
<ToolTipService.ToolTip>
<ToolTip Content="This decision can be changed by editing the file MetaMorpheus/GUIsettings.toml" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
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