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.

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Showing: limited to 100 messages
Remote server error 404 and Skyline Daily Runner exe error code 2
(1 response) dhardie 2024-04-17 13:45:46

Hello Panorama support;

I just started seeing this error this morning when trying to upload raw files with AutoQC. Multiple restarts and deletion of raw files in monitored data folder and in Skyline files did not fix the problem see error log entry below:

[2024-04-17 1:38:42 PM] Unknown error attempting to upload to Panorama.
[2024-04-17 1:38:42 PM] File was not uploaded to the server. Please try again, or if the problem persists, please contact your Panorama server administrator.
[2024-04-17 1:38:42 PM] The remote server returned an error: (404) Not Found.
[2024-04-17 1:38:42 PM] ERROR: Failure occurred. Exiting...
[2024-04-17 1:38:43 PM] ERROR: SkylineDailyRunner.exe exited with error code 2.
[2024-04-17 1:38:43 PM] Finished importing existing files...

Any suggestions


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2+ charge state not available for selection
(2 responses) ss 2024-03-21 03:46:09


I am building autoQC Skyline file and would like to select a 2+ precursor for one of the QC peptides but this is not availale in the SKyline precusor selection three (see attached). Other peptides in this list have the 2+ option available as 2+ is also listed in the transitions settings filter tab.

Thanks for you assistance.

 Precursor selection Skyline 1.png  Precursor selection Skyline 2.png 
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Authenticating user Credential on panorama
(2 responses) jean-christophe prost 2024-03-20 08:14:01

Hello Panorama,

I am able to login in Panorama, I was able to setup new AutoQC folders and everything, but I am not able to setup the server in skyline, and I used my panorama Login. Did I something wrong?

THank you for your help.
Kind regards

 Credential probelms.docx 
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Precursor Area visualisation in AutoQC
(3 responses) dhabaker 2024-03-06 09:05:45


I am having trouble visualizing both the precursor area and precursor mass error visualization for my QC replicates. However, the retention time visualization seems to work well for the same replicates. I have attached a file showing this error.

Can you please assist with this issue?

Please let me know if any further details are required regarding this.

Thank you.

Best regards,

 Precursor Area in Auto QC.PNG 
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Mass accuracy despaired
(1 response) Taher Elgierari 2024-02-29 08:53:42

Good morning
for some reason we are not seeing the mass accuracy metric on panorama, nothing changed on our end, is this metric no longer trackable on panorama?

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Problems with spectral library when uploading the project to Panorama Public
(1 response) Dorota Muth-Pawlak 2024-02-27 03:27:55


I would like to upload Skyline files with raw files to Panorama Public and Proteome Exchange. I receive the error indicating missing spectral library but I can see that the file is uploaded on Panorama web. Could you tell me what is the problem in current content of my folder? I attached the printscreen of the message I received. You can also find here project details.


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problem with Skyline version and installation
(2 responses) virginie imbault 2024-01-22 08:02:42

I have a TT5600 from Sciex and we have windows 7 on the acquisition computer.
So I have installed Skyline (32bit) and autoQCLoader.
But when I run autoQCLoader, I have an error and this warning message appears (see in attachment).

Can you help me?


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Error Downloading .NET Framework 4.7.2
(7 responses) justinsnider 2024-01-09 14:33:54


I tried downloading Skyline for a 64-bit Windows computer with internet and received an error message that .NET Framework 4.7.2 was needed for the download. When I download .NET Framework 4.7.2, I received the attached error message.

Any ideas on how to fix this error? Thanks!

 Skyline download error.pptx 
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How to become an admin
(1 response) vincent richard 2023-12-20 13:32:30

Hello! I would like to be added as an administrator for our lab's panorama projects (Borchers Lab), but the existing admin no longer works in our group (email is deactivated). How can we proceed managing the account?

Thanks very much,

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error in autoQC
(2 responses) wphipps5 2023-12-19 17:16:31

Hi there-- AutoQC loads our data fine into Panorama, but there are eventually errors...

[12/19/2023 5:00:37 PM] Y:\Chemistry\MassSpecFacility\STMS-AMC\7-STMS_Tuning\AutoQC\raw\PRM_raw\STMS_20231212_07.raw was acquired (12/15/2023 4:15:57 AM) before the acquisition date (12/15/2023 4:18:45 AM) on the last imported file in the Skyline document. Skipping...
[12/19/2023 5:00:37 PM] STMS_20231212_08.raw is ready
[12/19/2023 5:00:37 PM] Running SkylineRunner.exe with args:
[12/19/2023 5:00:37 PM] --in="Y:\Chemistry\MassSpecFacility\STMS-AMC\7-STMS_Tuning\AutoQC\" --import-file="Y:\Chemistry\MassSpecFacility\STMS-AMC\7-STMS_Tuning\AutoQC\raw\PRM_raw\STMS_20231212_08.raw" --import-on-or-after=12/15/2023 4:18:45 AM --save
[12/19/2023 5:00:38 PM] Opening file...
[12/19/2023 5:00:39 PM] File opened.
[12/19/2023 5:00:41 PM] Loading QEplus_HeLa_PRM.skyd cache
[12/19/2023 5:00:41 PM] 100%
[12/19/2023 5:00:41 PM] STMS_20231212_08 -> Y:\Chemistry\MassSpecFacility\STMS-AMC\7-STMS_Tuning\AutoQC\raw\PRM_raw\STMS_20231212_08.raw Note: The file has already been imported. Ignoring...
[12/19/2023 5:00:41 PM] Error: No files left to import.
[12/19/2023 5:00:41 PM] TAU_20231215_03.raw is ready
[12/19/2023 5:00:41 PM] Running SkylineRunner.exe with args:
[12/19/2023 5:00:41 PM] --in="Y:\Chemistry\MassSpecFacility\STMS-AMC\7-STMS_Tuning\AutoQC\" --import-file="Y:\Chemistry\MassSpecFacility\STMS-AMC\7-STMS_Tuning\AutoQC\raw\PRM_raw\TAU_20231215_03.raw" --import-on-or-after=12/15/2023 4:18:45 AM --save
[12/19/2023 5:00:42 PM] Opening file...
[12/19/2023 5:00:42 PM] File opened.
[12/19/2023 5:00:45 PM] Loading QEplus_HeLa_PRM.skyd cache
[12/19/2023 5:00:45 PM] 100%
[12/19/2023 5:00:45 PM]
[12/19/2023 5:00:45 PM] Adding results...
[12/19/2023 5:00:45 PM] 1. Y:\Chemistry\MassSpecFacility\STMS-AMC\7-STMS_Tuning\AutoQC\raw\PRM_raw\TAU_20231215_03.raw
[12/19/2023 5:00:45 PM]
[12/19/2023 5:00:47 PM] Successfully pinged Panorama server.
[12/19/2023 5:00:48 PM] [1] 10%
[12/19/2023 5:00:50 PM] [1] 20%
[12/19/2023 5:00:52 PM] [1] 25%
[12/19/2023 5:00:55 PM] [1] 30%
[12/19/2023 5:00:57 PM] [1] 35%
[12/19/2023 5:00:59 PM] [1] 41%
[12/19/2023 5:01:01 PM] [1] 50%
[12/19/2023 5:01:03 PM] [1] 60%
[12/19/2023 5:01:05 PM] [1] 93%
[12/19/2023 5:01:07 PM]
[12/19/2023 5:01:07 PM] Updating peak statistics
[12/19/2023 5:01:10 PM] 50% - Joining file Y:\Chemistry\MassSpecFacility\STMS-AMC\7-STMS_Tuning\AutoQC\TAU_20231215_03_2859473399.raw.skyd
[12/19/2023 5:01:11 PM] 100%
[12/19/2023 5:01:12 PM] Updating peak statistics
[12/19/2023 5:01:12 PM] Saving file...
[12/19/2023 5:01:14 PM]
[12/19/2023 5:01:14 PM] 100%
[12/19/2023 5:01:14 PM] File saved.
[12/19/2023 5:01:14 PM] SkylineRunner.exe exited successfully.
[12/19/2023 5:01:14 PM] TAU_20231215_17.raw is ready
[12/19/2023 5:01:14 PM] Running SkylineRunner.exe with args:
[12/19/2023 5:01:14 PM] --in="Y:\Chemistry\MassSpecFacility\STMS-AMC\7-STMS_Tuning\AutoQC\" --import-file="Y:\Chemistry\MassSpecFacility\STMS-AMC\7-STMS_Tuning\AutoQC\raw\PRM_raw\TAU_20231215_17.raw" --import-on-or-after=12/15/2023 4:18:45 AM --save
[12/19/2023 5:01:15 PM] Opening file...
[12/19/2023 5:01:16 PM] File opened.
[12/19/2023 5:01:18 PM] Loading QEplus_HeLa_PRM.skyd cache
[12/19/2023 5:01:18 PM] 100%
[12/19/2023 5:01:18 PM]
[12/19/2023 5:01:18 PM] Adding results...
[12/19/2023 5:01:18 PM] 1. Y:\Chemistry\MassSpecFacility\STMS-AMC\7-STMS_Tuning\AutoQC\raw\PRM_raw\TAU_20231215_17.raw
[12/19/2023 5:01:18 PM]
[12/19/2023 5:01:21 PM] [1] 10%
[12/19/2023 5:01:23 PM] [1] 19%
[12/19/2023 5:01:25 PM] [1] 24%
[12/19/2023 5:01:28 PM] [1] 29%
[12/19/2023 5:01:30 PM] [1] 35%
[12/19/2023 5:01:32 PM] [1] 41%
[12/19/2023 5:01:35 PM] [1] 48%
[12/19/2023 5:01:37 PM] [1] 58%
[12/19/2023 5:01:39 PM] [1] 68%
[12/19/2023 5:01:41 PM]
[12/19/2023 5:01:42 PM] Updating peak statistics
[12/19/2023 5:01:44 PM] 50% - Joining file Y:\Chemistry\MassSpecFacility\STMS-AMC\7-STMS_Tuning\AutoQC\TAU_20231215_17_2859473399.raw.skyd
[12/19/2023 5:01:45 PM] 100%
[12/19/2023 5:01:46 PM] Updating peak statistics
[12/19/2023 5:01:46 PM] Saving file...
[12/19/2023 5:01:48 PM] File saved.
[12/19/2023 5:01:48 PM] SkylineRunner.exe exited successfully.
[12/19/2023 5:01:48 PM] Running SkylineRunner.exe with args:
[12/19/2023 5:01:48 PM] --in="Y:\Chemistry\MassSpecFacility\STMS-AMC\7-STMS_Tuning\AutoQC\" --panorama-server="" --panorama-folder="/Hoofnagle/HeLa PRM QC" --panorama-username="WPHIPPS5@UW.EDU"
[12/19/2023 5:01:49 PM] ERROR: Unable to verify Panorama server information.
[12/19/2023 5:01:49 PM] There was an error authenticating user credentials on the server
[12/19/2023 5:01:49 PM]
[12/19/2023 5:01:49 PM] ERROR: Unexpected JSON response from the server: {{"currentUser":{{"canUpdateOwn":"false","canUpdate":"false","canDeleteOwn":"false","canInsert":"false","displayName":"wphipps5","canDelete":"false","id":5750,"isAdmin":"false","email":""}}
[12/19/2023 5:01:49 PM] URL:
[12/19/2023 5:01:49 PM]
[12/19/2023 5:01:49 PM] Exiting...
[12/19/2023 5:01:49 PM] ERROR: SkylineRunner.exe exited with error code 2.
[12/19/2023 5:01:49 PM] Finished importing existing files...
[12/19/2023 5:01:49 PM] Importing new files...
[12/19/2023 5:01:49 PM] ERROR: Uploads to Panorama have not been successful in over 24 hours. Stopping configuration.
[12/19/2023 5:01:49 PM] Finished running configuration.

