Hello,
My name is Kara Joseph with the Baker Lab at UNC Chapel Hill and we are working on expanding our library for PFAS with some new adducts, however the adducts listed below cause errors when inserting the Transition List. I have included the original adducts we prefer to use below. Do you have any suggestions on how to format these while retaining the structural information for the losses?
M-COOH-HF
M-C2H4-OH
M-CH2-COOH
The only way I can get the Transition List to import properly is as follows:
M-C-2H-2O-F
M-2C-5H-O
M-2C-3H-2O
Thank you!!! |
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| Nick Shulman responded: |
2024-09-27 16:33 |
Can you send us your entire transition list?
We will try to figure out what is going on.
-- Nick |
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| Brian Pratt responded: |
2024-09-27 17:30 |
I think it's just that Skyline is having trouble determining the charge (and isn't doing a good job of saying so, I'll work on that).
Try adding an explicit charge declaration, e.g. [M-COOH-HF]- instead of just [M-COOH-HF] (assuming it is actually z=-1, but you get the idea)
- Brian |
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| karamj33405 responded: |
2024-09-30 08:17 |
Brian was correct,
Specifying the charge for all the adducts worked to solve this issue. I appreciate you all working on getting Skyline to recognize the charge, and both of you for your help! Thanks!
- Kara |
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| Brian Pratt responded: |
2024-09-30 09:59 |
I'm glad that worked out. I'd still love to see that transition list, to get a proper sense of just what the experience was like when you tried to load it in to Skyline. It would also be helpful to have the modified list, if we're going to try to improve Skyline's ability to determine charges on more complicated adduct descriptions.
Thanks,
Brian |
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