No, there is no way to do "Apply peak to all" from the command-line.

However, we do have a new feature in the latest Skyline-daily which is supposed to help with scenarios where a peptide was easily identified in some replicates but not easily found in the others.
The feature is Peak Boundary Imputation and you can read about the feature here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=PeakImputation

-- Nick

Thank you Nick for the reply.
This sounds like a nice feature.

I am thinking about writing an external tool to achieve my goal. This external tool would do the following:
(1) first, for each peptide, compute the average lower-RT and upper-RT boundaries from 8 of the 96 runs;
(2) then, apply this lower-RT and upper-RT boundaries to the rest of the runs (for the computation of AUC).

Do you think this is feasible? Could I have your kind input on building this external tool :-)?

Kind regards, Bingwen

If you know what peak boundaries you want to set for each Peptide and Replicate, then you should create a .csv file with those boundaries in it and use the "--import-peak-boundaries" command-line option.
-- Nick

Thanks a lot!
I think this will work :-)

I have one more question to consult with you: How can I remove a peptide from s Skyline document when its AUC is too small (i.e., not meeting a minimal AUC requirement on our control samples)? Is there a SkylineRunner option to do it?

Kind regards, Bingwen

Just to clarify, I would like to apply this minimal AUC filtering by looking at the AUCs on the 8 control samples (out of the 96 samples) for each peptide.

Similarly, we wanted to filter our data applying a minimal dot-product on the 8 control samples (regardless of the dot-productions of the remaining 88 samples). I noticed you have this '--refine-min-dotp' option but it seems this filtering will apply to all 96 samples?


Thanks. Kind regards, Bingwen

The usual way to remove peptides matching a particular criteria is to create a custom report that includes the value of interest. Then, you filter and/or sort the report so that the selected rows are all of the peptides that you want removed, and then use the "Actions" dropdown at the top of the Document Grid to delete the selected peptides.
Here is the Custom Reports tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports

There is no way to delete peptides like this from the command line. The command line offers many other ways to delete peptides, such as "--refine-min-dotp", but there's no equivalent way to delete based on area.

If you are writing an interactive external tool, you could delete peptides based on what you see in report results. An external tool can communicate with the instance of Skyline that launched it using the Tool Service API, and the API includes a method to delete things based on their "locator".

It sounds like you are planning on writing an external tool for Skyline.
What programming language are you going to write your tool in?
The Tool Service API is most easy to use if you are writing your tool in C#.
However, for tools written in other programming languages, there does exist something you can execute which will send commands to the running instance of Skyline using the tool service API.
-- Nick

I haven't decided on the language yet. Perhaps I should go with C#?

Bingwen

Do you have a recommendation on the .NET SDK version I should use to compile C# files?

I am getting this error using .NET SDK 8.0.14 on Skyline's example interactive tool:

PS C:\data\git-clones\pwiz\pwiz_tools\Skyline\Executables\Tools\ExampleInteractiveTool_BW> dotnet.exe build
  Determining projects to restore...
  Nothing to do. None of the projects specified contain packages to restore.
C:\Program Files\dotnet\sdk\8.0.414\Microsoft.Common.CurrentVersion.targets(1259,5): error MSB3644: The reference assemblies for .NETFramework,Version=v4.7.2 were not found. To resolve this, install the Devel
oper Pack (SDK/Targeting Pack) for this framework version or retarget your application. You can download .NET Framework Developer Packs at https://aka.ms/msbuild/developerpacks [C:\data\git-clones\pwiz\pwiz_t
ools\Skyline\Executables\Tools\ExampleInteractiveTool_BW\ExampleInteractiveTool.csproj]

Build FAILED.

C:\Program Files\dotnet\sdk\8.0.414\Microsoft.Common.CurrentVersion.targets(1259,5): error MSB3644: The reference assemblies for .NETFramework,Version=v4.7.2 were not found. To resolve this, install the Devel
oper Pack (SDK/Targeting Pack) for this framework version or retarget your application. You can download .NET Framework Developer Packs at https://aka.ms/msbuild/developerpacks [C:\data\git-clones\pwiz\pwiz_t
ools\Skyline\Executables\Tools\ExampleInteractiveTool_BW\ExampleInteractiveTool.csproj]
    0 Warning(s)
    1 Error(s)

Time Elapsed 00:00:00.52
PS C:\data\git-clones\pwiz\pwiz_tools\Skyline\Executables\Tools\ExampleInteractiveTool_BW>


Thanks. Bingwen

Skyline uses .Net Framework 4.7.2 to build.

