dbwilburn
commented
10 months ago Hi Robbin.
I would have to double check, but this is likely very need the end of the gradient. RT alignment is a bit compressed on the tails because the spline function fit to the KDE map can not extrapolate beyond the last RT for which there was a Prosit-precitable peptide (or close to it). If we used a different alignment method, extrapolation would be an option, but that would likely have negative implications for the rest of the data, and most gradients are compressed on the tails anyway, so the empirical RT estimates are noisier too.
Best, Damien.
On Thu, Sep 7, 2023, 4:18 AM RobbinBouwmeester @.***> wrote:
Dear @dbwilburn https://github.com/dbwilburn,
There seems to be a slight issue with the "Zecha2019_TMT" data set.
There are many (different) peptides with the exact retention time of "101.48783141336828".
Could this maybe be due to your preprocessing steps?
Kind regards,
Robbin
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Dear @dbwilburn,
There seems to be a slight issue with the "Zecha2019_TMT" data set.
There are many (different) peptides with the exact retention time of "101.48783141336828".
Could this maybe be due to your preprocessing steps?
Kind regards,
Robbin