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Peptide format from IMS library not recognized

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Peptide format from IMS library not recognized Juan C. Rojas E.  2022-06-27 06:39
 

Hi all,

I tried creating an IMS library of cross-linked peptides with the "Use Results" option. After creating the library and re-importing the results I noticed that no IMS filtration was applied.

Closer inspection of the library shows that the name in the library does not include the appropriate notation to be recognized as a cross-linked peptide or the site of the cross-link and is only taking the "left peptide" sequence. Are there any extra steps I need to take or is this a bug?

I have provided some example files (raw data and Skyline project) in our private Panorama "MLU - AGSinz - Data Sharing" folder for testing in case it is a bug.

As always, thank you for your time and support.
Sincerely,
Juan C.
 
 
Brian Pratt responded:  2022-06-27 09:29

Hi Juan,

Most likely a bug - you may be the first to combine crosslinking and IMS. I'll have a look at your files, can you make sure that I (bspratt@protein.ms) have access?

Best regards,
Brian Pratt
 
Juan C. Rojas E. responded:  2022-06-28 01:56

Hi Brian,

Thank you very much for having a look. I just added you to the users list and I hope you'll receive an e-mail soon. Let me know if you don't.

Juan C.
 
Brian Pratt responded:  2022-06-28 10:21

Oops, I mis-typed my email - it's bspratt@proteinms.net, not bspratt @ protein.ms - sorry!
 
Brian Pratt responded:  2022-06-30 09:54

Hi Juan,

I'm still very interested to have a look at that data, but still have not received an email granting access (which is on me for initially giving you the wrong email, admittedly).

Best,

Brian
 
Juan C. Rojas E. responded:  2022-07-01 05:37

Hi Brian,

I added your corrected e-mail. I wonder why you did not get it :( Should I try to reach out to Vagisha to solve it?

Sincerely,
Juan C.
 
Brendan MacLean responded:  2022-07-07 06:20

By your request, I assume you have added him to the list of people with access to a folder on panoramaweb.org. This does not necessarily generate email. Though, that is an interesting idea, as I know that many apps like Google Drive to offer to send email when you initially share a folder or document with someone. PanoramaWeb.org (LabKey Server) does not.

So, you just need to email Brian the link to your folder on PanoramaWeb.org and he should be able to access it once he is signed in with the email address matching the one you have added in your Folder Permissions.

Interesting use case. Thanks for sharing.

--Brendan
 
Brian Pratt responded:  2022-07-18 11:59

Hi Juan,

Thanks for letting us know about this issue. This has been resolved (thanks, Nick!) and the fix will appear in the next Skyline-Daily.

Best regards,

Brian
 
Juan C. Rojas E. responded:  2022-07-19 00:26

Awesome news about the fix!

@Brendan, yeah...somehow I even managed to confuse Vagisha as to how I added Brian to the access list. She has kindly instructed me with the correct way of doing it. However, as you mentioned it would be nice to have the notification for the other users.

Danke Schön!