The instructions for building Skyline are on this page:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=HowToBuildSkylineTip

-- Nick

Thanks so much for the info.

I read the documentation, it seems that to compile "pwiz\pwiz_tools\Skyline\Executables\Tools\ExampleInteractiveTool\", I will need to compile the whole Skyline project?

Is my interpretation correct?

Thanks. Bingwen

Thanks so much Nick!

It worked! I follow the URL you provided and was able to use Visual Studio 2022 to run All Tests.

My next question is, how do I compile "pwiz\pwiz_tools\Skyline\Executables\Tools\ExampleInteractiveTool\"?

(Eventually I will have my own folder " "pwiz\pwiz_tools\Skyline\Executables\Tools\VVDTool\" but I wanted to use your provided example to try things out)

Thanks again. Kind regards, Bingwen

(P.S.: Visual Studio is pretty much new to me.)

Getting this error when try to build the example tool:

1>------ Build started: Project: ExampleInteractiveTool, Configuration: Debug|x86 ------
1>C:\data\Skyline\pwiz\pwiz_tools\Skyline\Executables\Tools\ExampleInteractiveTool\Graph.cs(24,7,24,18): error CS0246: The type or namespace name 'SkylineTool' could not be found (are you missing a using directive or an assembly reference?)
1>C:\data\Skyline\pwiz\pwiz_tools\Skyline\Executables\Tools\ExampleInteractiveTool\Graph.cs(25,7,25,15): error CS0246: The type or namespace name 'ZedGraph' could not be found (are you missing a using directive or an assembly reference?)
1>C:\data\Skyline\pwiz\pwiz_tools\Skyline\Executables\Tools\ExampleInteractiveTool\GraphUtilities.cs(23,7,23,15): error CS0246: The type or namespace name 'ZedGraph' could not be found (are you missing a using directive or an assembly reference?)
1>C:\data\Skyline\pwiz\pwiz_tools\Skyline\Executables\Tools\ExampleInteractiveTool\MainForm.cs(25,7,25,18): error CS0246: The type or namespace name 'SkylineTool' could not be found (are you missing a using directive or an assembly reference?)
1>C:\data\Skyline\pwiz\pwiz_tools\Skyline\Executables\Tools\ExampleInteractiveTool\GraphUtilities.cs(37,55,37,64): error CS0246: The type or namespace name 'GraphPane' could not be found (are you missing a using directive or an assembly reference?)
1>C:\data\Skyline\pwiz\pwiz_tools\Skyline\Executables\Tools\ExampleInteractiveTool\Graph.cs(107,29,107,44): error CS0246: The type or namespace name 'ZedGraphControl' could not be found (are you missing a using directive or an assembly reference?)
1>C:\data\Skyline\pwiz\pwiz_tools\Skyline\Executables\Tools\ExampleInteractiveTool\Graph.cs(107,53,107,62): error CS0246: The type or namespace name 'ZoomState' could not be found (are you missing a using directive or an assembly reference?)
1>C:\data\Skyline\pwiz\pwiz_tools\Skyline\Executables\Tools\ExampleInteractiveTool\Graph.cs(107,73,107,82): error CS0246: The type or namespace name 'ZoomState' could not be found (are you missing a using directive or an assembly reference?)
1>C:\data\Skyline\pwiz\pwiz_tools\Skyline\Executables\Tools\ExampleInteractiveTool\Graph.cs(140,53,140,65): error CS0246: The type or namespace name 'Chromatogram' could not be found (are you missing a using directive or an assembly reference?)
1>C:\data\Skyline\pwiz\pwiz_tools\Skyline\Executables\Tools\ExampleInteractiveTool\Graph.cs(37,26,37,41): error CS0246: The type or namespace name 'ZedGraphControl' could not be found (are you missing a using directive or an assembly reference?)
1>C:\data\Skyline\pwiz\pwiz_tools\Skyline\Executables\Tools\ExampleInteractiveTool\Graph.cs(42,22,42,37): error CS0246: The type or namespace name 'ZedGraphControl' could not be found (are you missing a using directive or an assembly reference?)
1>C:\data\Skyline\pwiz\pwiz_tools\Skyline\Executables\Tools\ExampleInteractiveTool\Graph.cs(171,34,171,49): error CS0246: The type or namespace name 'ZedGraphControl' could not be found (are you missing a using directive or an assembly reference?)
1>C:\data\Skyline\pwiz\pwiz_tools\Skyline\Executables\Tools\ExampleInteractiveTool\MainForm.cs(251,49,251,56): error CS0246: The type or namespace name 'IReport' could not be found (are you missing a using directive or an assembly reference?)
1>C:\data\Skyline\pwiz\pwiz_tools\Skyline\Executables\Tools\ExampleInteractiveTool\MainForm.cs(251,66,251,73): error CS0246: The type or namespace name 'IReport' could not be found (are you missing a using directive or an assembly reference?)
1>C:\data\Skyline\pwiz\pwiz_tools\Skyline\Executables\Tools\ExampleInteractiveTool\MainForm.cs(34,17,34,34): error CS0246: The type or namespace name 'SkylineToolClient' could not be found (are you missing a using directive or an assembly reference?)
1>C:\data\Skyline\pwiz\pwiz_tools\Skyline\Executables\Tools\ExampleInteractiveTool\MainForm.Designer.cs(215,17,215,25): error CS0246: The type or namespace name 'ZedGraph' could not be found (are you missing a using directive or an assembly reference?)
1>C:\data\Skyline\pwiz\pwiz_tools\Skyline\Executables\Tools\ExampleInteractiveTool\MainForm.Designer.cs(216,17,216,25): error CS0246: The type or namespace name 'ZedGraph' could not be found (are you missing a using directive or an assembly reference?)
========== Build: 0 succeeded, 1 failed, 0 up-to-date, 0 skipped ==========
Build failed.

