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

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

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

Best regards
Andreas

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

--------------------

Stack trace:

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

Exception caught at: 
   at System.Windows.Forms.Application.ThreadContext.OnThreadException(Exception t)
   at System.Windows.Forms.Control.WndProcException(Exception e)
   at System.Windows.Forms.NativeWindow.Callback(IntPtr hWnd, Int32 msg, IntPtr wparam, IntPtr lparam)
   at System.Windows.Forms.SafeNativeMethods.ShowWindow(HandleRef hWnd, Int32 nCmdShow)
   at System.Windows.Forms.SafeNativeMethods.ShowWindow(HandleRef hWnd, Int32 nCmdShow)
   at System.Windows.Forms.Control.SetVisibleCore(Boolean value)
   at System.Windows.Forms.Form.SetVisibleCore(Boolean value)
   at System.Windows.Forms.Form.Show(IWin32Window owner)
   at pwiz.Skyline.SkylineWindow.OpenLibraryExplorer(String libraryName) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Skyline.cs:line 2921
   at pwiz.Skyline.SkylineWindow.ViewSpectralLibraries() in C:\proj\pwiz_x64\pwiz_tools\Skyline\Skyline.cs:line 2871
   at pwiz.Skyline.SkylineWindow.spectralLibrariesToolStripMenuItem_Click(Object sender, EventArgs e) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Skyline.cs:line 2840
   at System.Windows.Forms.ToolStripItem.RaiseEvent(Object key, EventArgs e)
   at System.Windows.Forms.ToolStripMenuItem.OnClick(EventArgs e)
   at System.Windows.Forms.ToolStripItem.HandleClick(EventArgs e)
   at System.Windows.Forms.ToolStripItem.HandleMouseUp(MouseEventArgs e)
   at System.Windows.Forms.ToolStrip.OnMouseUp(MouseEventArgs mea)
   at System.Windows.Forms.ToolStripDropDown.OnMouseUp(MouseEventArgs mea)
   at System.Windows.Forms.Control.WmMouseUp(Message& m, MouseButtons button, Int32 clicks)
   at System.Windows.Forms.Control.WndProc(Message& m)
   at System.Windows.Forms.ToolStrip.WndProc(Message& m)
   at System.Windows.Forms.ToolStripDropDown.WndProc(Message& m)
   at System.Windows.Forms.NativeWindow.Callback(IntPtr hWnd, Int32 msg, IntPtr wparam, IntPtr lparam)
   at System.Windows.Forms.UnsafeNativeMethods.DispatchMessageW(MSG& msg)
   at System.Windows.Forms.UnsafeNativeMethods.DispatchMessageW(MSG& msg)
   at System.Windows.Forms.Application.ComponentManager.System.Windows.Forms.UnsafeNativeMethods.IMsoComponentManager.FPushMessageLoop(IntPtr dwComponentID, Int32 reason, Int32 pvLoopData)
   at System.Windows.Forms.Application.ThreadContext.RunMessageLoopInner(Int32 reason, ApplicationContext context)
   at System.Windows.Forms.Application.ThreadContext.RunMessageLoop(Int32 reason, ApplicationContext context)
   at pwiz.Skyline.Program.Main(String[] args) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Program.cs:line 305

Hi,

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

Thanks.

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

I already submitted data of another project to Panorama. I think, this time, I did it exactly the same way. I created a folder and two subfolders. In the main folder, I created the "targeted MS experiment" and included the subfolders. I checked the folder permissions. They are exactly the same as for the previous project. I also checked that the folders are "Panorama" folders and not Collaboration folders.
But now, the submit button is missing. I used Skyline version 19.1.0.193 and Mozilla Firefox.
I hope you can help me that I can submit my data.
Sabrina

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

Best regards
Andreas

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

An error occurred trying to download 'http://skyline.gs.washington.edu/software/AutoQC/AutoQC.application'.

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

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

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

Best regards
Andreas

Dear folks,

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

Hi Panorama people!!!

