An error like that means that something has gone wrong with your Skyline installation.
You should uninstall Skyline and install it again from the website.

The error has nothing to do with the specific type of raw file you are trying to read in Skyline.
Sometimes that sort of error will seem to depend on exactly how you launched Skyline. For instance, it might be that double-clicking on a .sky file in Windows Explorer will launch a different Skyline.exe compared to what you get if you launch Skyline from the Windows Start Menu.
Typically, the way you would fix something like this is to use Control Panel and go into "Programs and Features" and uninstall everything that looks like Skyline or Skyline-daily and then install Skyline and/or Skyline-daily again from the Skyline website.
-- Nick

Hi Nick,
I've tried uninstalling/reinstalling Skyline (making sure all instances of Skyline have been removed from the PC before re-installing) and now I'm getting a new error when I try to open some of my documents and in every document where I try to import data. The error is...

Skyline version: 23.1.0.380-cf25ad847 (64-bit)
Installation ID: 34b6f779-29c9-4273-9d5b-a54b642b7b23
Exception type: FileNotFoundException
Error message: Could not load file or assembly 'PrmPasefScheduler.dll' or one of its dependencies. The specified module could not be found.

--------------------

System.IO.FileNotFoundException: Could not load file or assembly 'PrmPasefScheduler.dll' or one of its dependencies. The specified module could not be found.
File name: 'PrmPasefScheduler.dll'
   at pwiz.Skyline.Controls.Graphs.RTGraphController.OnUpdateGraph()
   at pwiz.Skyline.Controls.Graphs.GraphSummary.UpdateGraph(Boolean selectionChanged) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Controls\Graphs\GraphSummary.cs:line 347
   at pwiz.Skyline.Controls.Graphs.GraphSummary.OnDocumentUIChanged(Object sender, DocumentChangedEventArgs e) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Controls\Graphs\GraphSummary.cs:line 238
   at System.EventHandler`1.Invoke(Object sender, TEventArgs e)
   at pwiz.Skyline.SkylineWindow.OnDocumentUIChanged(SrmDocument documentPrevious) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Skyline.cs:line 588


Exception caught at:
   at System.Windows.Forms.Application.ThreadContext.OnThreadException(Exception t)
   at System.Windows.Forms.Control.InvokeMarshaledCallbacks()
   at System.Windows.Forms.Control.WndProc(Message& m)
   at System.Windows.Forms.Form.WndProc(Message& m)
   at System.Windows.Forms.NativeWindow.Callback(IntPtr hWnd, Int32 msg, IntPtr wparam, IntPtr lparam)
   at System.Windows.Forms.UnsafeNativeMethods.DispatchMessageW(MSG& msg)
   at System.Windows.Forms.UnsafeNativeMethods.DispatchMessageW(MSG& msg)
   at System.Windows.Forms.Application.ComponentManager.System.Windows.Forms.UnsafeNativeMethods.IMsoComponentManager.FPushMessageLoop(IntPtr dwComponentID, Int32 reason, Int32 pvLoopData)
   at System.Windows.Forms.Application.ThreadContext.RunMessageLoopInner(Int32 reason, ApplicationContext context)
   at System.Windows.Forms.Application.ThreadContext.RunMessageLoop(Int32 reason, ApplicationContext context)
   at System.Windows.Forms.Form.ShowDialog(IWin32Window owner)
   at pwiz.Skyline.Alerts.AlertDlg.ShowAndDispose(IWin32Window parent) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Alerts\AlertDlg.cs:line 129
   at pwiz.Skyline.SkylineWindow.OpenFile(String path, FormEx parentWindow) in C:\proj\skyline_23_1\pwiz_tools\Skyline\SkylineFiles.cs:line 420
   at pwiz.Skyline.SkylineWindow.openMenuItem_Click(Object sender, EventArgs e) in C:\proj\skyline_23_1\pwiz_tools\Skyline\SkylineFiles.cs:line 208
   at System.Windows.Forms.ToolStripItem.RaiseEvent(Object key, EventArgs e)
   at System.Windows.Forms.ToolStripMenuItem.OnClick(EventArgs e)
   at System.Windows.Forms.ToolStripItem.HandleClick(EventArgs e)
   at System.Windows.Forms.ToolStripItem.HandleMouseUp(MouseEventArgs e)
   at System.Windows.Forms.ToolStrip.OnMouseUp(MouseEventArgs mea)
   at System.Windows.Forms.ToolStripDropDown.OnMouseUp(MouseEventArgs mea)
   at System.Windows.Forms.Control.WmMouseUp(Message& m, MouseButtons button, Int32 clicks)
   at System.Windows.Forms.Control.WndProc(Message& m)
   at System.Windows.Forms.ToolStrip.WndProc(Message& m)
   at System.Windows.Forms.ToolStripDropDown.WndProc(Message& m)
   at System.Windows.Forms.NativeWindow.Callback(IntPtr hWnd, Int32 msg, IntPtr wparam, IntPtr lparam)
   at System.Windows.Forms.UnsafeNativeMethods.DispatchMessageW(MSG& msg)
   at System.Windows.Forms.UnsafeNativeMethods.DispatchMessageW(MSG& msg)
   at System.Windows.Forms.Application.ComponentManager.System.Windows.Forms.UnsafeNativeMethods.IMsoComponentManager.FPushMessageLoop(IntPtr dwComponentID, Int32 reason, Int32 pvLoopData)
   at System.Windows.Forms.Application.ThreadContext.RunMessageLoopInner(Int32 reason, ApplicationContext context)
   at System.Windows.Forms.Application.ThreadContext.RunMessageLoop(Int32 reason, ApplicationContext context)
   at pwiz.Skyline.Program.Main(String[] args) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Program.cs:line 309

