Hi Panorama Team,

It looks like I might need project admin rights to create folders in our projects. Can this permission be granted for me in the UNC-CH-Metabolomics and Proteomics Core project folder? I'm unsure who is currently listed as our admin but I will be a primary user and will need the ability to create folders for our various projects

Thank you!

Dear Panorama Team,
Thank you for your advice on how to choose a file to upload. I tried to upload ABRF_sPRG_2013_QTOF_2014-01-10_15-06-15 according to your method and succeeded. But when I try to share my RAW file through Skyline (64-bit) (24.1.0.414 ), it did create a .zip file, but all my RAW data were lost. How to solve this question？If any assistance could be provided I would be grateful!

Dear Panorama Team, thank you for your help with the question about founding the correct folder to upload. I have found it now, and now I am trying to upload my proteome data to the website. But I have encountered another problem. I followed the protocol to share the file. However, the Skyline failed to create sharing file.How can I uploading data to panorama？If any assistance could be provided I would be grateful!

Hi Panorama team,

I try to set up automatic import of files for QC with AutoQC.
I have several error messages in the log (attached) but I don't well understand why. It says that my Skyline file is in use but it is not. I checked for all the permissions to modify the file. Moreover, the Panorama upload works, but not all the time.

Also, when I add a file to the folder to watch, I see in the log that a file was added to directory but nothing happens.

Do not hesitate if you need more information.

Thank you in advance for your help,
Pascaline

Dear Panorama Team, I have just registered an account, and now I am trying to upload my proteome data to the website. but I have encountered some problems when using Skyline to upload. Why I could not find the sub-folder of my project (Gannan Medical University-PDXO_Proteomics, Oba01 and Abem in CRC_PDXO) when I uploading data to panorama？If any assistance could be provided I would be grateful!

Dear Panorama Team,

I tried to submit a folder from Panorama Web to Panorama Public and got the following error message:

"At least one of the subfolders contains an experiment. Cannot add subfolder data to this experiment. "

The document has different subfolders. Initially each subfolder had an own experiment section. However, to meet the submission requirements, I deleted them and added the experiment to the main folder. However, now I cannot integrate the subfolders anymore getting the error message above.

How can I fix that?

Man thanks in advance!

Best
Ingo

I'm looking to download a table from Panorama that includes retention time and peak area for each peptide, similar to the transition results table that can be exported from Skyline. Does anyone know how I can obtain this type of data from Panorama?

I've run 3 concentrations of peptides in triplicate for 5 days and would like to create graphs like the reproducibility section of the CPTAC assay portal. I have Day and replicate set up as annotations - things seem to have uploaded properly, but I'm not getting a reproducibility report option anywhere in the Panorama Chromatogram library.

https://panoramaweb.org/Indiana%20U%20-%20Proteome%20Analysis/Reproducability%20and%20repeatability%20Aducanumab%20Assay/targetedms-showProtein.view?id=14140386

Is my current Panorama upload for this - thanks, not sure what I'm missing!

Please, I have a question. I am trying to submit my project to ProteomeXchange via Panorama. However, I am running into issues with the Spectral libraries section. It keeps showing as incomplete for one of my libraries. When expanding the INCOMPLETE section, this is what I get (see image attached).
Not sure about the types of file extensions that are needed.
Please, I would appreciate your help with this matter.
Best,
Omar.

Dear Support-Team,

would it be possible to also define a time range instead of a specific timepoint to fetch the custom trace metric? I am asking, because our loading pressure on the Neo Vanquish varies a bit due to clogging/aging of the needle seat. With the fixed value we are sometimes missing it completely. So if I could catch the max value within a defined RT range, this would be much more useful for us.

Best

Robert

Hello,

I'm aiming to implement AutoQC for our instrument here. Unfortunately due to the windows version on our instrument computer and the security requirements of the University I can only have limited internet access.

Therefore, our IT team needs some help with information so the computer can communicate with your server using Auto QC Loader. What's the server's name, and which ports need to be opened on our university firewall?

