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Choice of quantification marker resulted in better quantification if the retention time difference was minimized (12 out of 12 cases error factor < 4.0) rather than if the accurate mass difference was minimized (7 out of 12 cases error factor < 4.0).
Thus, we determined that the mass difference was derived from the difference in the chain lengths of the LCB, namely C18- and C20-sphingosine.
Since HGSNAT is predicted to have 5 potential N-linked glycosylation sites each potentially contributing ∼2 kDa to the size of the mature enzyme [11], this molecular mass difference was consistent with the hypothesis that inactive mutants lacked proper glycosylation.
The accepted error of mass difference was below 0.02 Da, while the accepted difference of abundances was below 10%%.
Although this body mass difference was not deemed significant, it could be argued that this difference may have played a role in adaptive responses to the resistance exercise program.
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The mass difference is slightly greater than 10 ppm and the peptide appears in a different mass retention time bin in the matrix, while it should be present in one bin.
The energy equivalent of this mass difference is given by the Einstein relation, E = mc2.
The mass of the particles that we react is slightly more than the particles we create and that mass difference is turned into energy.
This mass difference is defined as nuclear binding energy.
Therefore, this mass difference is avoided in the simulations by fixing water density at a constant value.
Thus, if the peptides are not fully sequenced with all fragment ions visible, it is not possible to assess if the observed 14 units mass difference is due to a methyl group modifying a lysine or arginine residue or to a polymorphism in the protein sequence.
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