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

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

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

Alex

Hello Dear,

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

Best regards,
Leandro

Dear Skyline and Panorama teams,

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

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

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

Cheers,
Chris

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

Dear PanoramaWeb team,

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

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

Sincerely,
Eisuke

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

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

Best regards
/Andreas

Dear Panorama team,

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

Greetings,
Tobi

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

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

Hi Panorama people,

I'm trying to set new folders for AutoQC of all instruments in my lab, but I cant seem to delete older folders. I get the following error when I try to delete the folders from the Folder Management page:
java.lang.NullPointerException
at org.labkey.pipeline.api.PipelineManager.purge(PipelineManager.java:240)
at org.labkey.pipeline.PipelineModule.containerDeleted(PipelineModule.java:237)
at org.labkey.api.data.ContainerManager.fireDeleteContainer(ContainerManager.java:2108)
at org.labkey.api.data.ContainerManager.delete(ContainerManager.java:1573)
at org.labkey.core.admin.AdminController$DeleteFolderAction.handlePost(AdminController.java:6823)
at org.labkey.core.admin.AdminController$DeleteFolderAction.handlePost(AdminController.java:6784)
at org.labkey.api.action.FormViewAction.handleRequest(FormViewAction.java:101)
at org.labkey.api.action.FormViewAction.handleRequest(FormViewAction.java:80)
at org.labkey.api.action.BaseViewAction.handleRequest(BaseViewAction.java:177)
at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:482)
at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:1266)
at org.labkey.api.view.ViewServlet._service(ViewServlet.java:204)
at org.labkey.api.view.ViewServlet.service(ViewServlet.java:131)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:38)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:1241)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:215)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:118)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:198)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:493)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81)
at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:650)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342)
at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:800)
at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:806)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1498)
at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:748)
request attributes
LABKEY.OriginalURL = http://localhost:8080/admin/Dalhousie University - Proteo and Metabolomics Core/QC_VelosPro/QTra5500_QC/deleteFolder.view?
LABKEY.StartTime = 1546973895452
LABKEY.action = deleteFolder
org.springframework.web.servlet.DispatcherServlet.CONTEXT = Root WebApplicationContext: startup date [Thu Dec 20 13:54:46 PST 2018]; parent: Root WebApplicationContext
LABKEY.controller = admin
LABKEY.Counter = 0
org.labkey.api.util.ExceptionUtil$exception = java.lang.NullPointerException
X-LABKEY-CSRF = f03e4fa741ccf58c794ea79555e0ac35
LABKEY.container = /Dalhousie University - Proteo and Metabolomics Core/QC_VelosPro/QTra5500_QC
LABKEY.RequestURL = /admin/Dalhousie%20University%20-%20Proteo%20and%20Metabolomics%20Core/QC_VelosPro/QTra5500_QC/deleteFolder.view?
LABKEY.OriginalURLHelper = /admin/Dalhousie%20University%20-%20Proteo%20and%20Metabolomics%20Core/QC_VelosPro/QTra5500_QC/deleteFolder.view?

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

Hi Vagisha,

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

Thanks so much in advance for your time and help!

Best,
Regine

Dear Panorama support,

our autoQC loader client reports:

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

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

Greetings,
Tobi

Dear PanoramaWeb team,

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

Sincerely,
Eisuke

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

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

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

Best, Klemens

Hello,

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

Thanks very much in advance for your help!
Best,
Regine

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

Best,
Jeremy

Dear Panorama team,

first of all, thank you so much for the great work you are doing! We have recently implemented QC for our QTrap 5500 system based on Skyline and Panorama employing the AutoQC client. I have to say that it greatly facilitates the workflow compared to manual data inspection in Skyline. However, since yesterday no QC Plots can be displayed on our dashboard ("no data to plot"). However, samples are being successfully uploaded into the specified Skyline document and also to Panorama, according to the AutoQC log (new sample names also appear in the QC summary, just the plots are gone, s. attached screenshot). When I enter the public Panorama project "U of Melbourne - Proteomics Facility", I can see and manipulate QC Plots there, so this does not seem to be a browser or a general issue. We use regular Skyline release 4.1.0.18169 combined with AutoQC Loader 1.1.0.11725, OS is Windows 7 Professional, 64-bit. Restarting the relevant configuration in the loader did not help. I would very much appreciate any suggestions since we are quite new to Panorama and have never encountered that issue before.

Best regards,

Roman

Hello

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

Thank you for your help! :)
JRC

I'm uploading an SRM experiment (Skyline project file, description, raw files). I uploaded the raw files but they are not being recognized, as it appears the associated raw file names linked to the Skyline project file all have some additional text added to the file names. Is there any way to get my uploaded raw files linked to the skyline project in Panorama? Thanks!

Hi Panorama Support,

I see it is possible to upload raw files to Panorama, however the Public Panorama projects I clicked on only seemed to have .sky.zip files (presumably the Skyline results files). And the tutorial for Panorama Public doesn’t mention raw files. Is it preferable to use something like PRIDE at EMBL to upload raw files, or can raw files be uploaded alongside Skyline files in Panorama Public?

Our DIA raw files are fairly large: 20 GB in total; 0.5 to 1.5 GB per raw file.