Or, is there another work around you can advise on?

Best Wishes,
James

Dear developers,

when plotting transition or product ion peak areas with log-scaling enabled, the y-axis for is displaying everything on a quite broad scale (see attached screenshot). Before, the limits have been a bit more tight. It is now really hard to see any trends on the lines. But without log-scaling the plots for lower intense peptides cannot be properly read as well. If I remember it correctly, this has been different in the past, were the y-axis limits were restricted to the min and max values? My preferred way of plotting would actually be if we could manually set the y-axis limits, as is the case for the x-axis (time).

Best and thanks for PanormaQC as well as Skyline.

Robert

Dear Panaorama Team,
Unfortunately my admin login, I always used to setup our AutoQC loader, tels me that my email address has no permission to upload in panorama.
Do you have an explanation to this problem?
In advance thank you for your help.
Best regards, Jean-Christophe

Dear Panorama team,

I am trying to fix a problem with AutoQC and I would really appreciate your help.

I use a few configurations in AutoQC (version 24.1.0.105). Some of them work, some of them do not (see log enclosed, I can mention error 502 Bad Gateway particularly as an example). I employ the same PC as my colleague, we have separate user accounts for Windows, our role assignments do not differ (see screenshot enclosed), our AutoQC configurations are completely the same (we performed the sharing of configurations, changing only user name and password). Using her account, everything works perfectly. Any ideas to solve the riddle successfully?

Kind regards,

Veronika Zihlova
PLK ProteoLab Krc - IPHYS IMG CAS

Hello! Is there a way to delete folders that were already created or at least change the projects name on PanoramaWeb? I do not want blank folders taking up viewing space if possible but cannot find the appropriate place to delete existing folders.

Thanks!

Orbitrap Exploris GC 240 MS is not currently listed when submitting data.
Please let me know when this is added.

Dear Panorama,

We started now to use Panorama to have homogenized control cards for our two research panel we are using.
It works really well. Thank you. I showed your tool to my collegue working with routine methods, and for here purposes, the concentrations are missing.
They would not need areas but concentrations of their QCs or at least the light/heavy ratio of them.

I found the metric "Light/Heavy Ratio". In my skyline file, the ratio is calculated as shown in the tif file "light_heavy_Ratio_skyline". When I enable the light/heavy metric, there is no indication, and it tells me "There were no records found. The date filter applied may be too restrictive". In the panorama gride, there is no possibility to indicate light or heavy transition.
Or should I do something in my skyline template? I send you my template I am using.

Let me know what I can do, to be able to use this "light/heavy ratio" metric.
In advance thank you for your help and wish you a nice start in the new day.

Jean-Christophe

Dear Panorama team,

I try to upload PRM data from Sykline (Skyline-daily (64-bit) 23.1.1.503 (16f52e48b)) to Panorama. The uploading itself seems to work, but then process crashes. If I first share my skyline document and then upload the zip file, the upload itsself works when I import the data I get the following error message: malformed input off : 6, length : 3

Enclosed I send you the whole log file.....

Do you know what crashes the upload?

Many thanks in advance,

best
Ingo

Thank you for the support with the previous question.

We managed to upload the Skyline file to PanoramaWeb but we would like to add the Panorama ID on the student's thesis before we submit the data to Panorama Public. Will the accession link below still be the same after we submit to Panorama Public? Or does it change? Thank you very much. Best.

https://panoramaweb.org/LNBio%20-%20Mas%20Lab/Ana%20Gabriela%20Costa%20Normando/PRM_runs_Saliva_OSCC/panoramapublic-showExperimentAnnotations.view?id=1886

Hi there,
we are piloting the use of autoQC and Panorama for automated evaluation of our LC-MS system's performance (system suitability). This is for small molecule analysis. We made a sample with a handful of metabolites that we run at the start of each LC-MS batch.

