Showing: all messages
Unknown error attempting to publish to Panorama
(1 response) fazeliniah 2018-02-12
Hi Panorama Team,
Our AutoQC has stopped uploading the results to PanoramaWeb. There is a remote server error (The remote server returned an error: (404) Not Found.). I 'd appreciate it if you could take a look. We are using skyline daily with the updated version of AutoQC. I have attached the log file for your review.
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AutoQC 404 error
(1 response) socall 2018-02-11

I'm trying to get AutoQC to talk to Panorama. The folder I'm trying to write to is here: (Yes I managed to spell Orbitrap with a 'b' when making the folder!)

For project folder name in the panorama settings in AutoQC i've tried "U of Melbourne – Proteomics Facility/Orbitrab_Elite_QC" , "project/U of Melbourne – Proteomics Facility/Orbitrab_Elite_QC", "U%20of%20Melbourne%20%E2%80%93%20Proteomics%20Facility/Orbitrab_Elite_QC", and just about everything else I can think of, but no joy.

The error I get is "The remote server returned and error: (404) Not Found", so I assume the address is wrong somehow.

Any ideas? Thanks, Sean
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Notification alert in AutoQC
(1 response) fazeliniah 2017-12-12
Hi Panorama Team,
Is it possible to set up notification alert for AutoQC? Ideally, we would like to get notified immediately (text or email) if some of our numbers are below user-specified values?
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Panorama Upload Error
(3 responses) mdowns2 2017-12-12
Hi Panorama Support Team,

I recently attempted to upload a new Skyline document to one of our PanoramaWeb folders, but I received the error below. Could you please help me figure out what is causing the issue?

Thank you,

12 Dec 2017 08:54:30,597 INFO : Starting to run task 'org.labkey.targetedms.pipeline.TargetedMSImportTask' at location 'webserver-high-priority'
12 Dec 2017 08:54:30,600 INFO : Starting to import Skyline document from
12 Dec 2017 08:54:30,600 INFO : Expanding 2016-11-11_LysozymeDiscoForPRM.blib
12 Dec 2017 08:54:30,601 INFO : Expanding 2016-11-11_LysozymeDiscoForPRM.redundant.blib
12 Dec 2017 08:54:30,603 INFO : Expanding 2017-12-06_Lysozyme-Wine_Spikes_pH_optimization_MD.skyd
12 Dec 2017 08:54:30,859 INFO : Expanding
12 Dec 2017 08:54:30,859 INFO : Expanding
12 Dec 2017 08:54:30,867 WARN : The version of this Skyline document is 3.7. This is newer than the highest supported version 3.62
12 Dec 2017 08:54:32,739 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask'
12 Dec 2017 08:54:32,741 ERROR: Uncaught exception in PipelineJob: (DONE) Skyline document import -
org.labkey.api.query.RuntimeValidationException: name: Value is too long for column 'name', a maximum length of 200 is allowed.
Caused by: name: Value is too long for column 'name', a maximum length of 200 is allowed.
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multiple users
(1 response) fazeliniah 2017-11-29
Hi Panorama team,
We have started to use AutoQC for our instruments. Thanks for this really amazing tool.
Is there a way to allow multiple people in our lab view the results of QC using their own login information? Ideally, I would like to add 2-3 users so they can view the results on PanoramaWeb.
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Import waiting indefinitely without anything happening
(3 responses) dkueltz 2017-11-29
Hi Vagisha,
I noticed that lately it takes a very long time to upload a Skyline document to Panorama and sometimes I was not able to upload at all since the document is wait-listed infdefinetly (I have been waiting more than a day before cancelling and trying again). This is different from before when it took only a few minutes and I tried both importing directly from Skyline and via the web interface. Could you please take a look at the document that is currently "import waiting" listed and check what is wrong with it and why it does not start running?. It is in my JoLi-01 folder.
Thank you,
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Backwards compatibility from 3.7 to 3.6 problem
(2 responses) dkueltz 2017-11-24
I am trying to upload a Skyline document to Panorama. I generated the document with the latest version of Skyline daily but saved the file as Share compatible with version 3.6 to enable Panorama upload. I can ope the document now with the regular Skyline 3.7 version but still cannot upload it to Panorama despite sharing it in Skyline version 3.6 format. I get the following error:
24 Nov 2017 20:48:23,848 WARN : The version of this Skyline document is 3.7. This is newer than the highest supported version 3.62
24 Nov 2017 20:48:28,314 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask'
24 Nov 2017 20:48:28,315 ERROR: Uncaught exception in PipelineJob: (DONE) Skyline document import -
org.labkey.api.query.RuntimeValidationException: aminoacid: Value is too long for column 'aminoacid', a maximum length of 30 is allowed.
Caused by: aminoacid: Value is too long for column 'aminoacid', a maximum length of 30 is allowed.
Thanks for any help with this issue!
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Organizing project in Panorama
(4 responses) natbat 2017-10-31

