From 62dd8e2fe95c390c34697bb100b455156e729a36 Mon Sep 17 00:00:00 2001 From: alchemistmatt Date: Wed, 21 Feb 2024 13:38:55 -0800 Subject: [PATCH] Add documentation comment referencing the MSGF Results Summarizer --- CreateMSGFPlusResultsFileFromPHRP/Program.cs | 2 +- .../SearchToolResults/ToolResultsBaseClass.cs | 5 +++++ Program.cs | 2 +- 3 files changed, 7 insertions(+), 2 deletions(-) diff --git a/CreateMSGFPlusResultsFileFromPHRP/Program.cs b/CreateMSGFPlusResultsFileFromPHRP/Program.cs index 58485df..4467555 100644 --- a/CreateMSGFPlusResultsFileFromPHRP/Program.cs +++ b/CreateMSGFPlusResultsFileFromPHRP/Program.cs @@ -378,7 +378,7 @@ private static void ShowProgramHelp() Console.WriteLine("E-mail: matthew.monroe@pnnl.gov or proteomics@pnnl.gov"); Console.WriteLine("Website: https://github.com/PNNL-Comp-Mass-Spec/ or https://panomics.pnnl.gov/ or https://www.pnnl.gov/integrative-omics"); - // Delay for 750 msec in case the user double clicked this file from within Windows Explorer (or started the program via a shortcut) + // Delay for 750 msec in case the user double-clicked this file from within Windows Explorer (or started the program via a shortcut) Thread.Sleep(750); } catch (Exception ex) diff --git a/PeptideHitResultsProcessor/SearchToolResults/ToolResultsBaseClass.cs b/PeptideHitResultsProcessor/SearchToolResults/ToolResultsBaseClass.cs index 20a5169..141eada 100644 --- a/PeptideHitResultsProcessor/SearchToolResults/ToolResultsBaseClass.cs +++ b/PeptideHitResultsProcessor/SearchToolResults/ToolResultsBaseClass.cs @@ -312,6 +312,11 @@ public abstract class ToolResultsBaseClass /// /// From column Q.Value for DIA-NN /// + /// + /// The MSGF Results Summarizer filters on QValue when computing PSM stats, which are stored in the database using procedure store_job_psm_stats + /// Stats are displayed on the Analysis Job Detail Report page, for example: + /// Spectra Searched: 23949, Total PSMs: 12317, Unique Peptides: 10439, Unique Proteins: 2247 (FDR < 1.00%) + /// /// public double QValue; } diff --git a/Program.cs b/Program.cs index 74d6238..9748827 100644 --- a/Program.cs +++ b/Program.cs @@ -91,7 +91,7 @@ public static int Main(string[] args) return 0; } - // Delay for 750 msec in case the user double clicked this file from within Windows Explorer (or started the program via a shortcut) + // Delay for 750 msec in case the user double-clicked this file from within Windows Explorer (or started the program via a shortcut) Thread.Sleep(750); return -1;