Upon reviewing the Skyline file that contains our system suitability samples and that is linked to Panorama, we noticed that for some samples peak integration was not performed correctly. We use explicit retention times and do observe some retention time shift from one experiment to another. We also have 2 isomers in our sample that have the same transitions and elute closely to each other although they are near baseline separated (see attached PDF). Depending on the retention time shift for that sample, the correct or incorrect peak may be integrated.

Here are my questions:

1. Is there a way to get more consistent peak integrations across the files and still use AutoQC, for instance be removing explicit retention times (I imagine this can work for some of our molecules although not for our isomer pair)
2. If the answer to the above question is no, how would your recommend to proceed? Not use AutoQC, but instead review peak integrations manually and then use 'upload to Panorama' under Files?

many thanks!

Hello Support team,

I am interested in monitoring the inverse mobility as a metric for the QC sample. I am using Bruker's timsTOF system (".d" raw data format). Can you please suggest me any documentation or a manual on this?

Thank you for the wonderful support.

BR,
D. Baker

Hello Support team,

I am interested to know if it is possible to add previously acquired QC runs (for instance a QC acquired in 2022) than the last imported QC run (from 2024) in the project folder on the Panorama web.

I modified the "Folder to Watch" settings in AutoQC to the folder where the desired 2022 QC run is located. However, it doesn't seem to work. I have attached a snip of the log file from the AutoQC while the modified configuration was run.

Please let me know if any additional information is required to address this issue.

BR,
D. Baker

Hi all,

I am new to Skyline / Panorama (it was recommended by a collaborator), but ultimately the goal is to use it for monitoring system suitability data on a variety of instruments, mainly Waters QToF instruments, but eventually our triple quad, and maybe UV instruments too if it is possible to get that to work, but it is not high priority at the moment.

So far I have just been using our Xevo ToF instrument to acquire some test SST data (we work with small molecules), and have used Skyline (in molecules configuration) on the instrument computer to get a quick overview of the data, and then Panorama to have a more detailed look once the data is backed up to a server and can be accessed online. In both cases I have been using AutoQC to import the data, to make it as automated as possible.

I have to say I have been quite impressed with what I have seen so far, and think this could be a really useful solution for us to take our SST use to another level, and make it more proactive rather than being used for troubleshooting when things look wrong....

However, I was really hoping that I would be able to also use the column backpressure as one of my SST criteria, and it seems that I should be able to do that from what I have read. Unfortunately, when I follow the instructions how to add a new or custom QC parameter, Panorama says that there are no traces found. If I look in Masslynx I can clearly see the pressure traces, so the UPLC SST method is correctly recording the pressure (and some other parameters) as I asked it to, but this doesn't seem be getting into the Skyline or Panorama files....

Is there some trick or setting somewhere that I am missing so that the pressure traces are also loaded? Or is there a known problem with importing this data from a Waters .raw file?

Any suggestions would be gratefully received... I feel I am probably doing something wrong, but I have no idea what it is....!

Thanks,

David

Dear Panorama,

Today I tried to upload files, but it did not work either using AutoQC or using skyline.

I attached you both error message I got.

Thank you in advance for the support.
Kind regards
Jean-Christophe

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

_Darryl

Hello,

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.

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
Jean-Christophe

Hello,

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,
Dhanwin

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?
thanks
Taher

Hi,

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.

BR
Dorota

Hello,
I have a TT5600 from Sciex and we have windows 7 on the acquisition computer.
So I have installed Skyline (32bit) 20.2.0.343 and autoQCLoader.
But when I run autoQCLoader, I have an error and this warning message appears (see in attachment).

Can you help me?

Regards
Virginie

Hello,

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!

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,
Vincent

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\QEplus_HeLa_PRM.sky" --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 QEplus_HeLa_PRM.sky 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\QEplus_HeLa_PRM.sky" --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 QEplus_HeLa_PRM.sky 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] QEplus_HeLa_PRM.sky
[12/19/2023 5:01:14 PM] 100%
[12/19/2023 5:01:14 PM] File QEplus_HeLa_PRM.sky 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\QEplus_HeLa_PRM.sky" --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 QEplus_HeLa_PRM.sky 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 QEplus_HeLa_PRM.sky 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\QEplus_HeLa_PRM.sky" --panorama-server="https://panoramaweb.org/" --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 https://panoramaweb.org/.
[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":"wphipps5@uw.edu"}}
[12/19/2023 5:01:49 PM] URL: https://panoramaweb.org/security/home/ensureLogin.view
[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.