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AutoQC with Thermo Chromeleon data vaults
(2 responses) paul mathews 2023-11-08 15:44:46

Hello all--

I am working with a skyline document/autoQC/panorama with some GCMS data generated on Thermo TSQ and ISQ GC-MS and Chromeleon 7.2.10 ES. We utilize Panorama on our LCMS systems (Bruker and Agilent) with no problem, if you've used Chromeleon, you know the file structure is a jungle.. Has anyone had success setting up AutoQC in such a way to pull from the Chromeleon data vault?

I have been exporting the Chromeleon files to a separate folder manually, but that sort of defeats the functionality of the AutoQC loader..


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Problem uploading targeted small molecule quantifications
(3 responses) Joerg 2023-09-20 05:27:37

Uploading my third data file to a novel folder results in the following error message which I can't interpret, unfortunately 8the previous two files worked smoothly): - Analytical Chemistry/Custodio et al.%2C Cells%2C 2023/pipeline-status-showFile.view?rowId=174298&filename=230512MyllysUrea_231247ff_2023-09-20_14-04-13.sky_2023-09-20_05-04-16.log&download=false

Any help is greatly appreciated!
Many thanks in advance,

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no results posted on Panorama
(1 response) Taher Elgierari 2023-09-14 18:08:31

we noticed today that nothing in being uploaded to panorama, the autoqc is working, but connection to the server seems to be down, is there anything we need to form users end?

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AutoQC successfully pings, but no upload?
(4 responses) lpino 2023-09-11 11:22:28

Hi team!

I previously had AutoQC working great for about 11 months, but at some point it stopped uploading to our Panorama page. The small icon button on our configuration does successfully launch the appropriate Panorama page, and the Skyline button opens the appropriate Skyline document. Here's an example of the log (attached). If there's any other information I can get you, please let me know!


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AutoQC feature request - add commands
(2 responses) jjotto 2023-06-14 09:05:33

I'd like to be able to trigger additional actions when AutoQC sees a new file that meets the conditions met in the configuration. For example, when new file is found, could it trigger a command line process using the filename and path as a variable? The AutoQC setup for monitoring works very well, and if I could trigger my standard Skyline report from the file as well as submitting a search via command line, that would be ideal. I'm currently using a powershell script that works intermittently to submit a file for search.

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Peak selection
(2 responses) ss 2023-05-23 01:50:05

Hello Skyline team,

I'm monitoring a peptide that elutes as a double peak (see attached), likely due to differing oxygen orientations of oxdised Methione.

I would like to obtain separate XICs for each of the peaks since to use as reporters for column performance.

Is there a way to do this in an automated manner without manual peak integration? Data is uplaoded via AutoQC and would like to avoid operator intervention.

The transitions are identical but since data is generated on a TIMS perhaps CCS can be applied as an additional filter. I'm not sure if can do this and also how to execute it in Skyline:


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Changed folder structure, AutoQC not processing files through Skyline
(3 responses) paul mathews 2023-04-24 15:41:14

I originally had all my data going to the main folder in this account. I have since created some organization based on instrument/column and ionization mode. I deleted all runs from my previous imports when doing this.

When I tried to apply autoQC to the new file directories, I got an error saying results had already been imported, but nothing shows up in my dashboard.

I then removed spectra uploads (manage results) in the skyline document. Now I get the error "no existing files found".

I have double checked the "skyline file path" and "folder to watch", and icnluded the right patterns (all QC runs save to the same folder but are differentiated by "_pos" or "_neg".

Any advice?

 no files error.PNG 
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Zeno wiff vs wiff2 and Skyline AutoQC import
(4 responses) ss 2023-04-18 05:21:07

Hi Skyline team,

I'm importing Zeno SWATH data into Skyline using AutoQC. For each run there are a wiff and wiff2 raw files generated that seem to contain the same data when extracted in Skyline (although wiff2 files are bigger in size). Is there a preference for which file format should be processed in Skyline?

Thanks for your feedback.

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Auto QC not importing older data
(2 responses) ss 2023-03-17 09:23:54


I've set up AutoQC but some of the files are not imported to Skyline/ uploaded to Panorama with the following message:

221103_Zeno1_S00187_MHE_QC_MNT_100SPD_EV1109_221025_HeLa_50ng_DIA_A6.wiff was acquired (11/3/2022 6:43:44 PM) before the acquisition date (3/6/2023 1:22:36 PM) on the last imported file in the Skyline document. Skipping...

How do I get around this?

Log file is attached



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Exporting data from AutoQC
(3 responses) janelle hancock 2023-02-13 16:10:24

Hello Everyone,
I would like to export a spreadsheet of performance metrics. I can't seem to find a way to export run statistics from AutoQC. Is this possible? Ultimately I need to set reasonable pass/fail criteria, and modelling based on our existing data seems like the best way to do this.

I have been using the associated skyline file to generate document grids, and am able to model RT variation from this. But the TIC and transition/ precursor area plots in Auto QC doesn't seem to have equivalent statistics in Skyline?

Can anyone let me know how to download these from Panorama, or how to get them in the document grid in Skyline?


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Add metric: Orbitrap injection time
(3 responses) romeally 2023-01-17 07:30:23

Hi Panorama team,

I was wondering if it was possible to add MS1 Orbitrap injection time as a trackable metric to Panorama for Thermo data. The data are in the .raw files, so I imagine it could be extracted. This would be helpful, because if the instrument is dirty and overall instrument performance is decreasing, Orbitrap injection time may experience a compensatory increase to meet AGC limits and MS1 signal may remain relatively stable. We have seen this, where we get low protein IDs or PSMs or MS2 signal, but MS1 signal does not appear to be suffering, although injection times are high. After instrument cleaning, performance in other metrics goes up but MS1 signal does not change much and injection times return down to baseline.


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QC Plots
(2 responses) witold szymanski 2023-01-09 01:06:25

Dear Panorama Team!
Thanks for the awesome platform! I have one question though:
Is it possible to have multiple plots in the Dashboard at once? Like different metrics below each other

  1. Retention time
  2. Mass Accuracy


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QC trend report
(18 responses) jean-christophe prost 2022-11-10 02:27:00

Dear Panorama Team,

I tried quite a long time to generate reports or grids to get a quick overview for SST measurements.
Currently we have to import the data in skyline and extract them a csv report, that is then imported in Excel to get a final SST (see attachment) report and tells you, if your system works properly to measure your run.

Of course, in case we could have everything directly in panorama, it would increase the easiness of our workflow. I do not know, since we use already a set up report from skyline, if we can import it in panorama? or how to set something similar, or a report that gives you the standard deviation of the retention tim, mass error, CV of area and height, in one shot.

In advance thank you for your support and help.
Best, Jean-Christophe

 Small molecule precursor list.docx 
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Problem with server
(4 responses) jean-christophe prost 2022-11-01 07:10:21

Dear PanaoramWeb Team,

Nat made me, few days ago, a new PanoramaWeb project. Today I tried, following your "import Data Into Panorama" to generate the zip, without success.
As you can see in the word file, I tested two url. and both of them did not worked

I was wondering what I did wrong

In advance thank you for your help and I wish you a nice day


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Unable to search for small molecules on Panorama Public
(1 response) chrashwood 2022-10-13 12:17:48

Dear Panorama team,

I hope you are doing well. I was trying to search for small molecules with the PanoramaPublic search function however I have noticed that recently small molecule assays are no longer coming up for searches. Previously, small molecule results would show up if I used the right keyword but now they no longer appear.

E.g. if I search for "arginine" under Protein search or Peptide search, only protein results appear. However, the following Panorama Public document has Skyline assays with arginine listed as a molecule ( as well as many others. Just checking in to see if this is a bug or perhaps there is a different way I should be searching for small molecules.