The ExampleInteractiveTool is looking for ZedGraph.dll in a place where it cannot be found.
If you want to build that tool you are going to need to remove the reference to ZedGraph and add another one which you get by browsing to ZedGraph.dll which you can find in the pwiz_tools\Skyline\bin\x64\Release folder after you have built Skyline.

Note that after you have built the ExampleInteractiveTool you cannot run it directly because it only works if it has been launched from Skyline. After you build it, a file called "ExampleInteractiveTool.zip" will get created on disk and you can use the "Add > From File" button in the "Tools > External Tools" dialog in Skyline to get the new menus item added to the Tools menu.

ExampleInteractiveTool is very old. I will ask around and find out if there are any newer resources which would provide better examples of how to do things.
-- Nick

Oh, by the way, the configuration type (e.g. "Debug" or "Release") of the ExampleInteractiveTool that you build needs to match what you built for Skyline, because it's looking for the "SkylineTool.dll" in a folder which will have Debug or Release in its path.
Usually you will want to be building Release for both Skyline and your tool, so choose "Release" in the dropdown in the "Build > Configuration Manager" dialog.
That will fix the problems where it's saying "SkylineTool" cannot be found.
For the ZedGraph errors you will need to browse for the ZedGraph dll because it's looking in a place where that dll really cannot be found.
-- Nick

Thanks so much for the tips!

