Dear Brandon,
I am working with a large modification that decays in MS/MS mode as a neutral loss of more than 600 Da. At the moment, Skyline limits neutral loss fragment to 600 Da. I can input 2 neutral losses for the same amino acid but skyline will not list fragments with the sum of the neutral losses (either one or the other). My go around has been to artificially modify another amino acid to compensate but of course the spectral library does not match anymore.
Any hope to raise the neutral loss mass limit? Or do you know of another go around?
Thanks, and best regards,
Axel |
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| Brendan MacLean responded: |
2015-02-05 03:45 |
Hi Axel,
I can raise the limit. Do you have a new suggested maximum? I can get this fix into a Skyline-daily release fairly quickly. Let me know what you think is a limit unlikely that anyone would hit in a reasonable case. 1000, 5000, 10,000?
Thanks for your post.
--Brendan |
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| axel ducret responded: |
2015-02-06 01:57 |
Hi Brendan,
Thank you for your post. The largest modification in Unimod is 3500 Da, so I guess a limit that is likely to be still reasonable for the very vast majority of us would be 4000 Da.
Thank you and best regards,
Axel |
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