Welcome to Panorama support 

Welcome to the Panorama support forum. If you have a question about using Panorama, or if you encounter a problem, you can post your questions here.

Support is provided by the creators of the software, as time allows, though we hope others will share their experience as the user community grows.

In order to post to the forum, you'll need to sign up for an account. If you already have an account but have forgotten your password, you can reset your password using the "Forgot your password?" link on the Sign-in page.

When you post a question, please include the following information:

  • A detailed description of your problem or question, including instructions for re-creating any problem that you are encountering
  • The web-browser you were using when you encountered the problem
  • If the problem occurred while publishing a document through Skyline please include the version of the Skyline software you were using, your operating system, and any other information that may help us to answer the question

If you are including text output from a tool, please attach files to your message, rather than pasting in long text.


You can also sign up to request a project on PanoramaWeb.

Showing: all messages
Panorama AutoQC not updating since 3/1
(2 responses) Will Thompson 2017-03-24
Hi Vagisha and team,

We have an issue with the most recent results not showing up in Panorama folder /Duke Proteomics Core/QC. Since 3/1, the AutoQC Loader on the PC loads the data into Skyline and then the log shows that it is pushed to Panorama, but the data never shows up in the Levy-Jennings or other plots. The data HAS been loaded to panorama because I can see them listed in the "RUNS" tab. Please take a look and let me know what you find. I have given admin access to that folder to vsharma@uw.edu.


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Error in Panorama Upload
(5 responses) Todd 2017-03-20

We have been uploading DDA runs to Panorama (through AutoQC) for several months now without any major issues. We have used the latest Skyline-daily builds (currently Since about 3/9/2017, we have been getting errors at the end of the skyline file upload both when using AutoQC, or when trying to manually upload the files from within the Skyline application. I have attached the logs for the AutoQC (v1.1.0.10005) and the Skyline applications, and an example sky.zip file. We can't remember exactly whether this error coincided with our latest upgrade of Skyline-daily to the most recent build, but it might be related.

 293_PRTC_std_2017-03-20_15-05-10.sky.log  AutoQC.log 
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AutoQC "stalling"
(7 responses) phains 2017-03-15

we have AutoQC setup to monitor several MS with a number of different configuration files. All of them work *most* of the time. We have noticed that after a few days (we are still working out how long), AutoQC stops working for some of the configurations. If you stop the individual configuration (as opposed to the AutoQC application) and restart it, the files are successfully processed. It is possible ALL the configurations are doing this, it’s just that we haven’t noticed as those particular configurations aren’t supposed to be processing any files at this point in time. As such, it may be a global issue, or a local issue, we aren't 100% sure as yet.

We have other software running on the same PC doing a very similar thing (syncing files) and it is not experiencing any issues, so we don’t think it’s related to computer sleep issues (the PC is set to stay wake all the time, ditto the HDD).

Any ideas?


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AutoQC not sending files to Panorama
(11 responses) n wildburger 2017-02-09
Currently, I am using AutoQC on our Fusion so we can monitor instrument performance with the PRTC mix from Thermo.
Auto QC runs fine, but no files or results are on our folder on Panorama.

Attached is the Skyline template for of PRTC peptides we monitor, which to me looks fine. However, the instrument method used for the PRTC standard is a targeted MS2, meaning there is no MS1. I think this is why the AutoQC fails since a lot of the metrics are from the MS1 (correct me if I'm wrong). And since there is no MS1 my database search with PEAKS fails so I cannot create a spectral library.

Any input would be appreciated.
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"unknown error connecting to the server panoramaweb.org"
(4 responses) nod2007 2016-11-15
I started getting the message:

"unknown error connecting to the server panoramaweb.org"

about a week ago and have been unable to upload any results since. I haven't made any changes to the AUTOQC settings.
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Publish to Panorama Error
(4 responses) mdowns2 2016-11-01
I am having an issue with using the Publish to Panorama option in Skyline to publish to our PanoramaWeb project. When I attempt the upload I can see the appropriate project and subfolders, but I receive the following 404 error message:"The remote server returned an error: (404) Not Found." I have attached a screen grab with details.

Any advice you can give would be appreciated.

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AutoQC Loader stuck - error message
(4 responses) allikrest 2016-10-05
I keep getting the error message below. Sometimes it appears as below but I have also had a pop-up error that causes the AutoQC Loader app to quit altogether, which is problematic since I have other configurations actively importing files when the Loader quits. I am trying to import a .raw file. I have made sure that it is newly added to the "watch" folder, that it is not in the skyline document, and that it is not already uploaded as a "sample file" on Panorama. Now, AutoQC Loader just seems to be stuck. It won't recognize any new raw files that I drop into the "watch" folder for this particular configuration. I have attached the log file showing the errors.