I just realized the .dll files were missing because the quick build did not work:
Build started at 13:11:17.14
Building pwiz (64-bit)...
ProteoWizard 3.0.25268. master x64 AMD64 NT
Generated C:\data\Skyline\pwiz\pwiz\data\msdata\Version.cpp
Generated C:\data\Skyline\pwiz\pwiz\analysis\Version.cpp
Generated C:\data\Skyline\pwiz\pwiz\data\identdata\Version.cpp
Generated C:\data\Skyline\pwiz\pwiz\data\tradata\Version.cpp
Generated C:\data\Skyline\pwiz\pwiz\data\proteome\Version.cpp
Generated C:\data\Skyline\pwiz\pwiz\Version.cpp
tar.list hdf5-1.8.7.tar.bz2
tar.extract hdf5-1.8.7.tar.bz2 (already extracted)
tar.list boost_1_86_0.tar.bz2
tar.extract boost_1_86_0.tar.bz2 (already extracted)
tar.list zlib-1.2.3.tar.bz2
C:/data/Skyline/pwiz/libraries\tar.jam:450: in extract-really
*** argument error
* rule path.exists ( location )
* called with: ( )
* missing argument location
(builtin):see definition of rule 'path.exists' being called
C:/data/Skyline/pwiz/libraries\tar.jam:343: in tar.extract
C:/data/Skyline/pwiz/libraries\ext-zlib.jam:32: in ext-zlib.init
C:/data/Skyline/pwiz/libraries/boost-build/src/build\toolset.jam:44: in toolset.using
C:/data/Skyline/pwiz/libraries/boost-build/src/build\project.jam:1104: in using
C:/data/Skyline/pwiz/libraries\ext-boost.jam:144: in ext-boost.init
C:/data/Skyline/pwiz/libraries/boost-build/src/build\toolset.jam:44: in toolset.using
C:/data/Skyline/pwiz/libraries/boost-build/src/build\project.jam:1104: in using
Jamroot.jam:581: in modules.load
C:/data/Skyline/pwiz/libraries/boost-build/src/build\project.jam:372: in load-jamfile
C:/data/Skyline/pwiz/libraries/boost-build/src/build\project.jam:64: in load
C:/data/Skyline/pwiz/libraries/boost-build/src/build\project.jam:142: in project.find
C:/data/Skyline/pwiz/libraries/boost-build/src\build-system.jam:618: in load
C:/data/Skyline/pwiz/libraries/boost-build/src/kernel\modules.jam:294: in import
C:/data/Skyline/pwiz/libraries/boost-build/src/kernel/bootstrap.jam:139: in boost-build
C:/data/Skyline/pwiz/libraries/boost-build/boost-build.jam:8: in module scope
Build failed: exit code was 1.
Build finished at 13:11:18.48
Elapsed time: 0:0:1

Any advice on how to fix this "*** argument error"? (see above)

BTW, this is the quick build command I used:
pwiz_tools\build-apps.bat 64 --i-agree-to-the-vendor-licenses toolset=msvc-14.3 %*

I am not familiar with the error that you are seeing, but this is the command I use to build:
quickbuild.bat --i-agree-to-the-vendor-licenses toolset=msvc-14.3 address-model=64 --without-compassxtract pwiz_tools\Skyline//Skyline.exe

If my command works, then use it instead of what you are using.
-- Nick

Thanks so much for the pointers!

I was able to move forward but now I am seeing these "Access is denied" messages. Any idea why?

