v3.9.0

MainForm.cs

@@ -46,8 +46,6 @@ public partial class MainForm : RCPA.Gui.Command.CommandForm
   {
     public static readonly string version = RcpaToolsAssembly.Version;
 
-    public static bool PublishVersion { get; set; }
-
     public MainForm()
     {
       InitializeComponent();
@@ -202,11 +200,6 @@ public MainForm()
 
       AddCommand(new ToolCommandSeparator(MenuCommandType.Quantification));
 
-      //AddCommand(new AgilentToMS1BuilderUI.Command());
-
-#if (!PublicVersion)
-      AddCommand(new ToolCommandSeparator(MenuCommandType.Quantification));
-
       //AddCommand(new SmallMoleculeDataPreparationProcessorUI.Command());
       //AddCommand(new SmallMoleculeDataMostIntensityBuilderUI.Command());
       //AddCommand(new SmallMoleculeSignificantPeakFinderUI.Command());
@@ -217,7 +210,6 @@ public MainForm()
       AddCommand(new ForwardReverseRatioCalibratorUI.Command());
 
       AddCommand(new ProteinChromotographViewer.Command());
-#endif
 
       //Statistic
       AddCommand(new ProteinDistributionUI.Command());
@@ -274,14 +266,12 @@ public MainForm()
       //AddCommand(new AgilentFileViewerUI.Command());
       AddCommand(new GenerateIsotopicFileUI.Command());
 
-#if (!PublicVersion)
       AddCommand(new ToolCommandSeparator(MenuCommandType.Misc));
       AddCommand(new PNovoSAPValidatorUI.Command());
       AddCommand(new MascotSAPValidatorUI.Command());
       AddCommand(new CombineQuantificationResultProcessorUI.Command());
       AddCommand(new SpectrumSAPValidatorUI.Command());
       AddCommand(new IdentifiedPeptideValidatatorUI.Command());
-#endif
 
       //20111017
       AddCommand(new DatabaseSAPValidatorUI.Command());
@@ -312,6 +302,9 @@ public MainForm()
       //Setup
       AddCommand(new ExternalProgramConfigUI.Command());
 
+      AddCommand(new ToolCommandSeparator(MenuCommandType.Misc));
+      AddCommand(new AminoacidInsertionBuilderUI.Command());
+
       //Help
       AddCommand(new HelpCommand());
 

Properties/RcpaToolsAssembly.cs

@@ -15,6 +15,6 @@ static class RcpaToolsAssembly
   internal const string Author = "Quanhu SHENG";
   internal const string Company = "RCPA/CQS";
   internal const string Copyright = "Copyright (C) 2006-2015 " + Company;
-  internal const string Version = "3.8.8";
+  internal const string Version = "3.9.0";
   internal const string InformationalVersion = Version;
 }