I would like to organize my project in Panorama more logically but do not know how to do it.
The idea is that I would like to have several subfolders under the same project. These subfolders would correspond to different experiments separately published in the scientific journals. Therefore, they have to have different access modes.
Historically it has happend so that the first experiments already published in JProtRes-2016 were not submitted in a subfolder. Now I would like to make a separate subfolder for these data (in open access)and move them there. I created this subfolder named "Phosphopeptides in Synechocystis_SRM verification". Could you move them there?
At present, I am writing another paper, and need to submit new experiment to Panorama with the access key for reviewers. The documnet is in subfolder named "SpkG in Synechocystis 6803 GT". However, I do not see the link to publish this separate subfolder.
Or should I re-publish the whole project?
Please advise:
Can you move the old data to the specified subfolder?
How can I get the access key for the reviewers to the subfolder "SpkG in Synechocystis 6803 GT"?

Best regards
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Small molecules in Skyline daily and Panorama upload
(4 responses) christopher ashwood 2017-10-27
Dear Panorama support,

I've been trying to upload small molecule assays from Skyline Daily (molecules defined by chemical formula rather than defined monoisotopic mass). The assay works fine but publishing it to Panorama gives me the following error:

27 Oct 2017 02:24:23,783 ERROR: Uncaught exception in PipelineJob: (DONE) (

java.lang.IllegalStateException: Missing attribute mass_monoisotopic for element molecule.

I understand a workaround might be to specify the monoisotopic mass but I would prefer if the mass derived from chemical formula/adduct could be used from Skyline Daily ( Am I doing something wrong that would cause this error?

Edit: I've tried a workaround of saving the Skyline assay as non-daily v3.7 but this causes errors when trying to open it in Skyline v3.7 ("Custom ions must specify a formula or valid monoisotopic and average masses"). So this workaround is not possible.

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Trying to make public a dataset
(4 responses) panorama sabido 2017-10-20
I have a dataset on Panorama that I want to make public. I am trying to follow step 2 on but I do not see the <Select Web Part> menu at bottom left on the page. How can I fix this?
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Chrom Lib "creates" new transitions
(9 responses) tvaisar 2017-10-18
I found what I think is a critical issue - I tried to recreate the Skyline document from a Panorama clib and uploaded the clib from Panorama into Skyline - in the list of peptides and transitions, a new transition/fragment ion appeared for a peptide which was not there in the Skyline document used to create the Panorama clib. See the attached powerpoint.
It is a b-ion for which m/z is the same as a y-ion which was in the original. The correct y-ion did not show up in the peptide/transition list.

This actually happened for several peptides - this is just an example.

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skyline crashes
(16 responses) Tobias Kockmann 2017-10-16
Hi support,

I am getting the following error message:

Problem signature:
  Problem Event Name:    CLR20r3
  Problem Signature 01:    Skyline.exe
  Problem Signature 02:
  Problem Signature 03:    593f676f
  Problem Signature 04:    Skyline
  Problem Signature 05:
  Problem Signature 06:    593f676f
  Problem Signature 07:    78f7
  Problem Signature 08:    6
  Problem Signature 09:    pwiz.Skyline.Util.Assumption
  OS Version:    6.3.9600.
  Locale ID:    1033
  Additional Information 1:    d0a3
  Additional Information 2:    d0a3a8f66f382cee6a91e8944b701130
  Additional Information 3:    5dc3
  Additional Information 4:    5dc3c9c471f74cb07429231ba6cb1284

Read our privacy statement online:

If the online privacy statement is not available, please read our privacy statement offline:

Can you tell me how to solve the issue?

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Results not being pushed to Panorama
(6 responses) pnlabsg 2017-09-20
Dear Panorama developers,

We have been using autoQC for just over a month, and found that our QC results not being pushed to Panorama for the past few days. I suspect a conflict in Skyline having to add a new file and remove a old file at the same time (a typical log with this problem is shown below).

