Have you planned to install any search engine such as X!Tandem in Skyline? I miss to be able to carry out the entire pipeline in a friendly (as Skyline offers) way... Another thing, is skyline able to process pepXML files, with peptideProphet and iProphet analysis, from TPP?

Thank you
Nothing definite yet, but we will keep this on the TODO list, and it may happen in the future. Thanks for your interest.

Could it be possible to add in the results grid exclude standards and if possible zooming on the calibration curve to see the low end of the curve cause right now its not so friendly.
The "Exclude From Calibration" column got added to the Peptide Results in the Document Grid last year.

A common complaint I heard at ASMS this year is that Skyline is hard to get started with because "it just sits there with its blank screen and stares at you". We see this on the support board too ("I wanted to load my raw data but it said I didn't have any transitions, what now?").

Several users agreed that if the Targets window had some kind of help text in it when a document is empty, that would be a big help. No need to go full Clippy, but something friendly that suggests a few different ways to get targets loaded would be an inexpensive but large usability boost.
Not sure what this would look like, but Alex won't be the one to do it. Maybe just a clickable region that brings up the Start Page?

Opportunistic feature that will require the right inspiration to get done. No deadline.

Hi Nick,
We have started seeing a new unhandled exception in the DataGridView (details below). Can you look into how we can catch this exception, and show a more friendly error message?

Hopefully, we can catch it somewhere below the global handler, although I don't see any Skyline code on the current stack trace.

--Brendan


User comments:
I will save the file.

I tried to export a transitionlist with 90.000 transitions.

Jeppe

Skyline version: 1.1.1.3167
Installation ID: 588cf6a0-00ee-4e35-815e-cf8fa196f2f9
Exception type: System.Runtime.InteropServices.ExternalException
Error message: Requested Clipboard operation did not succeed.

Stack trace:
   at System.Windows.Forms.Clipboard.ThrowIfFailed(Int32 hr)
   at System.Windows.Forms.Clipboard.SetDataObject(Object data, Boolean copy, Int32 retryTimes, Int32 retryDelay)
   at System.Windows.Forms.DataGridView.ProcessInsertKey(Keys keyData)
   at System.Windows.Forms.DataGridView.ProcessDataGridViewKey(KeyEventArgs e)
   at System.Windows.Forms.DataGridView.OnKeyDown(KeyEventArgs e)
   at System.Windows.Forms.Control.ProcessKeyEventArgs(Message& m)
   at System.Windows.Forms.DataGridView.ProcessKeyEventArgs(Message& m)
   at System.Windows.Forms.Control.ProcessKeyMessage(Message& m)
   at System.Windows.Forms.Control.WmKeyChar(Message& m)
   at System.Windows.Forms.Control.WndProc(Message& m)
   at System.Windows.Forms.DataGridView.WndProc(Message& m)
   at System.Windows.Forms.Control.ControlNativeWindow.OnMessage(Message& m)
   at System.Windows.Forms.Control.ControlNativeWindow.WndProc(Message& m)
   at System.Windows.Forms.NativeWindow.Callback(IntPtr hWnd, Int32 msg, IntPtr wparam, IntPtr lparam)
What is the status on this?

Lately we seem to get a lot of support requests where users are trying to just fire up Skyline then open a mass spec raw file. We issue an error like "the file contains an error at line 1 column 1", which only makes sense if the file is actually XML data.

Instead, we should:
 scan the first few hundred bytes to see if it contains "srm_settings" and "Skyline"
    if so, then throw that line/column error, fine.
 if not, see if we can identify it as mass spec data.
   if it is mass spec data, suggest they use File > Import Results, or if they don't have any targets, suggest they look into SeeMS.
Failing all that, issue an error like "this file does not appear to be a Skyline document."
Part of this is now implemented - we no longer just show the bare xml parser error. The bit about trying to identify raw data isn't there, but we do now offer a more friendly message about the file not being a skyline doc. Additionally if it's a .skyd file we'll find the .sky file next to it and load that without complaint.
Closing this - the important part is done, I doubt we'd ever get to the second half of this idea (about people trying to directly open raw data files instead of .sky files).
Just randomly looking at issues. The second part would be pretty easy for pwiz-recognized files. Just call ReaderList::identify on it and see if it returns non-empty. But that would add a ProteowizardWrapper dependency, where maybe you don't have one right now.

per https://skyline.ms/announcements/home/support/thread.view?rowId=72995

mauraisa (Members) created a new request    2025-10-28 13:38

I am trying use the "Copy Data" feature to copy the data from the "Full Scan" viewer that appears when you click on a chromotagram.

In general I think it is really useful to extract the underlying data from the visualizations in Skyline, however I am finding the way the output is formatted difficult to understand. What I would like to do is plot the data from the scan in R, but the format makes that difficult without moving a lot of things manually. At this point I am questioning whether the formatting is a feature or a bug.

I'm pretty sure the "Copy Data" feature is simply broken for scans with ion mobility data. I've attached a csv with the output that I am seeing when copying the data from a scan from a timsTOF. Columns for m/z and 1/K0 (Vs/cm^2) are repeated multiple times. It looks like the values for intensity are there but it not clear which rows they apply to. In row 3, 1/K0 (Vs/cm^2) is repeated in 57 columns.

I would think the best way to format the output would be a simple table with a single header and 3 columns: m/z, 1/K0 (Vs/cm^2), and intensity.

The first thing I tried to do was to look at what the output for a 2D scan without ion mobility data looks like. I think it a bit more comprehensible but still not very R/python friendly. There are 3 separate set of headers for each ion annotation.

Again I would think the best format would be a simple table with 3 columns: m/z, intensity, annotation.