PS C:\data\Skyline\pwiz> .\quickbuild.bat --i-agree-to-the-vendor-licenses toolset=msvc-14.3 address-model=64 --without-compassxtract pwiz_tools\Skyline//Skyline.exe
Build started at 9:31:03.62
Building pwiz (64-bit)...
ProteoWizard 3.0.25269.94868d3c1 master x64 AMD64 NT
Generated C:\data\Skyline\pwiz\pwiz\data\msdata\Version.cpp
Generated C:\data\Skyline\pwiz\pwiz\analysis\Version.cpp
Generated C:\data\Skyline\pwiz\pwiz\data\identdata\Version.cpp
Generated C:\data\Skyline\pwiz\pwiz\data\tradata\Version.cpp
Generated C:\data\Skyline\pwiz\pwiz\data\proteome\Version.cpp
Generated C:\data\Skyline\pwiz\pwiz\Version.cpp
tar.list hdf5-1.8.7.tar.bz2
tar.extract hdf5-1.8.7.tar.bz2 (already extracted)
tar.list boost_1_86_0.tar.bz2
tar.extract boost_1_86_0.tar.bz2 (already extracted)
tar.list zlib-1.2.3.tar.bz2
tar.extract zlib-1.2.3.tar.bz2 (already extracted)
Extracting vendor APIs...
Access is denied.
Access is denied.
Access is denied.
Access is denied.
Access is denied.
Access is denied.
Access is denied.
Access is denied.
Updating submodules for Hardklor etc...
Generated C:\data\Skyline\pwiz\pwiz_tools\Skyline\Properties\AssemblyInfo.cs
Generated C:\data\Skyline\pwiz\pwiz_tools\Skyline\SkylineCmd\Properties\AssemblyInfo.cs
Generated C:\data\Skyline\pwiz\pwiz_tools\Skyline\Executables\SkylineBatch\SkylineBatch\Properties\AssemblyInfo.cs
Generated C:\data\Skyline\pwiz\pwiz_tools\Skyline\TestRunner\Properties\AssemblyInfo.cs
Generated C:\data\Skyline\pwiz\pwiz_tools\Skyline\SkylineTester\Properties\AssemblyInfo.cs
Generated C:\data\Skyline\pwiz\pwiz_tools\Skyline\SkylineNightly\Properties\AssemblyInfo.cs
Generated C:\data\Skyline\pwiz\pwiz_tools\Skyline\SkylineNightlyShim\Properties\AssemblyInfo.cs
tar.list libpng-1.5.6.tar.bz2
tar.extract libpng-1.5.6.tar.bz2 (already extracted)
tar.list freetype-VER-2-13-3.tar.bz2
tar.extract freetype-VER-2-13-3.tar.bz2 (already extracted)
tar.list libgd-2.1.0alpha.tar.bz2
tar.extract libgd-2.1.0alpha.tar.bz2 (already extracted)
tar.list hdf5-1.8.7.tar.bz2
tar.extract hdf5-1.8.7.tar.bz2 (already extracted)
[pwiz/data/vendor_readers/ABI] Missing DLL: Reader_ABI can only identify files, not read them.
[pwiz/data/vendor_readers/ABI/T2D] 64-bit MSVC build: Reader_ABI_T2D can only identify files, not read them.
[pwiz/data/vendor_readers/Agilent] Missing DLL: Reader_Agilent can only identify files, not read them.
[pwiz/data/vendor_readers/Bruker] Missing DLL: Reader_Bruker can only identify files, not read them.
[pwiz/data/vendor_readers/Mobilion] Missing DLL: Reader_Mobilion can only identify files, not read them.
[pwiz/data/vendor_readers/Shimadzu] Missing DLL: Reader_Shimadzu can only identify files, not read them.
[pwiz/data/vendor_readers/Thermo] Missing DLL (did you download and install MSFileReader?): Reader_Thermo can only identify files, not read them.
error: Unable to find file or target named
error: '/C:/data/Skyline/pwiz/pwiz_aux/msrc/utility/vendor_api/UNIFI//C:\data\Skyline\pwiz/pwiz_aux/msrc/utility/vendor_api/ABI/protobuf-net.dll'
error: referred to from project at
error: '/C:/data/Skyline/pwiz/pwiz_aux/msrc/utility/vendor_api/UNIFI'

Build failed: exit code was 1.
Build finished at 9:31:10.63
Elapsed time: 0:0:7
PS C:\data\Skyline\pwiz>

I'll send you an email directly because that will be faster than discussing this on the support board.

That line:
[pwiz/data/vendor_readers/ABI] Missing DLL: Reader_ABI can only identify files, not read them.
is not supposed to be in the output.
(The subsequent line about not supporting Reader_ABI_T2D is supposed to be there)

That Reader_ABI warning probably explains why you it later can't find C:\data\Skyline\pwiz/pwiz_aux/msrc/utility/vendor_api/ABI/protobuf-net.dll.

It might be that you can fix this by doing:
clean.bat
and then doing that build command.

It might be that you tried to do an earlier build with different options, and whatever that did has left around some things that are breaking your build right now.
-- Nick

On a related/unrelated note, I also wanted to report a bug. The new version of Skyline (V25) is reporting 'File Name' in the first line of the CSV export report, instead of as a column. see below and attached. I also include .skyr we used.