We can get around this by removing the latest file in the Skyline document, then restarting autoQC again. Our AutoQC version is, and Skyline version is 64 bit.

Please advise on how to get automatic uploading working again.

Best regards,

[20-Sep-17 10:09:17 PM] Waiting for files...
[21-Sep-17 11:13:39 AM] 20170921_RS_BSA_PRM_1.raw added to directory.
[21-Sep-17 11:13:39 AM] 20170921_RS_BSA_PRM_1.raw is being acquired. Waiting...
[21-Sep-17 11:53:39 AM] 20170921_RS_BSA_PRM_1.raw is ready
[21-Sep-17 11:53:39 AM] Running SkylineRunner.exe with args:
[21-Sep-17 11:53:39 AM]
 --in="D:\Skyline autoQC\" --remove-before=22-Aug-17 --import-file="D:\MS_DATA_HF\20170921_RS_BSA_PRM_1.raw" --import-on-or-after=22-Aug-17 --save
 --panorama-server="" --panorama-folder="Nanyang Tech U – PN Lab/QC/HF" --panorama-username=""
[21-Sep-17 11:53:43 AM] Opening file...
[21-Sep-17 11:53:44 AM] File opened.
[21-Sep-17 11:53:44 AM]
[21-Sep-17 11:53:44 AM] Adding results...
[21-Sep-17 11:53:44 AM] 1. D:\MS_DATA_HF\20170921_RS_BSA_PRM_1.raw
[21-Sep-17 11:53:44 AM]
[21-Sep-17 11:53:48 AM] [1] 29%
[21-Sep-17 11:53:50 AM] [1] 45%
[21-Sep-17 11:53:52 AM] [1] 56%
[21-Sep-17 11:53:54 AM] [1] 64%
[21-Sep-17 11:53:57 AM]
[21-Sep-17 11:53:57 AM] Updating peak statistics
[21-Sep-17 11:53:57 AM] Joining file D:\Skyline autoQC\20170921_RS_BSA_PRM_1_453968865.raw.skyd
[21-Sep-17 11:53:57 AM] Removing results before 22-Aug-17...
[21-Sep-17 11:53:57 AM] Removed D:\MS_DATA_HF\20170821_RS_BSA_PRM_1.raw.
[21-Sep-17 11:53:57 AM] Saving file...
[21-Sep-17 11:53:57 AM] File saved.
[21-Sep-17 12:01:23 PM] SkylineRunner.exe exited successfully.
[21-Sep-17 12:01:23 PM] Waiting for files...
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Problem installing AutoQC
(8 responses) wfondrie 2017-09-19
Hi Panorama team,

I'm having trouble installing AutoQC on our instrument computers. I get an error message saying that application download did not succeed. Just to be sure I've tried installing it alongside either Skyline-daily or the latest stable version.

When I look at the log, it seems that it times out when trying to download Skyline Runner. I've attached one of the logs here. Thank you for your help.

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x axis for plots in autoQC folder are not kept const.
(3 responses) Tobias Kockmann 2017-09-14
Hi Panorama support,

I observed the following in

The QC plots that are displayed do not have the same x-axis (replicates). The DGL... peptides shows several datapoints for the the date 2017-09-03. For the ECC... there is several injections missing. How is this possible? If I co-plot all peptide it gets even more visible (see attachment).

Interestingly, all peptides that are missing belong to the same protein group.

 Levey-Jennings-EC[+57.0]C[+57.0]HGDLLEC[+57.0]ADDR.png  Levey-Jennings-DGLDAASYYAPVR.png  Levey-Jennings- All Series.png 
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Multiple accounts on Panorama
(1 response) fazeliniah 2017-09-13
Hi Vagisha,
I have two accounts on Panorama. One belong to our institution (I am the admin) and one is generated for me when I was at the Skyline Targeted Proteomics Course. I would like to use our institution account to share Skyline data but I can't sign out from my second account. I don't have the option to change the server name in the "Publish Document" window. Any advice? Can I ask to remove my personal account?
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Mass Accuracy of Fragment Ions
(3 responses) brown459 2017-09-07
Hi all-

Is there anyway that I can have a read out on panorama of the transition/fragment ion mass accuracy? Something that could allow us to determine the calibration of both parts of the fusion instrument (i.e. the mass accuracy in the OT and the IT)? This could be similar to a panorama dashboard view showing the mass accuracy of the MS1 data.


