Problems adding new chromatograms to assay library

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Problems adding new chromatograms to assay library Andreas Hober  2020-05-08 06:28:13
 

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

 
 
vsharma responded:  2020-05-08 06:47:46

Hi Andreas,

Can you please point me to the library folder where you are seeing this problem? I will take a look.

Thanks,
Vagisha

 
Andreas Hober responded:  2020-05-08 06:52:04
 
vsharma responded:  2020-05-08 13:35:59

Hi Andreas,

Thank you for sharing the link. I am able to duplicate the problem with some of the documents in your folder. I will get back to you on Monday with a solution.

Thanks,
Vagisha

 
vsharma responded:  2020-05-11 06:49:40

Hi Andreas,

The problem is due to a couple of bugs in the chromatogram library code. The root cause is that there are proteins in your documents that have the same sequence but different name / labels. For example:

Some documents have the protein "HPRR5000256" which has the same sequence as "QPrEST_Adiponectin_HPRR5000256" in another document.

The document with "QPrEST_Adiponectin_HPRR5000256" was uploaded first. And then a document with "HPRR5000256" was uploaded. I would have expected this to cause a conflict since the proteins have the same sequence. But due to the bug, the conflict was not reported. So, now the library had both proteins "HPRR5000256" and "QPrEST_Adiponectin_HPRR5000256".

Next, another document with "HPRR5000256" was uploaded, and this time, there was a conflict since the library already has a protein with the same name. When you try to resolve conflicts, all library proteins with the same sequence as "HPRR5000256" are listed in the UI. You will notice that there are two rows for "HPRR5000256". The conflict UI also needs to be fixed, by the way. The protein names in the "Current Library Proteins" cannot be read. Trying to resolve the conflicts fails with an error message is not helpful at all! Sorry about that.

I assume you don't want both "HPRR5000256" and "QPrEST_Adiponectin_HPRR5000256" in your library.

I will fix the bugs and we can, hopefully, have the server updated in the next few weeks. In the mean time, the workaround is to remove some of the older, single protein documents that have protein names that are not the same as the newer documents. I think if you delete the following documents, you should be able to get this folder to a working state.

QPrEST_Adiponectin_HPRR5000256_CE_2020-02-17_15-40-23.sky.zip
QPrEST_CystC_HPRR5000001_CE_2020-02-17_15-56-42.sky.zip
QPrEST_FAPa_HPRR1440042_CE_2020-02-17_16-00-26.sky.zip
QPrEST_Adiponectin_HPRR3790216_CE_2020-02-17_15-27-27.sky.zip
QPrEST_ComplementFactor_C3_HPRR280090_CE_2020-02-17_15-52-55.sky.zip
QPrEST_PlasminogenActivInhib_HPRR350091_CE_2020-02-17_16-17-06.sky.zip
QPrEST_RetinolB-4_HPRR350140_CE_2020-02-17_16-20-02.sky.zip
QPrEST_RetinolB-4_HPRR4190038_CE_2020-02-17_16-23-38.sky.zip
QPrEST_Thrombosp4_HPRR2400003_CE_2020-02-17_16-31-20.sky.zip
QPrEST_ PEDF_HPRR4340066_2nd digestion_CE_2020-02-18_11-29-33.sky.zip
QPrEST_Vitronectin_HPRR4030671_CE_2020-02-17_16-33-49.sky.zip

Thanks for using chromatogram libraries and reporting bugs!

-Vagisha