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Peptide 'header' and molecule name?
(1 response) Alejandro Cohen 2022-08-31 11:09:22

Hi Panorama people,

I'm setting up a QC workflow using a BSA digest standard on our Lumos LC-MSMS system. I am acquiring by PRM using both CID and HCD for different peptides. I have set a Skyline document with two different Protein Names/Labels (see attached image). When I upload the data to Panorama, the QC plots show the peptide precursor sequence and m/z (see also attached image), but there is no information on the protein name/label as per the Skyline document. Also, the peptides are ordered in alphabetical order.

Is there any way I can group the peptide based on the Proteins Names (as found in Skyline) or any way I can filter them using the protein name/label (BSA_CID or BSA_HCD)?

Hope I made myself clear! Thanks again for your support, the QC feature is KEY for running our lab and checking on instrument health :)



 Screenshot 2022-08-31 150624.png  Screenshot 2022-08-31 150722.png 
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QCannotations in Panoramaweb
(2 responses) hao pham 2022-06-02 13:05:59
Hi Panorama team,

First of all, thank you for your work in creating this platform to monitor instruments.

I'd like to bulk upload QCannotation for an instrument, but there is this error (image attached).
This is what I have tried.
-create a single line dummy annotation, export it as excel or text file, add in the desired annotations. When I upload this file, I received that error.
-download the template and fill out with the desired annotations. When I upload this file, I received that error.

We also want to look into R script for QCannotation, but is there a place to integrate this.

Thank you so much for your suggestion
 Screenshot 2022-06-02 125821.jpg 
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Are all peptides incl. iRTs used for normalization?
(2 responses) roberthardt 2022-05-31 09:16:19

Dear Skyline-team,

I am just curious to know if Skyline actually uses all peptides/precursors present in the document when I select "normalize medians" in the quantification settings? Or does it only use the target peptides and omits the iRTs? I am asking because I currently rely on the CiRt peptides, of which not all are present in all my samples at the same amounts. Thus taking also this peptides into account for normalization could potentially skew my results.



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ProteomeXchange submission UniMod ID Missing from Modification
(2 responses) ncl trostlab 2022-05-09 09:40:12

Hello, I'm trying to upload our Skyline method files and raw data from an experiment we're submitting with a paper, in this particular experiment we were using a SIL standard (QconCAT) and in Skyline we just modified our target peptides to have 15N atoms instead to include the heavy peptides in the method file. However, this modification is not accepted as a Unimod modification and I can't submit the data as a result. I've included a screenshot which shows the details of the error. I was wondering if you could offer some assistance as to how I can circumvent this problem. Thanks a lot for your help.

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Cannot create folder
(1 response) xfbubu 2022-04-14 22:07:33


I was trying to create a folder to upload skyline files and eventually deposit it to Panorama Public. However, I can only see the icon for Permalink but not the one to create folder. I am wondering if you could help me with it.

Thank you.

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Assay validation reports to chromatogram libraries
(2 responses) roman sakson 2022-01-25 10:20:18

Dear Vagisha,

I am exploring the capabilities of chromatogram libraries at the moment, which seem quite useful! Am I correct that there is no way to generate those libraries in Skyline directly, as for spectral libraries (without uploading data to Panorama first)? In a recent announcement to the subscribers you mentioned "Adding new assay validation reports to chromatogram libraries" as a new feature. I am not quite sure what you meant by that and would like to understand better.

Thank you for your time,

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Thank you for supporting my research
(2 responses) Azad Eshghi 2022-01-11 11:20:32


As there is no google review for Panorma Support, I just wanted to drop a line to express my gratitude for all of the research support I have received from the helpful folks that make up the Panorama team. I would especially like to thank Vagisha Sharma for her recent (patient) assistance with data upload to Panorama Public.

While this may not be a novel thought, there may be other researchers like me who have not previously considered thanking individuals in the acknowledgments section of a manuscript. However, now that the thought has dawned (for me) I have acknowledged Vagisha accordingly in a "to be submitted" manuscript and will remember to do so in all future manuscripts when appropriate.

Thanks again Vagisha and the rest of the Panorama support team.

All the best,

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uploading files to panorama
(2 responses) christoph baumgartinger 2021-11-24 06:43:55


i am just wondering if there is another way to upload files to panorama? In past i always uploaded my files directly from skyline to panorama.

Could you help me out with this?

Thank you very much in advance!


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Skyline Document Setup for MAM
(2 responses) david schmidt 2021-10-26 02:09:26

thank you very much for this excellent piece of software!

I'm trying to monitor PTMs within a MAM Folder.
Could you tell me whether this is possible with MS1 Full-Scan Filtering (DDA) and with DIA (all-ion) MS2-based quantification? In your example it seems that only precursors were used.

Upon import of my Skyline document, the %modified column of the PTM report remains empty. Also the Peptide Mapping report is completely empty. Do I need to specify certain parameters in the Skyline results or Document grid?

best wishes,


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Changing the system email address again
(7 responses) roman sakson 2021-10-20 13:04:56

Dear Panorama Team,

a former colleague of mine was the first one to be added to the PanoramaWeb project of my current institute. However, my colleague has left our team recently and his email has been deactivated by our IT department. Despite that, newly registered users within our project still receive a PanoramaWeb welcoming email that seemingly comes from my former colleague's email address and the (probably default) text also suggests to contact the PanoramaWeb team at my former colleague's email in case of questions. How could we change this default message?

Thank you,

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Boilerplate language for regulatory documents
(3 responses) brittany 2021-09-22 16:53:26


I was wondering if you provide and/or prefer standard language for use of AutoQC in describing quality control protocols in regulatory documents?

Thank you

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Fail to upload QC files into Panorama QC folders
(2 responses) kaitm 2021-09-16 14:04:10

QC folders require that all documents use the same molecule, but they did not match. Please create a new QC folder if you wish to work with different molecules. Attempted import: [C19H29N3O5, C27H38N2O4, C28H37N5O7, C32H41NO2, C33H40N2O9, C7H10N4O2S, C8H10N4O2, C8H9NO2]. Previously imported: [C12H14N4O4, C19H29N3O5, C27H38N2O4, C28H37N5O7, C32H41NO2, C33H40N2O9, C7H10N4O2S, C8H10N4O2, C8H9NO2].

QC folders require that all documents use the same molecule, but they did not match. Please create a new QC

This is an error message I'm getting when trying to upload new files onto QC Panorama. There were edits made to the original Skyline documents and the molecule was modified. I tried reverting the file back but it's still continuing to error when I use this Skyline file. I wanted to see what my options were with uploading a QC. Could I delete all the information already on the Panorama QC and then re-upload the files on processed through the Skyline method? How would I go about wiping the QCs already loaded?



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Importing R Markdown report
(2 responses) Juan C. Rojas E. 2021-09-14 02:30:54

Hi Panorama team!

I am wondering if there is a way to either display a R Markdown report in Panorama that was saved as an HTML file. I tried copying the generated HTML text to the Advanced Editor of a custom Wiki, but I got the following error after clicking "Save and Close":

Error: "There was a problem wile saving: Illegal element"

I have also just tried importing the file in a "Files" Web Part, but fort only the .html file I am getting the following error:

"You do not have privileges to upload"

For all other file types (so far) I have been able to upload.

Sorry if I am quite new to this whole web display and I am not approaching this right, but I hope you can help me with this.
Juan C. Rojas E.

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issues with uploading skyline file to Panorama Public
(3 responses) realjune 2021-08-23 02:15:18

Dear Panoramaweb team,

I submitted skyline files to Panorama Public on 8/14/21, and I found that the files are still on "Copy pending" status.
I realized some files from other teams were uploaded to Panorama Public on 8/16/21 or 8/17/21.
I am wondering why my skyline files are still not copied to Panorama Public.
The skyline file I submitted is on revision now, so I appreciate any help for solving this problem.

Injoon Yeo

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Collision Energy per transition displayed as "0.0000".
(5 responses) Roman Sakson 2021-07-20 13:37:43

Dear Panorama team,

I am now in the process of uploading a targeted MS Run to Panorama (preparation to publish). This is some MRM data where CEs were optimized for each transition. An optimized library ".optdb" as well as the usual CE Equation were selected in the transition settings in Skyline at the moment of data upload to the Panorama folder. When I click on the peptides in Panorama in the MS Run, one CE as well as one DP-value per peptide are being displayed, those values are probably derived from the equations. However, when I select transitions to be displayed and I customize the grid for CE values to be shown at transition level, I am getting a CE value of 0.0000 everywhere. I expected my optimized CE values to appear there, am I doing something wrong?

Thanks a lot in advance,

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issues with folder format and raw data upload
(2 responses) spacil 2021-07-14 02:49:33


I'm having persistent issues with the raw data upload in my folder named: "Profiling tryptophan catabolites and APP in DBS". Other folders have the same setting and work normally, please fix the bug.


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Column 'aminoacid' error importing a Skyline ZIP file into Panorama
(3 responses) Nathan Manes 2021-06-28 17:29:17

The ZIP:
NIH_NitaLazar / Manes_BMDM_TLR-Chemotaxis_2021 /

Uploading the Skyline "Share" ZIP worked fine. When I clicked "Import Data", It failed. Snippet of the log file:

28 Jun 2021 17:02:25,214 INFO : Expanding
28 Jun 2021 17:02:25,353 INFO : 1% Done
28 Jun 2021 17:03:03,307 ERROR: Import failed
28 Jun 2021 17:03:03,355 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask'
28 Jun 2021 17:03:03,357 ERROR: aminoacid: Value is too long for column 'aminoacid', a maximum length of 30 is allowed. Supplied value was 64 characters long.