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There was an error uploading the document to Panorama. Stopping...
(3 responses) Tobias Kockmann 2017-08-07
Hi support,

my AutoQC Loader reports this:

[8/7/2017 10:26:02 AM] Updating peak statistics
[8/7/2017 10:26:03 AM] Joining file Z:\QEXACTIVEHF_2\20170726_165_feller_autoQC_Fetuin_400amol_1.raw.skyd
[8/7/2017 10:26:03 AM] Saving file...
[8/7/2017 10:26:04 AM] File saved.
[8/7/2017 10:26:07 AM] Uploaded 1.11 MB of 15.56 MB
[8/7/2017 10:26:09 AM] 100% - Uploaded 15.56 MB of 15.56 MB
[8/7/2017 10:26:10 AM] Renaming temporary file on server
[8/7/2017 10:26:32 AM] ERROR: Error: Exception of type 'pwiz.Skyline.Util.PanoramaImportErrorException' was thrown.
[8/7/2017 10:26:32 AM] An error occurred on the Panorama server ( importing the file.
[8/7/2017 10:26:32 AM] ERROR: Error details can be found at Genomics Center Zurich - Proteomics %26 Protein Analysis Group/autoQC Server/QEXACTIVEHF2/details.view?rowId=20026
[8/7/2017 10:26:32 AM] ERROR: SkylineRunner.exe exited with code 0. Panorama upload failed.
[8/7/2017 10:26:32 AM] Finished importing existing files...
[8/7/2017 10:26:32 AM] ERROR: There was an error uploading the document to Panorama. Stopping...

What can I do? I restarted the corresponding config. No change.

 Screen Shot 2017-08-07 at 10.32.17.png 
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set password does nothing
(5 responses) Tobias Kockmann 2017-07-20
Hi there,

I am trying to set a pw for a new user, but nothing happens after hitting the return key. Who should I contact?

A more general question: We are using autoQC and during the test phase all uploading of data was done using my personal account. Now, I would like to release the system to the whole group. Which user status is required for

- uploading data to autoQC folders?
- adding annotations/guide sets?
- viewing the data

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Upload error
(5 responses) phains 2017-07-18

I am having similar issues to those already described. First off, I'm using LabKey 17.2 (just upgraded, but the issues were occurring with the prior version), AutoQC is V and Skyline is V3.7.0.10940, all 64-bit, Win 10 for AutoQC and Skyline or Win server 2012 for LabKey.

All my current AutoQC methods are working fine. These were made sometime ago with an earlier version of Skyline. The problem occurs when I try to make a NEW AutoQC config. I opened up one of my working methods, saved the Skyline file using the latest version of Skyline and now it does not work.

The symptoms: When I start the config in AutoQC it does not make an AutoQC.log file. If I make one manually this part then works fine. The file are imported in to Skyline but the Panorama upload fails.

The AutoQC log and Panorama log are attached.

By the way, we still have the issue with AutoQC giving up the ghost every few days when monitoring network drives. It’s annoying, but we just stop the config and start it again...


 AutoQC.log  Panorama.log 
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Skyline 3.7 Support
(3 responses) mdowns2 2017-06-14
Hi Panorama Team,

I've just recently updated to Skyline 3.7, and I'm unable to import data to a QC folder on Panorama. (See error messages below.)

Do you know when Skyline 3.7 files will be supported in the QC folders? Or is there some other issue going on?