An exception occurred while importing the file.
   at System.IO.__Error.WinIOError(Int32 errorCode, String maybeFullPath)
   at System.IO.FileStream.Init(String path, FileMode mode, FileAccess access, Int32 rights, Boolean useRights, FileShare share, Int32 bufferSize, FileOptions options, SECURITY_ATTRIBUTES secAttrs, String msgPath, Boolean bFromProxy, Boolean useLongPath, Boolean checkHost)
   at System.IO.FileStream..ctor(String path, FileMode mode, FileAccess access, FileShare share)
   at AutoQC.AutoQcLogger.WriteToFile(String message)
   at AutoQC.AutoQcLogger.LogError(String message)
   at AutoQC.AutoQcLogger.LogException(Exception ex)
   at AutoQC.ConfigRunner.RunConfiguration(Object sender, DoWorkEventArgs e)
   at System.ComponentModel.BackgroundWorker.OnDoWork(DoWorkEventArgs e)
   at System.ComponentModel.BackgroundWorker.WorkerThreadStart(Object argument)
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no mass accuracy data
(1 response) allikrest 2016-10-04
Is mass accuracy data stored in skyline or controlled by a setting in the skyline document? I have 4 AutoQC folders and can see mass accuracy data for the runs in all of them except for one ("AutoQC_BSA_Fus") (see attached screen shot). I have compared the settings in all four skyline documents and cannot seem to find anything that is different in the file associated with the folder in which runs have no mass accuracy data.

 Weekly BSA_Fus.sky  no mass accuracy.jpg 
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Error: test library not found in settings
(7 responses) allikrest 2016-09-30

I am getting this error whenever AutoQC Loader tries to import my skyline document to Panorama. I am using Skyline version, 64-bit. Any idea what is going on?


30 Sep 2016 07:14:18,818 INFO : Starting to import Skyline document from Weekly_Yeast_QEx_2016-09-30_10-13-58.sky.zip
30 Sep 2016 07:14:18,818 INFO : Expanding Weekly_Yeast_QEx.skyd
30 Sep 2016 07:14:18,859 INFO : Expanding Weekly_Yeast_QEx.sky.view
30 Sep 2016 07:14:18,860 INFO : Expanding Weekly_Yeast_QEx.sky
30 Sep 2016 07:14:18,861 WARN : The version of this Skyline document is 3.5. This is newer than the highest supported version 2.62
30 Sep 2016 07:14:19,525 INFO : Inserting peptides1
30 Sep 2016 07:14:19,570 ERROR: Skyline document import failed
java.lang.IllegalStateException: 'test' library not found in settings.
    at org.labkey.targetedms.SkylineDocImporter.insertPrecursor(SkylineDocImporter.java:1244)
    at org.labkey.targetedms.SkylineDocImporter.insertPeptideOrSmallMolecule(SkylineDocImporter.java:1040)
    at org.labkey.targetedms.SkylineDocImporter.insertPeptideGroup(SkylineDocImporter.java:923)
    at org.labkey.targetedms.SkylineDocImporter.importSkylineDoc(SkylineDocImporter.java:533)
    at org.labkey.targetedms.SkylineDocImporter.importRun(SkylineDocImporter.java:149)
    at org.labkey.targetedms.pipeline.TargetedMSImportPipelineJob.run(TargetedMSImportPipelineJob.java:85)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
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Programmatic access to data in Panorama
(4 responses) gabe 2016-09-09
Hi, I'm wondering where I can find descriptions or documentation on APIs or programmatic access to Skyline data in Panorama. This PDF suggests that APIs exist (page 23) but I can't find any more info anywhere. Thanks Gabe
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AutoQC: Error getting status of file
(2 responses) Christian.Frese 2016-08-02

I get the following error message when I start runnign AutoQC:

ERROR: Error getting status of file D:\Data\BSA\20160726_UC_ColID_163_CKF_BSA_50fmol_test2.raw
ERROR: Exception details can be found in the AutoQC log in C:\Users\Q1\Documents\PRM
Adding D:\Data\BSA\20160726_UC_ColID_163_CKF_BSA_50fmol_test2.raw to re-import queue.

I atached the logfile. Any idea what's going on?

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Problems with Autoqc
(1 response) mhardt 2016-04-28
Hi there,

ive set up a skyline file with MRM transitions for 8 small molecules and the data is successfully imported by the autoqc daemon and uploaded to the panorama server. Unfortunaterly, panorama doesnt display the data and gives an error message...

There were no records found. The date filter applied may be too restrictive.

But there is no filter set up. Can anybody help?


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*_annotated_minimized_* vs *_minimized_annotated_*
(1 response) c.chung 2016-04-15
On Apr 14, 2016 8:27 AM, c.chung wrote:

In the Panorama pagehttps://panoramaweb.org/labkey/project/LINCS/GCP/begin.view?TargetedMSRuns.sort=Created the GCP files can be:
I sorted by date, three out of the 15 files the naming is swapped.
Is there a difference in the protocol for naming them slightly different?

On Apr 14, 2016 2:20 PM, PCCSE support wrote:

Thank you for your question, there are no protocol differences between these two naming conventions, just user error in naming them in the wrong order.

I will shortly be reuploading these files in the correct order (annotated_minimized)
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Skyline with discovery content (DDA)
(1 response) An Staes 2016-01-19

We have a skyline file containing discovery data (DDA runs of which we build a spectral lib with the dat files from mascot) and no target data. When importing into panorama, it puts this skyline file in the "targeted MS runs" section. Is there a way to annotate that this is a discovery experiment, present in skyline?