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Array dimension Error
(1 response) dkueltz 2021-05-01 11:09:27

I am getting an error with the latest Skyline daily release that I had not seen before. This pops up when I import a results file with a large RT range specified. The assay library contains less than 200,000 transitions - so it should not be a problem. I did not see this error with previous versions even though the assay libraries I had used before were much larger (>1 million transitions). The error message is below. FYI - i am only allowing for about 15 or so PTMs in the corresponding document. I am using a workstation with 64GB RAM, which in my mind makes it unlikely that memory limitation is the issue. The results file import also crashed a couple of times already with the latest release and it kept hanging up on me when trying to close -reopen - I had to completekly uninstall and reinstall Skyline daily to render it to respond properly again - something seems to have changed that renders the import of results files more error-prone.
Thanks for looking into the array dimension limit errror pasted below,

At 10:57 AM:
Failed importing results file 'E:\EAM0025_Oremo-Testes_V8-AmBic\DIA\EAM0021_CnF1T_V8AmBic_1-C,2_01_3712.d'.
Array dimensions exceeded supported range.
pwiz.Skyline.Model.Results.ChromCacheBuildException: Failed importing results file 'E:\EAM0025_Oremo-Testes_V8-AmBic\DIA\EAM0021_CnF1T_V8AmBic_1-C,2_01_3712.d'.
Array dimensions exceeded supported range. ---> System.OverflowException: Array dimensions exceeded supported range.
at pwiz.Skyline.Model.Results.ChromGroups.ReleaseChromatogram(Int32 chromatogramIndex, Single retentionTime, ChromCollector collector, TimeIntensities& timeIntensities) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Results\ChromCollector.cs:line 625
at pwiz.Skyline.Model.Results.SpectraChromDataProvider.Collectors.ReleaseChromatogram(Int32 chromatogramIndex, ChromGroups chromGroups, TimeIntensities& timeIntensities) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 1298
at pwiz.Skyline.Model.Results.SpectraChromDataProvider.GetChromatogram(Int32 id, Target modifiedSequence, Color peptideColor, ChromExtra& extra, TimeIntensities& timeIntensities) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 609
at pwiz.Skyline.Model.Results.ChromData.Load(ChromDataProvider provider, Target modifiedSequence, Color peptideColor) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Results\ChromData.cs:line 77
at pwiz.Skyline.Model.Results.ChromDataSet.Load(ChromDataProvider provider, Target modifiedSequence, Color peptideColor) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Results\ChromDataSet.cs:line 234
at pwiz.Skyline.Model.Results.PeptideChromDataSets.Load(ChromDataProvider provider) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Results\PeptideChromData.cs:line 143
at pwiz.Skyline.Model.Results.ChromCacheBuilder.Read(ChromDataProvider provider) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 439
at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 252
--- End of inner exception stack trace ---

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Problems uploading files and them being recognized
(1 response) mmart137 2021-03-15 16:43:51

I'm trying to publish a full dataset for a paper. When I hit submit, it says that there are files missing that have clearly been uploaded. In addition, it is asking for new, different raw files that it says are missing every time I hit 'resubmit'. Can you please help here? Thanks!

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Problem uploading Skyline file to home folder
(1 response) michael-e-wright 2021-03-02 10:21:47

Can't access home folder to upload a Skyline file. Am I doing something wrong? Also, how do I control permissions to view the folder?

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Problems with AutoQC loader
(5 responses) a gorol 2021-01-05 01:35:08


since yesterday i have problems with uploading QC Files to Panorama. We are using the AutoQC loader since May last year and it worked perfectly for us. Since yesterday i can not start the configuration anymore. The log File gives me several error messages but i don`t know how to solve this issue. I attached the LogFiles.
I assume there is a problem with the skyline document but since this is the same one we are using since May I am not sure. Can you help us?



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Uploading error to Panorama
(2 responses) roberthardt 2021-01-04 06:16:41

Dear Skyline-Team,

I cannot upload any sky-zip files to the Panorama server anymore. I'm pretty confident that this has been caused by myself while using the "Cancel upload" button within Skyline daily. I also tried by myself cleaning the upload queue within Panorama, but this is also not working. I guess the server itself somehow got stuck?



 panorama canceling.PNG  panorama canceling2.PNG 
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Error while uploading data to Panorama from Skyline-daily
(1 response) hana kucharikova 2020-11-06 06:58:32


I have encountered an error while uploading data from Skyline-daily ( to Panorama.
I am using GoogleChrome web-browser and Windows 10 OS (OS build 18363.1139).

I have opened my Skyline document, in section File press Upoload to Panorama, selected folder and start uploading the file. At the end of upload (when 98% was finished) an error message appear.

"Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask'
ERROR: SqlExecutor.execute(); uncategorized SQLException for SQL []; SQL state [25P02];"

There was also warning about Skyline versions incompatibility: "The version of this Skyline document is 20.14. This is newer than the highest supported version 4.1".

I have tried the upload again into new folder and after the notes in Skyline were removed, neither helped.

Detail information about the error log are in the attachment.

Can you, please, help me?
Thank you,

 Panorama upload_log_error 
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AutoQC loader disconnects from local servers
(2 responses) David Kotol 2020-10-20 05:14:53

I have been struggling with the AutoQC for some time now. It works great but just for about 24 hours. Then I lose connection to local server where the data, in this case Thermo raw files, is stored. The connection to server remains lost until the PC is restarted.

To describe the problem:
1. QC sample is measured
2. Resulting file is automatically pushed to MassStorage local server (using
scheduler and .bat script) and to a designated folder
3. Another computer is running the AutoQC Loader and is paired
with the designated folder on the server
4. The QC software locates the result file on the server and uploads it
to the Panorama

This works for about 24 hours and then connection to the server is lost. The connection is restored by restarting the computer. But just for another 24 hours or so.

What I tried with always the same result:
- reinstall AutoQC Loader
- update AutoQC Loader
- use different computer
- reinstall and update Skyline

Is this a known issue or is it something with the servers of my institution, please? The institutional IT guys claim it is the software so I just want to check if anyone experienced this issue when loading raw files from servers and not the local storage.

All the best,
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AutoQC and skyline stuck at IMPORT WAITING
(2 responses) DennisGoldfarb 2020-10-06 06:51:13

I created a new AutoQC folder, but am having trouble uploading to it. I tried cancelling everything in the data pipeline, but those are now stuck in "cancelling". Any help would be appreciated. Thanks.

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Unable to authenticate my panorama site password and email within Auto QC
(2 responses) chris brown-2 2020-09-29 14:01:19

Hello - I am unable to sign in to my panorama account and password in AutoQC to upload QC data.

Skyline account:
AutoQC loader

Location of Panorama Folder: /Corteva Agrisciences - MSCOE/Lumos-Daily QC

Exact error message:
Configuration Validation Error
The username and password could not be authenticated with the panorama server.

Let me know what else you need.

Thanks, cjb

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Panorama for AutoQC
(1 response) imene bousahba 2020-09-17 03:23:10

I wanted to know if it is necessary to use panorama for AutoQC (to publish my files in purpose to view the results)
If not how can i do ?
Thank you very much

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New Auto-QC install and transferring Configurations
(1 response) Alejandro Cohen 2020-09-01 10:19:07


I'm transferring my configurations from one computer to another in a new installation of AutoQC ( I followed the instructions as per your email and get the error attached. The passwords are there in the original configurations. I tried editing the .xml file with the correct password, but that does not seem to work either

Is there a way around this?


 Trouble Shoot Auto QC_Screen shots.docx 
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Error uploading from skyline-daily but not skyline
(2 responses) d foschepoth 2020-08-06 11:47:01
I want to upload a bunch of skyline files and all but two of them I could readily upload using Skyline without issues. But two files provided by a colleague were opviously edited with a newer version so I used skyline-daily to upload. Upon Üpload to Panorama" I get this error message of a connection error (The program added some german text in the error report):
Brief german list of ingredients:
Zeile = Line
bei =at
Ende der internen Ausnahmestapelüberwachung = End of internal exception stack monitoring (or so)

System.Reflection.TargetInvocationException: Failed attempting to retrieve information from the following servers: ---> System.Exception: Failed attempting to retrieve information from the following servers:
   bei pwiz.Skyline.FileUI.PublishDocumentDlg.PublishDocumentDlgLoad(List`1 listServerFolders) in C:\proj\pwiz_x64\pwiz_tools\Skyline\FileUI\PublishDocumentDlg.cs:Zeile 139.
   bei pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action`1 performWork) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:Zeile 254.
   --- Ende der internen Ausnahmestapelüberwachung ---
   bei pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Util\Util.cs:Zeile 1942.
   bei pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:Zeile 202.
   bei pwiz.Skyline.FileUI.PublishDocumentDlg.PublishDocumentDlg_Load(Object sender, EventArgs e) in C:\proj\pwiz_x64\pwiz_tools\Skyline\FileUI\PublishDocumentDlg.cs:Zeile 88.

I tried with the most recent versions of skyline-daily on multiple computers. Always same outcome. The current version is of skyline-daily.

Any ideas what could be the cause for this?
Thanks in advance
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Manuscript on Biotin Acceptor Peptide
(3 responses) akulyyasov 2020-08-06 05:40:33

Dear Skyline/Panorama team and users,
I have uploaded the graphical abstract of the manuscript which I prepared during lockdown time.
In this paper, I summarized the application of Biotin Acceptor Peptide 1070 which is used in proximity utilizing biotinylation method.
The paper contains the description of its design, construction, and quantitation by Skyline software on the example of DNA dependent interaction of Sox2 and Oct4.
If someone would like to read the text of the article, please send a message to my address
I will be very grateful for any help in improving the text, remarks, and comments on this manuscript.

With best regards,

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Creating folders
(1 response) weixiandeng1990 2020-07-24 18:39:07

I can't see creating folder tab on the dashboard where it is supposed to be. Is it because I'm not an administrator of the lab account?

