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


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

Any input would be appreciated.
 
 
vsharma responded:  2017-02-09
Hi Norelle,

I looked at the files that you sent as attachments to Nat. Your Skyline docment is set up for MS1 filtering (Look under Transition Settings > Full Scan) so when I import your raw file (JGB_OTF1_02_04_2017.raw) I get this message:

"At 4:21 PM:
No scans in C:\Users\vsharma\WORK\MacCoss\AutoQC\Norelle_Data\JGB_OTF1_02_04_2017_32.raw match the current filter settings."

Since your instrument method is set up for targeted MS2 you should change the settings in your Skyline document for MS/MS filtering so that data from your raw files can be imported.

AutoQC Loader simply calls Skyline in the background to import raw files to the given Skyline document. If no data gets imported (as in this case), the document is not uploaded to Panorama.

I hope this helps.

Thanks,
Vagisha
 
n wildburger responded:  2017-02-20
Hi Vagisha,

I changed the settings for MS/MS filtering and now I can open the Skyline template and see my QC runs (which I couldn't before). However, the runs are still not being uploaded to Panorama. I can see that Panorama is being pinged, so that works, but nothing else.

Best,

Norelle
 
vsharma responded:  2017-02-21
Hi Norelle,

Can you please send me the AutoQC log file (AutoQC.log)? You will find it in the directory where you have your template Skyline document. Information in this file may help me figure out what is going on.


Thanks,
Vagisha
 
n wildburger responded:  2017-02-21
Hi Vagisha,

Attached are the AutoQC log and the QC skyline template files that were update to reflect that I am doing targeted MS/MS.

On interesting thing to note now is that I can see the most recent QC files (2/17-2/19/17) and their product ions when I open the Skyline document, however not the ones from further back (with the same QC instrument method).

Best,

Norelle
 
vsharma responded:  2017-02-21
Hi Norelle,

The AutoQC.log attachment didn't make it through. Can you please attach it again?

I don't think I need the Skyline document. But if I need it I will ask you to create a shared zip file through the File > Share menu. This will create a zip archive of all the files I need to open the document in Skyline (.sky, .skyd, .sky.view etc.) You can find some more information here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=manuscript_sharing

You will have to re-import the older raw files to be able to see data from those files.

Thanks,
Vagisha
 
n wildburger responded:  2017-02-21
 
vsharma responded:  2017-02-21
Hi Norelle,

The log just says "unknown error connecting to the server panoramaweb.org". Not very helpful! I've seen this before when the Windows operating system on the computer was not up to date. To confirm that is the case can you please try a couple of things?

1. On your instrument computer upload a document to Panorama directly from Skyline ("Publish to Panorama" button in the toolbar OR File > Publish to Panorama)

This will likely fail too, but let me know if it succeeds.

2. If 1) fails, try to install an external tool in Skyline from the tool store: Tools > Tool Store... menu

If 2) fails with this error message: "Error connecting to the Tool Store: The request was aborted: Could not create SSL/TLS secure channel." it means that your operating system does not support the protocol Skyline is using for SSL connections. In this case you will have to go through Windows updates. See this support board request on the Skyline website:
https://skyline.ms/issues/home/issues/details.view?issueId=481&_docid=issue%3A481
You may be able to get a stand-alone package for the update here: https://support.microsoft.com/en-us/kb/3140245

Let me know how this goes.

Thanks,
Vagisha
 
n wildburger responded:  2017-02-21
Thanks Vagisha,

Currently someone is running samples on the instrument so these steps will have to wait for the time being.
But I am attaching a screenshot of the AutoQC method set up. Maybe the URL is written incorrectly?
 
vsharma responded:  2017-02-21
Hi Norelle,

Thanks for the screenshot. I was able to see the URL in the log file as well. You don't need the full URL of your project in the URL field. Just https://panoramaweb.org is enough. However, even if you have the longer URL, AutoQCLoader will get the relevant part and build the correct URL. That is why pining the server is working fine.

Thanks,
Vagisha
 
n wildburger responded:  2017-02-22
Hi Vagisha,

I tried both suggests and neither work (attached).
I am not sure if I want to go through Windows updates. We have had problems in the past with Windows updates messing up how the MS software talks to the instrument etc.

Best,

Norelle
 
vsharma responded:  2017-02-23
Hi Norelle,

Unfortunately, Skyline and AutoQCLoader will not be able to communicate with PanoramaWeb without having support for the TLS protocols for secure connections. I think you can get a stand-alone package just for enabling TLS protocols here: https://support.microsoft.com/en-us/kb/3140245. I hope this works for you.

The first message you see when you try to publish to Panorama from Skyline is just telling you that you need to configure a Panorama server that Skyline can communicate with. So in the dialog that says: "There are not Panorama servers to publish to..." click on "Continue" and you will be presented with a dialog where you can enter your PanoramaWeb user name and password. After that you will be able to upload documents to PanoramaWeb (once you have support for TLS).

I hope this helps.

-Vagisha