The basic residues (if they are there at all) typically are not at a termini.
You may see a lot of peptides that only go to z = 1.
They often fragment like crap.
Should you go ahead and do it with DIA? (Yikes. Y'all try it first and write up how it went and I'll think about it). Well...here you go!
PEAKS vs Skyline vs DIA-NN vs SpectroNaut!
Who comes out on top? To be honest, it is sort of a mixed bag with pros and cons of each.
Figure 3 is a highlight for me because the consistency between all 4 is a whole lot higher than I would have guessed. The numbers are all within about 10% of each other.
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