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AutoQC problem
(1 response) eversa 2020-07-23 13:11:49

Hi, I tried to run a AutoQC and got the below error message:

--in="C:\ZWC-autoQC\" --remove-before=6/23/2020 --import-file="C:\ZWC-autoQC\ZWC_459_a1b3_10uMOPD.raw" --import-on-or-after=6/23/2020 --save
--panorama-server="" --panorama-folder="Washington University STL - Evers Lab/AutoQC" --panorama-username=""
[7/23/2020 2:26:58 PM] Opening file...
[7/23/2020 2:26:59 PM] File opened.
[7/23/2020 2:27:00 PM]
[7/23/2020 2:27:00 PM] Adding results...
[7/23/2020 2:27:00 PM] 1. C:\ZWC-autoQC\ZWC_459_a1b3_10uMOPD.raw
[7/23/2020 2:27:00 PM]
[7/23/2020 2:27:01 PM] ERROR: Error: Failed importing the results file C:\ZWC-autoQC\ZWC_459_a1b3_10uMOPD.raw.
[7/23/2020 2:27:01 PM] Message: pwiz.Skyline.Model.Results.MissingDataException: The file C:\ZWC-autoQC\ZWC_459_a1b3_10uMOPD.raw does not contain SRM/MRM chromatograms. To extract chromatograms from its spectra, go to Settings > Transition Settings > Full-Scan and choose options appropriate to the acquisition method used. ---> pwiz.Skyline.Model.Results.NoFullScanFilteringException: The file C:\ZWC-autoQC\ZWC_459_a1b3_10uMOPD.raw does not contain SRM/MRM chromatograms. To extract chromatograms from its spectra, go to Settings > Transition Settings > Full-Scan and choose options appropriate to the acquisition method used.
[7/23/2020 2:27:01 PM] at pwiz.Skyline.Model.Results.SpectraChromDataProvider..ctor(MsDataFileImpl dataFile, ChromFileInfo fileInfo, SrmDocument document, IRetentionTimePredictor retentionTimePredictor, String cachePath, IProgressStatus status, Int32 startPercent, Int32 endPercent, IProgressMonitor loader) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 98
[7/23/2020 2:27:01 PM] at pwiz.Skyline.Model.Results.ChromCacheBuilder.CreateSpectraChromProvider(MsDataFileImpl dataFile, ChromFileInfo fileInfo) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 1265
[7/23/2020 2:27:01 PM] at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 237
[7/23/2020 2:27:01 PM] --- End of inner exception stack trace ---
[7/23/2020 2:27:01 PM]
[7/23/2020 2:27:01 PM] ERROR: SkylineRunner.exe exited with code 0. Skyline document import failed.
[7/23/2020 2:27:01 PM] Adding C:\ZWC-autoQC\ZWC_459_a1b3_10uMOPD.raw to the re-import queue.
[7/23/2020 2:27:01 PM] Attempting to re-import C:\ZWC-autoQC\ZWC_459_a1b3_30uMOPD_200719145246.raw.
[7/23/2020 2:27:01 PM] ZWC_459_a1b3_30uMOPD_200719145246.raw is ready
[7/23/2020 2:27:01 PM] Running SkylineRunner.exe with args:
[7/23/2020 2:27:01 PM]

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Insufficient system resources
(18 responses) Tobias Kockmann 2020-07-23 02:24:44

Hi Panorama support,

I am getting the following error message when trying to execute autoQC:

	Windows 			: 6.3.9600.0 (Win32NT)
	Common Language Runtime 	: 4.0.30319.42000
	System.Deployment.dll 		: 4.7.3062.0 built by: NET472REL1
	clr.dll 			: 4.7.3221.0 built by: NET472REL1LAST_C
	dfdll.dll 			: 4.7.3062.0 built by: NET472REL1
	dfshim.dll 			: 6.3.9600.16384 (winblue_rtm.130821-1623)

	Deployment url			: file:///C:/Users/autoQC_user/AppData/Roaming/Microsoft/Windows/Start%20Menu/Programs/AutoQC/AutoQC.appref-ms%7C
	Deployment Provider url		:

	Below is a summary of the errors, details of these errors are listed later in the log.
	* Activation of C:\Users\autoQC_user\AppData\Roaming\Microsoft\Windows\Start Menu\Programs\AutoQC\AutoQC.appref-ms| resulted in exception. Following failure messages were detected:
		+ Insufficient system resources exist to complete the requested service. (Exception from HRESULT: 0x800705AA)

	No transaction error was detected.

	There were no warnings during this operation.

	* [7/23/2020 11:07:47 AM] : Activation of C:\Users\autoQC_user\AppData\Roaming\Microsoft\Windows\Start Menu\Programs\AutoQC\AutoQC.appref-ms| has started.
	* [7/23/2020 11:07:47 AM] : Performing necessary update check as specified by the deployment.

	Following errors were detected during this operation.
	* [7/23/2020 11:07:49 AM] System.Runtime.InteropServices.COMException
		- Insufficient system resources exist to complete the requested service. (Exception from HRESULT: 0x800705AA)
		- Source: mscorlib
		- Stack trace:
			at System.Deployment.Internal.Isolation.IsolationInterop.CreateActContext(CreateActContextParameters& Params)
			at System.Deployment.Internal.Isolation.IsolationInterop.CreateActContext(IDefinitionAppId AppId)
			at System.ActivationContext.CreateFromName(ApplicationIdentity applicationIdentity)
			at System.Deployment.Application.ApplicationActivator.Activate(DefinitionAppId appId, AssemblyManifest appManifest, String activationParameter, Boolean useActivationParameter)
			at System.Deployment.Application.ApplicationActivator.ProcessOrFollowShortcut(String shortcutFile, String& errorPageUrl, TempFile& deployFile)
			at System.Deployment.Application.ApplicationActivator.PerformDeploymentActivation(Uri activationUri, Boolean isShortcut, String textualSubId, String deploymentProviderUrlFromExtension, BrowserSettings browserSettings, String& errorPageUrl, Uri& deploymentUri)
			at System.Deployment.Application.ApplicationActivator.PerformDeploymentActivationWithRetry(Uri activationUri, Boolean isShortcut, String textualSubId, String deploymentProviderUrlFromExtension, BrowserSettings browserSettings, String& errorPageUrl)
--- End of stack trace from previous location where exception was thrown ---
			at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw()
			at System.Deployment.Application.ApplicationActivator.PerformDeploymentActivationWithRetry(Uri activationUri, Boolean isShortcut, String textualSubId, String deploymentProviderUrlFromExtension, BrowserSettings browserSettings, String& errorPageUrl)
			at System.Deployment.Application.ApplicationActivator.ActivateDeploymentWorker(Object state)

	No transaction information is available.

Any idea what this might indicate?

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DIA can't demultiplex
(1 response) wendy white 2020-06-18 11:35:55
I made a DIA overlap method on the instrument- but when I use MS Convert GUI, it fails and reports this error:
Opening file "C:\Users\WHITEW01\Desktop\Histones\2020_0617_histones.raw" for read...
Calculating SHA1 checksum...
Writing "C:\Users\WHITEW01\Desktop\Histones\2020_0617_histones.mzML"...
Failed - System.Exception: SpectrumToIndices() Number of demultiplexing windows changed. Minimum window size or window boundary tolerance may be set too low.
   at pwiz.CLI.msdata.MSDataFile.write(MSData msd, String filename, WriteConfig config, IterationListenerRegistry iterationListenerRegistry)
   at MSConvertGUI.MainLogic.processFile(String filename, Config config, ReaderList readers, Map`2 usedOutputFilenames)
   at MSConvertGUI.MainLogic.Go(Config config, Map`2 usedOutputFilenames).
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Building Overlap DIA on Thermo Exploris 480
(1 response) wendy white 2020-06-18 11:34:50
I want to quantitate histone modifications using Thermo Exploris 480. When I make the acquisition method from Skyline, this error is displayed: Columns don’t match:
 error DIA exploris.docx 
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Problems adding new chromatograms to assay library
(4 responses) Andreas Hober 2020-05-08 06:28:13

I have a Panorama Assay Library to which I have uploaded several runs from one of our mass spectrometers. However, recently we have had some problems while rerunning some samples. Since the proteins already exist in the library we get prompted with the following message: "There are 36 conflicting proteins in this folder. Resolve conflicts", but when we try to update these proteins an error occurs (see attached screenshot).

How can we resolve this issue?

Best regards,

 Screen Shot 2020-05-08 at 15.23.03.png 
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Recurring Error pinging Panorama server
(7 responses) Roman Sakson 2020-05-04 01:04:52

Dear Panorama Team,

we seem to have recurring troubles pinging the Panorama server (it started already before Easter and goes on). Remarkably, it seems to work every now and then, so that we can upload our QC files, however, delays do occur and I would like to understand where this error comes from (to my knowledge, we did not change anything regarding our internet connection). A typical error message looks like this (could go on for hours or even days):

[5/4/2020 5:20:42 AM] ERROR: [5/4/2020 5:20:42 AM] Error pinging Panorama server
System.Net.WebException: Unable to connect to the remote server ---> System.Net.Sockets.SocketException: A connection attempt failed because the connected party did not properly respond after a period of time, or established connection failed because connected host has failed to respond
at System.Net.Sockets.Socket.DoConnect(EndPoint endPointSnapshot, SocketAddress socketAddress)
at System.Net.ServicePoint.ConnectSocketInternal(Boolean connectFailure, Socket s4, Socket s6, Socket& socket, IPAddress& address, ConnectSocketState state, IAsyncResult asyncResult, Exception& exception)
--- End of inner exception stack trace ---
at System.Net.WebClient.UploadValues(Uri address, String method, NameValueCollection data)
at AutoQC.WebClientWithCredentials.Post(Uri uri, NameValueCollection postData)
at AutoQC.WebPanoramaClient.PingPanorama(String folderPath, String username, String password)
at AutoQC.PanoramaPinger.PingPanoramaServer()

Thank you very much in advance!


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ERROR: Index 0 out of bounds for length 0
(3 responses) Maithreyan 2020-04-27 08:21:41

When I try to upload the QC data from Skyline to panorama, I am getting the following error, I have attached the log file. I think it is something to do with our data. Could you please explain it. Also, Auto QC is not uploading the data automatically to Panorama even after giving the required details for panorama.