RCPA.Tools.csproj

@@ -44,6 +44,7 @@
     <BootstrapperEnabled>true</BootstrapperEnabled>
     <SolutionDir Condition="$(SolutionDir) == '' Or $(SolutionDir) == '*Undefined*'">..\</SolutionDir>
     <RestorePackages>true</RestorePackages>
+    <NuGetPackageImportStamp>cc088643</NuGetPackageImportStamp>
   </PropertyGroup>
   <PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Debug|AnyCPU' ">
     <DebugSymbols>true</DebugSymbols>
@@ -68,7 +69,7 @@
     </DefineConstants>
     <ErrorReport>prompt</ErrorReport>
     <WarningLevel>4</WarningLevel>
-    <PlatformTarget>AnyCPU</PlatformTarget>
+    <PlatformTarget>x86</PlatformTarget>
     <CodeAnalysisRuleSet>AllRules.ruleset</CodeAnalysisRuleSet>
     <AllowUnsafeBlocks>true</AllowUnsafeBlocks>
     <Prefer32Bit>false</Prefer32Bit>
@@ -97,13 +98,29 @@
     <Reference Include="DigitalRune.Windows.Docking">
       <HintPath>..\SQH.Lib\DigitalRune.Windows.Docking.dll</HintPath>
     </Reference>
+    <Reference Include="EntityFramework">
+      <HintPath>..\packages\EntityFramework.6.1.1\lib\net45\EntityFramework.dll</HintPath>
+    </Reference>
+    <Reference Include="EntityFramework.SqlServer">
+      <HintPath>..\packages\EntityFramework.6.1.1\lib\net45\EntityFramework.SqlServer.dll</HintPath>
+    </Reference>
     <Reference Include="System" />
     <Reference Include="System.ComponentModel.DataAnnotations" />
     <Reference Include="System.Configuration" />
     <Reference Include="System.Core">
       <RequiredTargetFramework>3.5</RequiredTargetFramework>
     </Reference>
     <Reference Include="System.Data" />
+    <Reference Include="System.Data.SQLite, Version=1.0.94.0, Culture=neutral, PublicKeyToken=db937bc2d44ff139, processorArchitecture=MSIL">
+      <SpecificVersion>False</SpecificVersion>
+      <HintPath>..\packages\System.Data.SQLite.Core.1.0.94.0\lib\net45\System.Data.SQLite.dll</HintPath>
+    </Reference>
+    <Reference Include="System.Data.SQLite.EF6">
+      <HintPath>..\packages\System.Data.SQLite.EF6.1.0.94.0\lib\net45\System.Data.SQLite.EF6.dll</HintPath>
+    </Reference>
+    <Reference Include="System.Data.SQLite.Linq">
+      <HintPath>..\packages\System.Data.SQLite.Linq.1.0.94.1\lib\net45\System.Data.SQLite.Linq.dll</HintPath>
+    </Reference>
     <Reference Include="System.Deployment" />
     <Reference Include="System.Design" />
     <Reference Include="System.DirectoryServices" />
@@ -200,6 +217,7 @@
       <SubType>Designer</SubType>
       <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
     </None>
+    <None Include="packages.config" />
     <None Include="Properties\Settings.settings">
       <Generator>SettingsSingleFileGenerator</Generator>
       <LastGenOutput>Settings.Designer.cs</LastGenOutput>
@@ -309,4 +327,11 @@
 </PreBuildEvent>
   </PropertyGroup>
   <Import Project="$(SolutionDir)\.nuget\nuget.targets" />
+  <Import Project="..\packages\System.Data.SQLite.Core.1.0.94.0\build\net45\System.Data.SQLite.Core.targets" Condition="Exists('..\packages\System.Data.SQLite.Core.1.0.94.0\build\net45\System.Data.SQLite.Core.targets')" />
+  <Target Name="EnsureNuGetPackageBuildImports" BeforeTargets="PrepareForBuild">
+    <PropertyGroup>
+      <ErrorText>This project references NuGet package(s) that are missing on this computer. Enable NuGet Package Restore to download them.  For more information, see http://go.microsoft.com/fwlink/?LinkID=322105. The missing file is {0}.</ErrorText>
+    </PropertyGroup>
+    <Error Condition="!Exists('..\packages\System.Data.SQLite.Core.1.0.94.0\build\net45\System.Data.SQLite.Core.targets')" Text="$([System.String]::Format('$(ErrorText)', '..\packages\System.Data.SQLite.Core.1.0.94.0\build\net45\System.Data.SQLite.Core.targets'))" />
+  </Target>
 </Project>

README.md

@@ -18,20 +18,20 @@ ProteomicsTools software suite contains a bunch of tools used in proteomics rese
 
 Currently, there are three major softwares with full documents:
 
-<a name="BuildSummary">
+<a name="BuildSummary"/>
 - **BuildSummary** [[Full documents](BuildSummary)] : The target-decoy database search strategy is widely accepted as a standard method for estimating the false discovery rate (FDR) of peptide identification, based on which peptide-spectrum matches (PSMs) from the target database are filtered. To improve the sensitivity of protein identification given a fixed accuracy (frequently defined by a protein FDR threshold), a post-processing procedure is often used that integrates results from different peptide search engines that had assayed the same dataset. In this work, we show that PSMs that are grouped by the precursor charge, the number of missed internal cleavage sites, the modification state, the numbers of protease termini and the proteins grouped by their unique peptide count should be filtered separately according to the given FDR. We also develop an iterative procedure to filter the PSMs and proteins simultaneously, according to the given FDR. Finally, we present a general framework to integrate the results from different peptide search engines using the same FDR threshold. Our method was tested with several shotgun proteomics datasets that were acquired by multiple LC/MS instruments from two different biological samples. The results showed a satisfactory performance. 
 
-<a name="SRMBuilder">
+<a name="SRMBuilder" />
 - **SRMBuilder** [[Full documents](SRMBuilder)] :
 With high sensitivity and reproducibility, selected reaction monitoring (SRM) has become increasingly popular in proteome research for targeted quantification of low abundance proteins and post translational modification. SRM is also well accepted in other mass-spectrometry based research areas such as lipidomics and metabolomics, which necessitates the development of easy-to-use software for both post-acquisition SRM data analysis and quantification result validation. Here, we introduce a software tool SRMBuilder, which can automatically parse SRM data in multiple file formats, assign transitions to compounds, match light/heavy transition/compound pairs and provide a user-friendly graphic interface to manually validate the quantification result at transition/compound/sample level. SRMBuilder will greatly facilitate processing of the post-acquisition data files and validation of quantification result for SRM. 
 