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..

thanks,

Hi,
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):
https://panoramaweb.org/IfADO%20-%20Analytical%20Chemistry/Custodio%20et%20al.%2C%20Cells%2C%202023/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,
Joerg

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?

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!

Thanks,
Lindsay

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.

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:

Thanks.

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?

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.

Hello,

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

Cheers,

Stoyan

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?

Thanks
Janelle

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.

Thanks!
Bob

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
   etc.

Greets!
Witek

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

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

Jean-Christophe

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 (https://panoramaweb.org/tczcoD.url) 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.

Cheers,
Chris

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 :)

Cheers

Alejandro

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.

Best

Robert

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.

Hello,

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.

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,
Roman

Hello,

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,
Azad

Hello,

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!

Best,
Christoph

Hi,
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,

David

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,
Roman

Hello

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
Brittany

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?

Thanks,

Kaitlyn

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.
Sincerely,
Juan C. Rojas E.

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

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,
Roman

Hi,

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.

Best
Zdenek

Hi,
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,
Dietmar

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 ---

Hi,
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!
Best,
Marissa

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?

Hello,

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?

Best,

Alex

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?

Best

Robert

Hello,

I have encountered an error while uploading data from Skyline-daily (20.1.1.299) 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,
Hana

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.

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

Skyline account: 20.1.0.31
AutoQC loader 1.1.0.20237

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

Hello,
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

Hi!!

I'm transferring my configurations from one computer to another in a new installation of AutoQC (1.1.0.20237). 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?

Thanks

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 kulyyasov@biocenter.kz
I will be very grateful for any help in improving the text, remarks, and comments on this manuscript.

With best regards,
Arman

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?

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

--in="C:\ZWC-autoQC\test.sky" --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="https://panoramaweb.org/" --panorama-folder="Washington University STL - Evers Lab/AutoQC" --panorama-username="eversa@wustl.edu"
[7/23/2020 2:26:58 PM] Opening file...
[7/23/2020 2:26:59 PM] File test.sky 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]

Hi Panorama support,

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

PLATFORM VERSION INFO
	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)

SOURCES
	Deployment url			: file:///C:/Users/autoQC_user/AppData/Roaming/Microsoft/Windows/Start%20Menu/Programs/AutoQC/AutoQC.appref-ms%7C
	Deployment Provider url		: http://skyline.gs.washington.edu/software/AutoQC/AutoQC.application

ERROR SUMMARY
	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)

COMPONENT STORE TRANSACTION FAILURE SUMMARY
	No transaction error was detected.

WARNINGS
	There were no warnings during this operation.

OPERATION PROGRESS STATUS
	* [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.

ERROR DETAILS
	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)

COMPONENT STORE TRANSACTION DETAILS
	No transaction information is available.

Any idea what this might indicate?

Hi,
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,
Andreas

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 https://panoramaweb.org/
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 128.95.55.201:443
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!

Roman

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

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?

Cheers,
Markus

Hi,

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.

Best,

Emmanuel

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 QC_Xevo-ACN_LCMS_QCmix_PrecOnly_2020-04-23_18-52-59.sky.zip
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 QC_Xevo-ACN_LCMS_QCmix_PrecOnly.sky.view
23 Apr 2020 09:53:26,464 INFO : Expanding QC_Xevo-ACN_LCMS_QCmix_PrecOnly.sky
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.

Hi,

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,
Srujana

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

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
Ferdinando

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
Ferdinando

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.
thanks.
taher

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; https://panoramaweb.org/contaminants.url
thanks.
taher

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.

Josh