27 Apr 2020 08:12:43,074 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask'
27 Apr 2020 08:12:43,079 ERROR: Index 0 out of bounds for length 0
java.lang.IndexOutOfBoundsException: Index 0 out of bounds for length 0

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Error when resubmitting data
(1 response) Markus 2020-04-25 14:21:31

Dear Panoramaweb team,

during revision we have added a second dataset to a project, which had already received a ProteomeXchange ID for review before. I have now added all data to the existing project and then tried to resubmit but I get the following error:
You are not authorized to edit the short URL 'fK1Nbw'

The former submission was done by a colleague of mine (who has meanwhile left) but I have full rights for the project - could that still be the problem?

Many thanks in advance for your help with this! BTW, would the PX-ID remain the same or would a new one be assigned?


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Upload to Panorama error - ERROR: MoleculeId: Value is too long for column 'MoleculeId'
(1 response) emmanuel varesio 2020-04-23 10:06:31


I'm setting up two similar autoQC configurations for either ACN or MeOH gradient SST with the same LCMS QC mix for a Waters H-Class - G2 TOF MS.

Raw data filenames are similar, folder names for each solvent are similar, the two Skyline template files have the same molecule names and transitions for MH+ .... in brief everything is the same except that it's either ACN or MeOH written in the names.

When running the MeOH AutoQC loader config this works fine, but when switching to ACN dataset I got the following error message at the stage when the Skyline zip file is apparently uploaded to Panorama server.

Any help appreciated.



23 Apr 2020 09:53:26,365 INFO : Starting to run task 'org.labkey.targetedms.pipeline.TargetedMSImportTask' at location 'webserver-high-priority'
23 Apr 2020 09:53:26,392 INFO : Starting to import Skyline document from
23 Apr 2020 09:53:26,395 INFO : Expanding QC_Xevo-ACN_LCMS_QCmix_PrecOnly.skyd
23 Apr 2020 09:53:26,451 INFO : Expanding
23 Apr 2020 09:53:26,464 INFO : Expanding
23 Apr 2020 09:53:26,476 WARN : The version of this Skyline document is 20.11. This is newer than the highest supported version 4.1
23 Apr 2020 09:53:26,486 INFO : 8% Done
23 Apr 2020 09:53:26,851 INFO : 11% Done
23 Apr 2020 09:53:26,852 INFO : Inserting QC-Xevo_LC_ACN
23 Apr 2020 09:53:26,865 INFO : 16% Done
23 Apr 2020 09:53:26,895 INFO : 19% Done
23 Apr 2020 09:53:26,918 INFO : 27% Done
23 Apr 2020 09:53:26,939 INFO : 31% Done
23 Apr 2020 09:53:26,978 INFO : 39% Done
23 Apr 2020 09:53:27,001 INFO : 43% Done
23 Apr 2020 09:53:27,021 INFO : 50% Done
23 Apr 2020 09:53:27,102 INFO : 55% Done
23 Apr 2020 09:53:27,630 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask'
23 Apr 2020 09:53:27,633 ERROR: MoleculeId: Value is too long for column 'MoleculeId', a maximum length of 200 is allowed. Supplied value was 241 characters long.
Caused by: MoleculeId: Value is too long for column 'MoleculeId', a maximum length of 200 is allowed. Supplied value was 241 characters long.
23 Apr 2020 09:53:27,729 ERROR: MoleculeId: Value is too long for column 'MoleculeId', a maximum length of 200 is allowed. Supplied value was 241 characters long.
org.labkey.api.query.RuntimeValidationException: MoleculeId: Value is too long for column 'MoleculeId', a maximum length of 200 is allowed. Supplied value was 241 characters long.
Caused by: MoleculeId: Value is too long for column 'MoleculeId', a maximum length of 200 is allowed. Supplied value was 241 characters long.

view message
Auto QC Trend report
(4 responses) Srujana 2020-04-16 13:11:03


I am working on Metabolomics data files for Skyline/PanoramaWeb/AutoQC. I am looking for answers for below queries.

  1. While installation of AutoQC Loader I am having issues with updated version, which is different from the tutorial version. I don.t see create new configuration tab or panorama settings and has different tabs like import and export. How do I use autoQC loader updated version.
  2. While creating QC trend report, run date tab is showing blocked and without that report doesn't proceed to next step.

Thank you,

view message
AutoQC Loader
(2 responses) Srujana 2020-04-07 11:59:08

Hi Panorama development team,

I have recently got access to ParamaWeb. I am working on "Sharing Skyline Document" tutorial. While uploading a file, "IMPORT WAITING" prompt appearin. And in Panorama page also i am seeing the same information. Could you please suggeste me if I need to get additonal acess to use this tutorial? As mentioned in the tutorial overiwe section, I didnt fid a TOTUORIAL folder but I have created a folder in Icahn Scool of Medicine page.
I have a uploaded word document with screen shots.

Thanks- Srujana

view message
Upload raw data
(1 response) ferdinando cerciello 2020-04-04 09:15:40

Hi Vagisha,

I have another question: I m now trying to upload the raw data related to the Skyline files, but when I go to the Raw Data page it tells it is not possible to upload data. Indeed I can t drop and drag anything or even upload by browsing to them. Also, I can t create subfolders. The error report is something like...file root web to this part could not be found.

Is there any setting I need to change in the file settings in order to be able to upload the raw files?

Thank you

view message
Errror: Aminoacid value
(2 responses) ferdinando cerciello 2020-03-30 14:43:09

Hi all,
I m trying to upload my files on panorama, but when submitting the import button, I get this error back: AminoAcid: value is too long for column "AminoAcid", a maximum length of 1 is allowed. Supplied value was 4 characters long. I can t understand to what it refers. I tried by shortening the name of the files, but it did not help. The aminoacids within the files are normally visible within the Skyline file.

Thank you

view message
Error configuring new instrument in Panorama
(1 response) Taher Elgierari 2020-03-26 14:05:14

just configured a new instrument in Panorama, that went fine, but when configuring the AutoQC I kept getting the an error saying the folder i entered is not a Panorama folder, i confirmed the folder directory and name matches what in Panorama.

view message
Error when adjusting
(4 responses) Taher Elgierari 2020-02-07 17:35:49

when using "Monitoring molecular contaminants and interferences in proteomic data sets" document i get error every time i try to adjust the resolution to accommodate Sciex 6600 instruments , it is fixed on orbtrap 60,000 at 400, is there a way to change it, or it doesn't matter sense it contains MS1 data only.
the link to the document;

view message
Errors uploading XL data to Panorama
azelter 2020-01-10 14:53:40
I have successfully uploaded one skyline document to Panorama which contains XL targets created by Nick's crosslinker tool. Two subsequent runs failed with different errors (see below).
Any insight into what the problem might be would be much appreciated! Thanks very much for your help!

10 Jan 2020 14:36:18,683 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask'
10 Jan 2020 14:36:18,684 ERROR: SqlExecutor.execute(); uncategorized SQLException for SQL []; SQL state [25P02]; error code [0]; ERROR: current transaction is aborted, commands ignored until end of transaction block; nested exception is org.postgresql.util.PSQLException: ERROR: current transaction is aborted, commands ignored until end of transaction block
Caused by: org.postgresql.util.PSQLException: ERROR: current transaction is aborted, commands ignored until end of transaction block
Caused by: org.postgresql.util.PSQLException: ERROR: duplicate key value violates unique constraint "uix_auditlogentry_document"
  Detail: Key (documentguid, entryhash)=(f13e38db-d3d1-483f-9157-a8ed31613ac8, R5jGBMHhj59meKIGY6s1/mns8Z4=) already exists.
10 Jan 2020 14:44:39,469 INFO : Done parsing Skyline document.
10 Jan 2020 14:44:41,209 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask'
10 Jan 2020 14:44:41,209 ERROR: Index 0 out of bounds for length 0
view message
Issue with Unimod modification IDs needed for ProteomeXchange submission
(5 responses) j hamey 2019-12-10 13:39:36

Hi there,

I'm having an issue submitting data to Panorama public that I would like to get a ProteomeXchange ID for.

In order to analyse my data in Skyline, I had to create custom modifications. In particular, I created two modifications that are essentially the same as two existing unimod modifications (accessions 1291 and 298), but which were not findable in Skyline.

The submission process says that the modifications must have a Unimod ID in order to get a ProteomeXchange ID, and that the remedy is to edit the modifications in Skyline and reupload everything. However, this seems like it would be untenable given the number of Skyline documents and peptides in my dataset, and the modification names in Unimod would also make the dataset more confusing. Is it possible to simply associate the data with the two relevant Unimod modifications rather than change every instance of these modifications?

Thank you for your help.


view message
Not possible to view chromatogram library
(2 responses) Andreas Hober 2019-11-26 07:19:17

I have been working quite a lot with Panorama for building chromatogram libraries and it has worked splendidly. However, the libraries that I have downloaded lately have all been corrupt in some way and I cannot view the chromatograms in Skylines, but I can clearly view them in the corresponding Panorama project.

Is there anything I can do in order to solve this or is there some issue which the creation of the .clib on the server?
I have attached the error message that I receive below.

Best regards

Installation ID: cfcf80a6-7631-4cba-8bf1-6cbb20a1ff50
Exception type: NullReferenceException
Error message: Object reference not set to an instance of an object.


