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Software settings were the following: frames = up to 1000 with signal threshold > 500 000; m/z start = 200; m/z stop = 350; m/z width = 0.02; Retention time start = 0 min; Retention time stop = 7.5 min; Retention time width = 1 min. Maximum number of frames and intensity threshold were set to limit the identification process to only major OTPs.
Other pixels with intensity lower than the threshold were set to zero.
The other pixels with intensity lower than the threshold were set to zero.
The ion scores threshold were set to 33, which yielded final peptide false positive rate below 1%.
The decyder spot detection algorithm ratio and threshold were set to a 1.5-fold change for calculations.
This single threshold was applied to each image to identify pixels within fibers by creating a pair of masks (one for F, one for B), in which all of the pixels above threshold were set to 1, and all of the pixels below threshold were set to zero.
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All settings were kept as default except the minimum threshold was set to 60.
The threshold is set to revert to A- in 2011.
And the threshold is set to go up in line with inflation".
The frequency threshold is set to three.
TSE threshold was set to 0.15.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com