A couple of people have reported that new error about "PrmPasefScheduler.dll" a few times going all the way back to August 2021.
These errors were reported anonymously through Skyline's Unhandled Error reporting dialog, so I do not have any more information about what might have caused it for them.

Which version of Windows do you have?

One thing that you might want to try is installing Skyline-daily which you can get by pushing the "Skyline-daily (beta)" button on the main Skyline page:
https://skyline.ms/project/home/software/Skyline/begin.view

Depending on whether you end up seeing the same sorts of errors with Skyline-daily that might give us more information about what might be causing your errors.
One drawback about Skyline-daily is that it produces documents which are incompatible with Skyline 23.1. You can work around this by using the "File > Share" and choosing an older version in the "Skyline file format" dropdown.

-- Nick

Hi Nick,
I've just downloaded Skyline Daily and I'm getting the below error. We're using Windows 10.


At 3:46 PM:
Could not load file or assembly 'pwiz_data_cli.dll' or one of its dependencies. The specified module could not be found.
System.IO.FileNotFoundException: Could not load file or assembly 'pwiz_data_cli.dll' or one of its dependencies. The specified module could not be found.
File name: 'pwiz_data_cli.dll'
   at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache()
   at pwiz.Skyline.Model.Results.ChromatogramCache.Build(SrmDocument document, String documentFilePath, ChromatogramCache cacheRecalc, String cachePath, MsDataFileUri msDataFileUri, IProgressStatus status, ILoadMonitor loader, Action`2 complete) in C:\proj\pwiz\pwiz_tools\Skyline\Model\Results\ChromatogramCache.cs:line 732

Unfortunately, I have never figured out a good way to determine what is causing the "Could not load file or assembly 'pwiz_data_cli.dll' or one of its dependencies" error. There hundreds of possibly missing files that could be the cause of that error, and the message gives no hint as to which file that might be.

What I usually try is:
1. Download Dependency Walker:
https://www.dependencywalker.com/depends22_x64.zip
2. Extract all the files from that .zip file. If you are using Windows to do the extraction you should first right-click on the .zip file in Windows explorer and choose "Properties" and then check the "Unblock" checkbox in the Properties window.
3. Run depends.exe
4. Use the "File > Open" menu item to open the "pwiz_data_cli.dll" file in the Skyline installation folder.
It's tricky to find Skyline's installation folder because it is deep under the AppData folder in your home directory. I usually use "Task Manager" to figure out where Skyline.exe while Skyline is running.
5. On my computer it usually takes about 20 minutes for Dependency Walker to open "pwiz_data_cli.dll". It also always says that there were some errors, and I ignore that. After Dependency Walker has finished you can use the "File > Save" menu item to save a ".dwi" file which will contain some information about which dll's could and could not be found.

If you send me that .dwi file I might be able to figure out what is going wrong, but it's actually a long shot because I barely understand the information that Dependency Walker is trying to convey.

There are other ways to install Skyline, and you might want to try those before going down the Dependency Walker path:
1. Unplugged installer:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=install-64-disconnected_23_1
2. "Administrator" installer:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=install-administator-64

I will also send you an email in case this should be diagnosed over a Zoom meeting.
-- Nick