Stack trace:

   at pwiz.Skyline.Model.Lib.ChromLib.ChromatogramLibrary.ReadChromatogram(ChromLibSpectrumInfo info) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Lib\ChromLib\ChromatogramLibrary.cs:line 96
   at pwiz.Skyline.Model.Lib.CachedLibrary`1.LoadChromatogramData(Object spectrumKey) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Lib\Library.cs:line 1044
   at pwiz.Skyline.SettingsUI.ViewLibraryDlg.UpdateUI(Boolean selectionChanged) in C:\proj\pwiz_x64\pwiz_tools\Skyline\SettingsUI\ViewLibraryDlg.cs:line 697
   at pwiz.Skyline.SettingsUI.ViewLibraryDlg.listPeptide_SelectedIndexChanged(Object sender, EventArgs e) in C:\proj\pwiz_x64\pwiz_tools\Skyline\SettingsUI\ViewLibraryDlg.cs:line 1070
   at System.Windows.Forms.ListBox.OnSelectedIndexChanged(EventArgs e)
   at System.Windows.Forms.ListBox.set_SelectedIndex(Int32 value)
   at pwiz.Skyline.SettingsUI.ViewLibraryDlg.UpdateListPeptide(Int32 selectPeptideIndex) in C:\proj\pwiz_x64\pwiz_tools\Skyline\SettingsUI\ViewLibraryDlg.cs:line 512
   at pwiz.Skyline.SettingsUI.ViewLibraryDlg.UpdateViewLibraryDlg() in C:\proj\pwiz_x64\pwiz_tools\Skyline\SettingsUI\ViewLibraryDlg.cs:line 311
   at pwiz.Skyline.SettingsUI.ViewLibraryDlg.ViewLibraryDlg_Load(Object sender, EventArgs e) in C:\proj\pwiz_x64\pwiz_tools\Skyline\SettingsUI\ViewLibraryDlg.cs:line 222
   at System.Windows.Forms.Form.OnLoad(EventArgs e)
   at pwiz.Skyline.Util.FormEx.OnLoad(EventArgs e) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Util\FormEx.cs:line 198
   at System.Windows.Forms.Form.OnCreateControl()
   at System.Windows.Forms.Control.CreateControl(Boolean fIgnoreVisible)
   at System.Windows.Forms.Control.CreateControl()
   at System.Windows.Forms.Control.WmShowWindow(Message& m)
   at System.Windows.Forms.Control.WndProc(Message& m)
   at System.Windows.Forms.Form.WmShowWindow(Message& m)
   at System.Windows.Forms.NativeWindow.Callback(IntPtr hWnd, Int32 msg, IntPtr wparam, IntPtr lparam)

Exception caught at: 
   at System.Windows.Forms.Application.ThreadContext.OnThreadException(Exception t)
   at System.Windows.Forms.Control.WndProcException(Exception e)
   at System.Windows.Forms.NativeWindow.Callback(IntPtr hWnd, Int32 msg, IntPtr wparam, IntPtr lparam)
   at System.Windows.Forms.SafeNativeMethods.ShowWindow(HandleRef hWnd, Int32 nCmdShow)
   at System.Windows.Forms.SafeNativeMethods.ShowWindow(HandleRef hWnd, Int32 nCmdShow)
   at System.Windows.Forms.Control.SetVisibleCore(Boolean value)
   at System.Windows.Forms.Form.SetVisibleCore(Boolean value)
   at System.Windows.Forms.Form.Show(IWin32Window owner)
   at pwiz.Skyline.SkylineWindow.OpenLibraryExplorer(String libraryName) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Skyline.cs:line 2921
   at pwiz.Skyline.SkylineWindow.ViewSpectralLibraries() in C:\proj\pwiz_x64\pwiz_tools\Skyline\Skyline.cs:line 2871
   at pwiz.Skyline.SkylineWindow.spectralLibrariesToolStripMenuItem_Click(Object sender, EventArgs e) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Skyline.cs:line 2840
   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\pwiz_x64\pwiz_tools\Skyline\Program.cs:line 305

view message
Upload to Panorama Public
michael plank 2019-10-01 11:19:41


could anyone please tell me what 'Drag and drop to the files browser in the Raw Data tab to upload files' means when trying to do an upload to Panorama Public. (I encounter this after selecting 'Submit'.)
When I press 'Upload Raw Data', I always get reverted to the project folder, but I don`t see a Raw Data tab'.


view message
Folder on Panorama
(2 responses) romeally 2019-09-20 12:00:16

I am trying to set up AutoQC and when I input the path to my folder on Panorama it says it is not a Panorama folder. I can get on Panorama and navigate to the folder so it does exist. Do AutoQC folders need a special designation? I am attaching the error I received as a screen capture. How do I connect to my folder?
Bob O'Meally

view message
Submit button is missing
(2 responses) Sabrina Geisslitz 2019-09-16 23:32:54

I already submitted data of another project to Panorama. I think, this time, I did it exactly the same way. I created a folder and two subfolders. In the main folder, I created the "targeted MS experiment" and included the subfolders. I checked the folder permissions. They are exactly the same as for the previous project. I also checked that the folders are "Panorama" folders and not Collaboration folders.
But now, the submit button is missing. I used Skyline version and Mozilla Firefox.
I hope you can help me that I can submit my data.

view message
Updating chromatogram libraries with metadata
(1 response) Andreas Hober 2019-08-19 07:52:32

I was only wondering if it would be possible to update chromatogram libraries on Panorama with metadata from e.g. a background proteome.
It would be very useful when looking at the overviews for protein coverage etc. I am currently working with quite a few Skyline files where all the proteins are named based on the standards that have been used for the method development and it would be great if I would be able to add a background proteome for grouping of the peptides once they have been added to assay project on Panorama, since now I have quite a few "proteins" which actually map towards the same actual protein.

Best regards

view message
AutoQC Loader Fails to download
(1 response) romeally 2019-08-05 13:39:41

Is anyone else getting this error when they try to run setup? I am getting the same error when I try to upgrade Skyline and I have never had any issues with that in the past. Could there be a firewall issue?

An error occurred trying to download ''.

See the setup log file located at 'C:\Users\BobO\AppData\Local\Temp\VSDEF38.tmp\install.log' for more information.

view message
Building assay libraries using Panorama
Andreas Hober 2019-07-24 18:11:55

I have gone through the tutorial material for storing chromatogram libraries using Panorama and that seems to be working great from a perspective of continuously expanding your assay library. I was wondering if it is possible to store iRT libraries and Collision energy libraries in a similar way using Panorama.

If not, is this something that you plan on implementing in the future?

Best regards

view message
Error message when trying to view chromatogram in Panorama
(4 responses) Azad Eshghi 2019-07-04 14:29:17

Dear folks,

I've "successfully" uploaded data to Panorama, however when I try to view chromatograms I receive an error message. I have attached a screenshot of the message. Thanks in advance.

 Panorama error message trying to view chromatogram.pdf 
view message
AutoQC Multiple (at least 2?) Metrics Side by side??
(10 responses) Alejandro Cohen 2019-06-07 05:47:25

Hi Panorama people!!!

Wonderful job with AutoQC, one of the best tools I've used for QC in the lab... for more than 25 years!!! (I used to plot Shewhart cotrol chart rules by hand!)

So, here suggestion that might work. Due to the generous real state of large screens, it would be very helpful if you could choose more than one metric (eg Rt and Area) side my side for each target. That would sometimes help quickly identifying and diagnosing problems, as switching from metric to metric for a big list of targets makes it hard to visualize. Of course, I could just split the browser into to screens, but then you have to synchronize scrolling (me?? ?lazy???)

You are doing a great job!!! Keep it up!!!


view message
Inaccurate peak picking by AutoQC
(1 response) LeandroXNeves 2019-06-05 13:01:16

Hello Dear,

A System Suitability workflow is being implemented in the lab but we are experience an issue with the data uploaded to Panorama using AutoQC. A few peptides are being inaccurately picked over different runs (screenshot enclosed). We double checked opening the files into Skyline and the correct peak was always present. Is it possible to provide the correct peak boundaries or scheduling the acquisition is the best option?

Best regards,

 Picture1.png  Picture2.png 
view message
Small molecules and Panorama chromatogram libraries
Chris 2019-05-13 14:29:06

Dear Skyline and Panorama teams,

I'm interested in the chromatogram library feature of Panorama for small molecules but my small molecule assays don't seem to be compatible with the existing targeted MS runs web part. I've checked the chromatogram library file generated in the fileset folder but it appears to be empty except for the LibInfo table.

Are there current efforts underway to get chromatogram library functionality for small molecule assays on Panorama? If not, I would like to let you know that there is at least one person interested in this feature.

I originally posted this in the Skyline support section but figure this is a more appropriate place for it.


view message
Question about peptide identification
(3 responses) fazeliniah 2019-03-29 12:59:53

Hi Panorama team,
We have been using the AutoQC for montoring 9 peptides (Scheduling PRM) in our standard sample. In the past few days, I have noticed that one of our peptides in the sample behave differently. Please check the attached picture. I believe that Skyline picks a wrong peak for this peptide. Is there an easy fix for this problem?
I don't think this is sample related issue since we have been using an aliquot of the same standard sample for few years now.
Thanks again for your work on this amazing tool.

 Levey-Jennings- All Series.png 
view message
Would you tell me how to prepare Skyline document to publish to a library folder on Panorama?
(7 responses) eisuke miyauchi 2019-03-27 19:36:50

Dear PanoramaWeb team,

I couldn't import my library downloaded from Panorama into Skyline for DIA analysis.

Would you tell me how to prepare Skyline document to publish to a library folder on Panorama?


view message
Unable to upload Skyline file
(1 response) Andreas Hober 2019-03-19 09:10:13

I've been trying to upload a Skyline file to one of my Panorama projects without any success.
I've tried uploading it through Skyline, as well as directly uploading the zipped Skyline file through the web interface, but neither works.
I get an error message in the Data Pipeline stating "No transition match!".

The particular data set is due for submission and any help with managing to upload the data would be much appreciated.