Kind regards,
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error on import
(1 response) Giel Vandemoortele 2016-01-18

We wanted to import our skyline files on our subfolder on Panorama, but we managed to import only 2 out of 10.
All the rest of the files throw the same error (see screenshot): java.lang.IllegalArgumentException: No enum constant org.labkey.targetedms.parser.DataSettings.AnnotationType.-1

Can you help us on this?

Thank you!

Kind regards,
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Display of ms/ms in Panorama
(1 response) Ida Suppanz 2015-10-30
I imported a skyline document to Panorama that I zipped via the "share"-> "minimal" option. In my skyline document I have several replicates with ms/ms information. In the Panorama view only one ms/ms is displayed for a given peptide. How can I see which replicate (and wich r.t. if there are several ms/ms for one replicate) it belongs to?
Is it possile to choose which ms/ms will be displayed in Panorama before zipping the file? Or can I display the ms/ms information for all replicates?
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Error Same Key
(6 responses) bphinney 2015-10-22
So I duplicated my skyline file and removed the results and re saved it. I wanted to add a few more peptides to my QC. When I run autoQC again (pointing to the new skyline file and uploading to a new sub directory on Panorama) I get "An Item with the same key has already been added" and then an Error failed importing. Any ideas on how to fix this?


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Auto QC Project
(4 responses) bphinney 2015-10-22
Hi, i'm trying to set up autoqc and publish to panaroma, but I can't figure out my project name to put in the "Folder on Panorama" box. I think my project has spaces in it which may be causing the problem


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autoQC client software
(1 response) Tobias kockmann 2015-10-21
Dear panorama support,

where can I find the panorama autoQC client software that needs to be installed on the instrument PC?

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Empty Group Name??
zaulim3 2015-08-02
One year ago, I registered the panoramaWeb at Jul 18, 2014.
At that time, I didn't make the group name in spite of your recommendation.

I want to make a group in panoramaWeb to publish my MRM data.
Could you make a new group, LMP_KIST, in my account??

Thank you.

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Error 412 Precondition failed
(4 responses) ykim 2015-07-27
Hi, I've been uploading files into Panorama without any issues, except that there are two files that give me this error: Error renaming temporary zip file: A remote server returned an error: (412) Precondition Failed. Any idea of how to fix this would be great! Thanks.
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Trouble uploading files
(1 response) brian flatley 2014-12-30
Hi Guys,

I am just getting some errors while trying to upload a file to Panorama from Skyline. I have tried to import the file using both manual upload of a zipped Skyline file and also uploading from Skyline directly to Panorama.

I have attached a screen shot of the error log.

"value too long for type character varying"


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The message to view email to fake email does not appear
(3 responses) yngvild bjorlykke 2014-10-02
I am following the tutorial for publishing data in Panorama. When doing: "If you use a fake email
address you can set the password for the account by clicking on a link to the email message that gets
generated for the new user.", the link to the message does not appear, instead I have:
"System membership status for new group members:
test@test.ts added as a new user to the system and emailed successfully."

Any idea on how to get unstuck?

Thank you!
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Error retrieving server folders
(1 response) brian flatley 2014-07-29

When I try and publish files from Skyline to Panorama, I get the following error message

Error retrieving server folders:
Value cannot be null.
Parameter name:value

If I select "ok" to this error message the folder structure for panorama appears but is absent of any of our folders
e.g. UCD Pennington Lab or any of the subfolders.

I have attached a screenshot of both the error message and the file structure of Panorama.

Any help would be great,

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RE: Panorama URL
(2 responses) tsbatth 2014-01-23
Hey Panorama team,

Thanks for good work. We're getting ready to upload a data set with a submition of apublication soon and we were wondering if it's possible to trim our current URL from


to something like


If it isn't too much trouble. Originally when I applied for panorama project I gave full name of the institution, but I think an abbreviation would be nicer. Thanks for your time.


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Cannot view or download the result (zip file)
(2 responses) mh167 2014-01-13
Hi there,

My collaborator just upload our MRM data to Panorama and I was able to view the result in the morning. After tried to download the Zip file and failed many times, I cannot see my result anymore ( I can still see the folder and the file but cannot see the chromatogram or other parts). Once I click the peptide, the panoroma stop working. I tried to download the zip file but always stopped after very long waiting. The web browser indicated some server error. Could you please give me some suggestions? Very appreciate.

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Duplicate webparts
(1 response) tsbatth 2013-05-22

I have a question regarding the Targeted MS Runs webpart in my project. I seem to be unable to remove webparts in a 'Targeted MS' folder. I have duplicate parts but seem to be unable to remove them (I'm admin for the project currently), I don't see the 'x' at top right of part title.


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Changing filenames
(2 responses) tsbatth 2013-05-20

Is it possible to rename files once they've been uploaded to Panorama via Skyline?


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How to add a new user account to an existing project
(4 responses) Tobias kockmann 2013-04-09
Hello Panorama support,

how to add a new user to an existing project? In the Admin tool one can only add pre-defined/default users. There is no function like create/invite user.

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