Thanks,

Steve

Hello-

I was wondering if there were a way to assay the ETD reagent ion signal on a Thermo Fusion Lumos using AutoQC. Currently we look through the individual scan headers output checking the "number of LM found" and the "LM correction (ppm)." This assay requires the instrument method to run Easy-IC. While we have a script that completes this task, it requires a little bit more work than we would like. The reason we want this installed is because we can clean the cathode (ETD source) and restore reagent ion signal when it decays-- increasing our LM accuracy and increasing our signal ETD fragment efficacy. Furthermore, this last point seems to be a great use of the AutoQC system.

Cheers,

CJB

Is there a way to change the QC plot headers (typically a peptide sequence) to a m/z? Or have it write out "PEPTIDE, m/z" as the header?

Thanks,

CJB

I am adding a data set to Panorama and having issues with the Instrument field. There is no drop-down list and it is not accepting my manual entry for Waters Xevo Tq-S. Can you clarify the correct way to enter this instrument so that I don't receive the error message "unrecognized instrument" when I hit submit?

Thank you!

Our setup;

Win 10 64 bit running
AutoQC: 1.1.0.11725
Skyline: 4.1.0.18169

Win server 2012, 64-bit, running LK v18.1

Since the LK update to v18.1 the uploads are failing. The files are loaded into Skyline fine, but then the upload to the server LK fails.

I’ve attached a number of log files;
AutoQC_log_PC6.txt the log for one specific configuration.
AutoQCProgram.log the log from the AutoQC install directory
LK_log.txt the log from LK for the specific AutoQC configuration above

Any help on this would be appreciated.

Peter

I'm trying to use AutoQC-daily to control chart our daily instrument QC data in Panorama. Each day we submit the same batch, but change the date on the output *.wiff file. As such, the QC data all has the same name and the AutoQC log file shows the error:
"The replicate MRM 100ng_mL 001 already exists in the given document and the --import-append option is not specified. The replicate will not be added to the document."

Is there a workaround?

Hi Panorama team,

as discussed at the skyline user meeting I would like to suggest some new features for Panorama + autoQC. I am not sure how other people use this tool, but our sample for system suitability testing contains iRT peptides. We accordingly use iRT regression as a performance measure, since the parameter estimates (slope and intercept) tell us if our LCs really deliver the commanded gradients. Unfortunately, we always have to do this offline, since Panorama does not monitor these parameters, although the skyline doc records the iRT regression on the fly. What about including diagnostic plots for RT regression in Panorama?

Another feature request: Panorama ignores the protein/peptide list context of targets. Our targets lists during autoQC runs contain a mixture of matrix peptides (BSA) and iRTs. Unfortunately, they are all displayed alike and in alphabetic order. Some sort of filtering/grouping according to peptide list/protein context would help very much! Also sorting according to hydrophobicity or iRT value would be a cool feature.

Let me know what you think about my suggestions,
Tobi

Hi Panorama support,

is it possible to run the autoQC loader application from the command line? We would like to script the complete autoQC pipeline and the loader application seems to be the missing part in the pipeline.

Greetings,
Tobi

I'm just getting started using AutoQC to load QC data into skyline. I successfully created a configuration but it appears that AutoQC is only loading the first scan into my skyline file. Is there anyway to get it to load more than one scan from a *.wiff file? Better yet, can I add just the scans from the *.wiff file that contain a particular text string in their name?

Hi Panorama people,

I'm using AutoQC and Loader, and I am marveled by it.... a long overdue solution to QC in MS laboratories. I'm using it with an aliquoted BSA digest using MS1 filtering on Skyline (VeloPro acquisition) and this has given me a great tool to assess the overall LC-MS performance prior to running real samples, KUDOS to ALL your team!!!

Now my suggestions:

-Is it possible to add to the QC plots types an additional parameter such as Xcorr or some other output parameter to assess the MSMS quality for DDA acquisitions?? This would be great!!! You already now the sequence of the target peptides, and it is likely you can pull out the MSMS for that precursor in each file. If you could monitor the additional parameter to follow over time, it would be a great source to assess the 'health' of the MSMS.

-Have you considered selling/distributing a QC sample (protein digest?) to be used as an external QC like done typically in clinical labs? It would be great to not only have internal QCs, but also external QCs and evaluate how your instrument is performing compared to identical (or not) instruments in other labs (anonymous). I imagine the huge variability as everyone is using different LC conditions, but if this could be minimally standardized, it could be a source of precious information to evaluate inter-laboratory variability

Cheers

Alex