Property,,,,01_A1_C,,,,,,10_A2_C,,,,,
File Name,,,,18246_KK_150835_QE4_01_A1_C.raw,,,,,,18246_KK_150835_QE4_10_A2_C.raw,,,,,

Protein Name,Peptide Sequence,Peptide Modified Sequence,Precursor Charge,01_A1_C Library Dot Product,01_A1_C Total Area Fragment,01_A1_C Peptide Retention Time,01_A1_C Predicted Result Retention Time,01_A1_C Min Start Time,01_A1_C Max End Time,10_A2_C Library Dot Product,10_A2_C Total Area Fragment,10_A2_C Peptide Retention Time,10_A2_C Predicted Result Retention Time,10_A2_C Min Start Time,10_A2_C Max End Time
RTS1_(),NMMAACDPR,NM[+16]M[+16]AAC[+324.2]DPR,2,0.8794,3481441,2.12,2.48,1.91,2.25,0.9092,3563590,2.02,2.39,1.87,2.13
RTS2_(),KVVGCSCVVVK,KVVGC[+57]SC[+324.2]VVVK,2,0.9746,13103905,2.88,2.77,2.73,3.34,0.9876,12669244,2.82,2.68,2.64,3.11
RTS3_(),INISEGNCPER,INISEGNC[+324.2]PER,2,0.8122,669568448,3.53,3.42,3.35,3.93,0.7996,616304576,3.45,3.33,3.29,3.84
RTS4_(),NMMAACDPR,NMMAAC[+324.2]DPR,2,0.8305,1137803008,3.56,3.37,3.34,4,0.8388,860190976,3.48,3.28,3.3,3.94
RTS5_(),KPTDGASSSNCVTDISHLVR,KPTDGASSSNC[+324.2]VTDISHLVR,3,0.9754,258197856,4.37,4.48,4.2,4.78,0.9742,235692416,4.26,4.39,4.1,4.77
RTS6_(),LLDLVQQSCNYK,LLDLVQQSC[+324.2]NYK,2,0.9055,45510080,5.52,5.46,5.33,5.95,0.9114,35894728,5.43,5.38,5.23,5.9
RTS7_(),TCLPGFPGAPCAIK,TC[+324.2]LPGFPGAPC[+57]AIK,2,0.9082,61900728,6.18,6.03,5.91,6.45,0.9051,52399776,6.1,5.96,5.91,6.44
RTS8_(),WCNVQSTQDEFEELTMSQK,WC[+324.2]NVQSTQDEFEELTMSQK,2,0.9657,9434648,6.71,6.75,6.44,6.94,0.9602,11094930,6.63,6.67,6.45,6.9
RTS9_(),LVSSPCCIVTSTYGWTANMER,LVSSPC[+57]C[+324.2]IVTSTYGWTANMER,2,0.9647,91456656,7.22,7.17,7.06,7.35,0.9631,103404928,7.14,7.1,6.92,7.27
RTS10_(),IIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYK,IIPTLEEGLQLPSPTATSQLPLESDAVEC[+324.2]LNYQHYK,3,0.8983,61101676,8.75,8.76,8.6,9.13,0.8897,107068928,8.68,8.69,8.55,9.13
RTS11_(),LCYVALDFEQEMATAASSSSLEK,LC[+324.2]YVALDFEQEMATAASSSSLEK,2,0.9738,13149412,8.67,9.05,8.47,9.17,0.9729,24287140,8.6,8.98,8.42,9.07
RTS12_(),VFIMDSCDELIPEYLNFIR,VFIMDSC[+324.2]DELIPEYLNFIR,2,0.9613,1575341,9.9,9.68,9.74,10.25,0.992,20190686,9.86,9.61,9.71,10.18

The different sort of report output that you are seeing with 25.1 is because of a new way that Skyline handles reports where the "Pivot replicate name" checkbox was checked in the Report Editor.

You can read about that feature here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=replicate_pivot_ui

Unfortunately, there is no way to turn this feature off. If your report is pivoted by replicate name, then all of the Replicate and Result File columns will appear in the separate grid above the main grid, and when you export to CSV it will essentially be two CSV grids separated by a blank line.
-- Nick