Melanie Downs

14 Jun 2017 15:17:10,169 INFO : Starting to run task 'org.labkey.targetedms.pipeline.TargetedMSImportTask' at location 'webserver-high-priority'
14 Jun 2017 15:17:10,172 INFO : Starting to import Skyline document from
14 Jun 2017 15:17:10,172 INFO : Expanding 2016_09_07_6ProteinDigest.blib
14 Jun 2017 15:17:10,174 INFO : Expanding 2016_09_07_6ProteinDigest.redundant.blib
14 Jun 2017 15:17:10,186 INFO : Expanding 2017-05-05_P6P_PRM-3.skyd
14 Jun 2017 15:17:10,953 INFO : Expanding
14 Jun 2017 15:17:10,953 INFO : Expanding
14 Jun 2017 15:17:10,973 WARN : The version of this Skyline document is 3.7. This is newer than the highest supported version 3.6
14 Jun 2017 15:17:11,033 INFO : Updating previously imported data for sample file F:\RawDataQE\20161215_P6P.raw in QC folder.
14 Jun 2017 15:17:11,157 INFO : Inserting sp|P02769|ALBU_BOVIN
14 Jun 2017 15:17:12,951 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask'
14 Jun 2017 15:17:12,952 ERROR: Uncaught exception in PipelineJob: (DONE) Skyline document import -
org.postgresql.util.PSQLException: ERROR: insert or update on table "generalmoleculechrominfo" violates foreign key constraint "fk_gmchrominfo_samplefile"
  Detail: Key (samplefileid)=(375166) is not present in table "samplefile".
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Signal Data Module on PanaramaWeb
(1 response) Jim Collett 2017-05-08
Would it be possible for the PanoramaWeb admin team to install to the LabKey Signal Data Module on PanoramaWeb?


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Feature Request - Manual Reference Ranges
(1 response) Will Thompson 2017-04-18
Hi Skyline Panorama Team,

We have been using AutoQC for a few years now (wow time flies!) and we have noticed that the most difficult portion of using the tool in practical 'go/no go' decisions is defining the "guide set" of runs. This is because it is very difficult to find a set of runs which have enough variation for all the metrics, without having too much variation for any of them, to properly capture the reference range. A good example would be retention time; If you perform 5 injections on 5 separate days, while running samples, you might get a good handle on most of the metrics for AutoQC. However if you are using commercial columns the retention time may be extremely tight within that window (say <15-30 seconds variability) which is too narrow to accommodate a column change or larger drifts over time, which may be somewhere in the neighborhood of +/- 1 minute. If we then start using larger sets of runs for guide sets, it is very difficult to find a set of runs over weeks or maybe even a month, which do not contain a single outlier for any of the metrics (and we in theory would not want to have outliers in the 'guide set'). Additionally, some metrics (such as mass accuracy) would make sense to have an 'absolute' cutoff window as opposed to a guide set in any case; for instance, we want all ions to have standard deviation of +/- 1.5 ppm. Allowing the user to utilize historical data to manually set a range for each metric may be more time-consuming for the user to set up, but it would perhaps lead to more accurate go/no go decisions. Another (slightly less appealing) option might be to still use the software to establish a 'guide set', but allow the user to exclude specific runs from specific individual metrics.


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No upload to Panorama from AutoQC
(6 responses) michael plank 2017-04-12
Hi all,
I`m trying to use AutoQC, but the data do not end up on Panorama. I`m wondering if you might have a look at my settings if I`m getting anything wrong: Screenshots attached.
I set the 'Expected acquisition duration' short, as the files are not written to the folder by the instrument, but I copy-paste them there.

AutoQC says "running", already for several hours on this configuration.
Panorama says "
No sample files imported"

I`m also attaching a copy of today`s log entries.

Thanks a lot for your help.
 sc1.png  sc2.png  20170411_todaysLog.txt 
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log file does not exist
(5 responses) n wildburger 2017-04-09

I keep getting an error message "log file does not exist" when ever I try to start AutoQC after building a configuration.

I have never seen this error before, and the is not the first time I have installed AutoQC on a system before granted this is an older computer.


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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


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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 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.

Todd  AutoQC.log 
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AutoQC "stalling"
(12 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"
(4 responses) nod2007 2016-11-15
I started getting the message:

"unknown error connecting to the server"

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  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
30 Sep 2016 07:14:18,818 INFO : Expanding Weekly_Yeast_QEx.skyd
30 Sep 2016 07:14:18,859 INFO : Expanding
30 Sep 2016 07:14:18,860 INFO : Expanding
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(
    at org.labkey.targetedms.SkylineDocImporter.insertPeptideOrSmallMolecule(
    at org.labkey.targetedms.SkylineDocImporter.insertPeptideGroup(
    at org.labkey.targetedms.SkylineDocImporter.importSkylineDoc(
    at org.labkey.targetedms.SkylineDocImporter.importRun(
    at java.util.concurrent.Executors$
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(
    at java.util.concurrent.ScheduledThreadPoolExecutor$
    at java.util.concurrent.ThreadPoolExecutor.runWorker(
    at java.util.concurrent.ThreadPoolExecutor$
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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 page 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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