Best regards

view message
Bruker tdf support
(2 responses) Tobias Kockmann 2019-03-04 07:16:53

Dear Panorama team,

could it be that the autoQCLoader app is not yet ready for Bruker tdf files? There is no instrument type "Bruker" selectable. Skyline-daily processes the data already and manual uploads 'to PanoramaWeb work.


view message
Unknown error connecting to the server
(4 responses) EvgenyKanshin 2019-02-16 07:45:50

Dear PanoramaWeb team,
since yesterday all configurations stopped working and gave this weir error message. We haven't changed anything on our side. I've attached the log file (error happened for a first time @ 2/15/2019 9:21:18 AM).

view message
Getting stuck importing data.
(3 responses) tkeppel 2019-01-18 10:39:13

I'm trying to upload results for a QC template project, but no matter if I'm uploading via the "Upload to Panorama" from within Skyline, or I try to manually drag and drop the generated .zip file or the skyline document itself, I'm getting stuck at "IMPORT WAITING".
Is there a command I need to toggle to send it through to upload into my project?
Thank you,

view message
Delete folders?
(9 responses) Alejandro Cohen 2019-01-08 11:00:27

Hi Panorama people,

I'm trying to set new folders for AutoQC of all instruments in my lab, but I cant seem to delete older folders. I get the following error when I try to delete the folders from the Folder Management page:
at org.labkey.pipeline.api.PipelineManager.purge(
at org.labkey.pipeline.PipelineModule.containerDeleted(
at org.labkey.core.admin.AdminController$DeleteFolderAction.handlePost(
at org.labkey.core.admin.AdminController$DeleteFolderAction.handlePost(
at org.labkey.api.action.FormViewAction.handleRequest(
at org.labkey.api.action.FormViewAction.handleRequest(
at org.labkey.api.action.BaseViewAction.handleRequest(
at org.labkey.api.action.SpringActionController.handleRequest(
at org.labkey.api.module.DefaultModule.dispatch(
at org.labkey.api.view.ViewServlet._service(
at org.labkey.api.view.ViewServlet.service(
at javax.servlet.http.HttpServlet.service(
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(
at org.apache.catalina.core.ApplicationFilterChain.doFilter(
at org.apache.tomcat.websocket.server.WsFilter.doFilter(
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(
at org.apache.catalina.core.ApplicationFilterChain.doFilter(
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(
at org.apache.catalina.core.ApplicationFilterChain.doFilter(
at org.labkey.api.module.ModuleLoader.doFilter(
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(
at org.apache.catalina.core.ApplicationFilterChain.doFilter(
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(
at org.apache.catalina.core.ApplicationFilterChain.doFilter(
at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(
at org.apache.catalina.core.ApplicationFilterChain.doFilter(
at org.apache.catalina.core.StandardWrapperValve.invoke(
at org.apache.catalina.core.StandardContextValve.invoke(
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(
at org.apache.catalina.core.StandardHostValve.invoke(
at org.apache.catalina.valves.ErrorReportValve.invoke(
at org.apache.catalina.valves.AbstractAccessLogValve.invoke(
at org.apache.catalina.core.StandardEngineValve.invoke(
at org.apache.catalina.connector.CoyoteAdapter.service(
at org.apache.coyote.http11.Http11Processor.service(
at org.apache.coyote.AbstractProcessorLight.process(
at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(
at java.util.concurrent.ThreadPoolExecutor.runWorker(
at java.util.concurrent.ThreadPoolExecutor$
at org.apache.tomcat.util.threads.TaskThread$
request attributes
LABKEY.OriginalURL = http://localhost:8080/admin/Dalhousie University - Proteo and Metabolomics Core/QC_VelosPro/QTra5500_QC/deleteFolder.view?
LABKEY.StartTime = 1546973895452
LABKEY.action = deleteFolder
org.springframework.web.servlet.DispatcherServlet.CONTEXT = Root WebApplicationContext: startup date [Thu Dec 20 13:54:46 PST 2018]; parent: Root WebApplicationContext
LABKEY.controller = admin
LABKEY.Counter = 0
org.labkey.api.util.ExceptionUtil$exception = java.lang.NullPointerException
X-LABKEY-CSRF = f03e4fa741ccf58c794ea79555e0ac35
LABKEY.container = /Dalhousie University - Proteo and Metabolomics Core/QC_VelosPro/QTra5500_QC
LABKEY.RequestURL = /admin/Dalhousie%20University%20-%20Proteo%20and%20Metabolomics%20Core/QC_VelosPro/QTra5500_QC/deleteFolder.view?
LABKEY.OriginalURLHelper = /admin/Dalhousie%20University%20-%20Proteo%20and%20Metabolomics%20Core/QC_VelosPro/QTra5500_QC/deleteFolder.view?

core schema database configuration
Server URL jdbc:postgresql://localhost/labkey
Product Name PostgreSQL
Product Version 10.3
Driver Name PostgreSQL JDBC Driver
Driver Version 42.2.5

view message
"Missing raw data" error message when trying to publish to Panorama Public
(2 responses) rschoenh 2018-12-19 10:42:24

Hi Vagisha,

I'm trying to publish Skyline files to Panorama Public to receive reviewer logins for a manuscript submission, but Panorama is giving me an error message stating that there are "Missing raw data." It's listing the Skyline document .zip files alongside the Missing raw data .wiff files. I thought at first that this was the case because the Skyline files I uploaded were located in a different file folder (on my computer) than the wiff files, but I tested that by adding the wiff file to the folder that contained the Skyline file and uploading the data to Panorama again, but it still gave me the same error message. It's also curious that for this particular Skyline file, it's listing only 1 wiff file as missing, whereas there are data from 2 wiff files in the Skyline file.

Thanks so much in advance for your time and help!


view message
[12/9/2018 10:40:31 AM] User does not have permissions to upload to the Panorama folder /Functional Genomics Center Zurich - Proteomics & Protein Analysis Group/Qcloud/QEXACTIVEHF_2
(4 responses) Tobias Kockmann 2018-12-09 04:33:22

Dear Panorama support,

our autoQC loader client reports:

[12/9/2018 10:40:31 AM]    User does not have permissions to upload to the Panorama folder /Functional Genomics Center Zurich - Proteomics & Protein Analysis Group/Qcloud/QEXACTIVEHF_2

Did somebody mess with my Panorama account? I have used it to upload data for months and now all of a sudden I am lacking permissions?


view message
Can we get logs?
(2 responses) eisuke miyauchi 2018-11-26 18:28:27

Dear PanoramaWeb team,

Can we get logs (ex. operation logs, event logs, and so on) in order to detect unauthorized accesses?


view message
Account permissions
(2 responses) Klemens Fröhlich 2018-11-14 09:57:41

Dear PanoramaWeb Team,
I was part of the Skyline Course in August this year. We there got an account from Vagisha Sharma. I now want to use AutoQC to establish an automated QC report system for our targeted peptide panels on a TSQ vantage.
However, I have great troubles following tutorials and webinars on that matter, because I do not seem to have a GROUP in panorama? I cannot access any projects of my own which makes it impossible for me to create folders (If I hover over the HOME directory in the upper left corner of the website I simply do not see any "add folder" button). I also cannot manage any permissions as described.

As already mentioned I think this could be linked to the fact that I do not have any GROUP status in my account.

I would appreciate any feedback on the matter. I would be perfectly happy with an account on the MacCoss Server as described on the sharing_documents#subfolder page.

Best, Klemens

view message
Inquiring about PanoramaWeb
(2 responses) eisuke miyauchi 2018-10-29 01:07:11
I have 4 questions in order to operate PanoramaWeb in our company.

1. Has the data remaining on the cloud definitely erased to prevent reuse or misuse by a third party after withdrawing from PanoramaWeb?

2. Can University of Washington access and use our data on the cloud?

3. How much storage capacity of the cloud?

4. What will become of the data on the cloud when PanoramaWeb is terminated? Can Spectral libraries exported from PanoramaWeb be used in other softwares?
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File name information shown above a chromatogram
(2 responses) rschoenh 2018-10-24 11:01:28


I'm trying to simplify the information that's shown above the peptide chromatograms for targeted MS runs. At the moment the information seems to include Sample or Replicate name, wiff file name, date of acquisition, peptide sequence, etc. I'm wondering if there is a way to not show the wiff file names, since mine happened to be quite long and it makes the information a bit convoluted.

Thanks very much in advance for your help!

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How to Download All Data Points for Plots?
(1 response) loffredoj 2018-10-18 15:18:13

Is it possible to download the data points on the 'Peak Area' Metric for all the uploaded files of each ion being targeted, using PanoramaWeb? (as a .txt or .xls) The downloaded data points would have fields like the name of each ion and the Peak Area, for a specific date. I uploaded a picture of the plot I am referring to. Our data is uploaded from TripleTOF 6600 systems and have been uploaded using the AutoQC client, and I am using Google Chrome to view PanoramaWeb.


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QC Plots are not Displayed
(7 responses) s merker 2018-10-12 02:10:20

Dear Panorama team,

first of all, thank you so much for the great work you are doing! We have recently implemented QC for our QTrap 5500 system based on Skyline and Panorama employing the AutoQC client. I have to say that it greatly facilitates the workflow compared to manual data inspection in Skyline. However, since yesterday no QC Plots can be displayed on our dashboard ("no data to plot"). However, samples are being successfully uploaded into the specified Skyline document and also to Panorama, according to the AutoQC log (new sample names also appear in the QC summary, just the plots are gone, s. attached screenshot). When I enter the public Panorama project "U of Melbourne - Proteomics Facility", I can see and manipulate QC Plots there, so this does not seem to be a browser or a general issue. We use regular Skyline release combined with AutoQC Loader, OS is Windows 7 Professional, 64-bit. Restarting the relevant configuration in the loader did not help. I would very much appreciate any suggestions since we are quite new to Panorama and have never encountered that issue before.

Best regards,


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Adding Users - No Email Received
(2 responses) chapmanj 2018-10-05 09:38:59


I added my 2 lab members as users to our laboratory QC Panorama Project and in the instructions it says they should receive an email inviting them to create an account. I initially did this on 9/14/18 and they never received any communication. We have checked all junk and spam folders. Any suggestions or work arounds to get them up and running so I am not the sole person able to access our AutoQC?

Thank you for your help! :)

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