Brian Pratt responded: |
2021-10-25 12:47 |
We'll have a look at this, thanks.
In the meantime, what's that non-ASCII character (hex code 0xB0) that shows up in the peptide.MatchedProductsString and fragment.str columns? Probably not related to the problem, but it's unusual.
Thanks for using the Skyline support board!
Brian Pratt
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dwwilk02 responded: |
2021-10-25 13:21 |
Hi Brian,
Thanks for your response and offer to help. I believe that character is an indicator of a fragment with a water neutral loss (e.g., b5° indicates a b5 ion with water neutral loss). Thanks,
Daniel Wilkey
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Brian Pratt responded: |
2021-10-25 14:16 |
It would be helpful to see the original file, but looking at the code, it seems the parser is expecting something more like "SILAC 13C(6) 15N(2)" than "Label:13C(6)15N(2)". I wonder if something has changed in PLGS and the way it represents these modifications?
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dwwilk02 responded: |
2021-10-25 14:42 |
Thanks Brian:) In the test file I sent earlier, Skyline was able to recognize the the modification when I changed it to "SILAC 13C(6) 15N(2)+K(15)". The original final fragment file is attached.
Daniel Wilkey
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dwwilk02 responded: |
2021-10-25 14:52 |
I possibly added the mods Label:13C(6)15N(2) (K) and Label:13C(6)15N(4) (R) into our version of PLGS. I used them instead of the SILAC mods in PLGS for the search. Thanks for your help with this,
Daniel Wilkey
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Brian Pratt responded: |
2021-10-25 15:08 |
Ah, OK. It's hard to know what to do with user-created values.
Thanks
Brian
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