-<a name="O18Quant">
+<a name="O18Quant" />
 - **O18Quant** [[Full documents](O18Quant)] : Proteolytic 18O-labeling has been widely used in quantitative proteomics since it can uniformly label all peptides from different kind of proteins. There have been multiple algorithms and tools developed over the last few years to analyze high-resolution proteolytic 16O/18O labeled mass spectraanalyze high-resolution proteolytic 18O-labeled mass spectra. We have developed a software tool: O18Quant, which addresses two major issues in the previous developed tools.  First, O18Quant uses robust linear model (RLM) for peptide-to-protein ratio estimation. RLM can minimize the effect of outliers instead of iteratively removing them which is a common practice in other approaches. Second, the existing approaches lack applicable implementation which O18Quant is implemented using C# under Microsoft .net framework and R. It automatically calculates the peptide/protein relative ratio and provides a friendly graphic user interface (GUI) which allows the user to manually validate the quantification result at scan, peptide and protein levels. The intuitive GUI O18Quant can greatly enhance the user’s visualization and understanding of the data analysis. 
 
-<a name="TurboRaw2MGF">
+<a name="TurboRaw2MGF" />
 - **TurboRaw2MGF** [[Full documents](TurboRaw2MGF)] : Isobaric labelling technique coupled with high resolution mass spectrometry has been widely employed in proteomic workflows requiring relative quantification. For each high resolution tandem mass spectrum (MS/MS), it can be used not only to quantify the peptide from different samples by reporter ions，but also to identify the peptide it derived from. Since the ions related to isobaric labeling may act as noise in database searching, the MS/MS spectrum should be preprocessed before peptide/protein identification. In this paper, we demonstrate that there are a lot of high frequency, high abundance isobaric related ions in MS/MS spectrum, and combining removing isobaric related ions with deisotoping and deconvolution in MS/MS preprocessing procedure improves the peptide/protein identification sensitivity significantly. 
 
-<a name="Prerequisites"/>
+<a name="Prerequisites" />
 #Prerequisites
 Two libraries are required for executing the software:	
 - [MSFileReader library](http://sjsupport.thermofinnigan.com/public/detail.asp?id=703)
@@ -60,7 +60,12 @@ The c# source code is also provided at following repositories. Visual Studio 201
 
 <a name="Changes"/>
 #Changes
-
+- 2015/02/26 Version 3.9.0
+ 1. Enhanced: MaxQuant Evidence To Peptide Converter: remove the PSM from decoy and contaminant proteins.
+- 2015/02/16 Version 3.8.9
+ 1. Enhanced: BuildSummary: extract phosphorylation site probability from ProteomeDiscoverer MSF file.
+ 2. Enhanced: Isobaric Labelling Peptide Statistic Builder: Filter phosphorylation peptides by site probability.
+ 3. New: Aminoacid Insertion Builder
 - 2015/02/13 Version 3.8.8
  1. Bugfix: Null reference exception of Mascot SAP Validator.
 - 2015/01/21 Version 3.8.7

app.config

@@ -3,6 +3,7 @@
   <configSections>
     <!-- For more information on Entity Framework configuration, visit http://go.microsoft.com/fwlink/?LinkID=237468 -->
     <section name="entityFramework" type="System.Data.Entity.Internal.ConfigFile.EntityFrameworkSection, EntityFramework, Version=6.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" requirePermission="false" />
+    <!-- For more information on Entity Framework configuration, visit http://go.microsoft.com/fwlink/?LinkID=237468 -->
   </configSections>
   <runtime>
     <assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1">
@@ -30,4 +31,19 @@
       <provider invariantName="System.Data.SQLite.EF6" type="System.Data.SQLite.EF6.SQLiteProviderServices, System.Data.SQLite.EF6" />
     </providers>
   </entityFramework>
-</configuration>
+  <system.data>
+    <!--
+        NOTE: The extra "remove" element below is to prevent the design-time
+              support components within EF6 from selecting the legacy ADO.NET
+              provider for SQLite (i.e. the one without any EF6 support).  It
+              appears to only consider the first ADO.NET provider in the list
+              within the resulting "app.config" or "web.config" file.
+    -->
+    <DbProviderFactories>
+      <add name="SQLite Data Provider" invariant="System.Data.SQLite" description=".NET Framework Data Provider for SQLite" type="System.Data.SQLite.SQLiteFactory, System.Data.SQLite" />
+      <remove invariant="System.Data.SQLite" />
+      <remove invariant="System.Data.SQLite.EF6" />
+      <add name="SQLite Data Provider (Entity Framework 6)" invariant="System.Data.SQLite.EF6" description=".NET Framework Data Provider for SQLite (Entity Framework 6)" type="System.Data.SQLite.EF6.SQLiteProviderFactory, System.Data.SQLite.EF6" />
+    </DbProviderFactories>
+  </system.data>
+</configuration>

packages.config

@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="utf-8"?>
+<packages>
+  <package id="EntityFramework" version="6.1.1" targetFramework="net45" />
+  <package id="System.Data.SQLite" version="1.0.94.1" targetFramework="net45" />
+  <package id="System.Data.SQLite.Core" version="1.0.94.0" targetFramework="net45" />
+  <package id="System.Data.SQLite.EF6" version="1.0.94.0" targetFramework="net45" />
+  <package id="System.Data.SQLite.Linq" version="1.0.94.1" targetFramework="net45" />
+</packages>