The remaining spectra containing UStags were subjected for further processing to explain mass shifts with known PTMs.
The metabolic incorporation of the isotope-labeled amino acids leads to a mass shift of corresponding peptides, with the ratio of the peak intensities reflecting the relative protein amount.
As the Cys316Ala mutant of AlmE was capable of adenylating and subsequently transferring glycine and l-alanine with nearly equal specificity, one could predict that l-alanyl-AlmF could serve as a substrate for AlmG for transfer onto lipid A. However, our MS analysis of V. cholerae lipid A expressing AlmE Cys316Ala did not show mass shifts consistent with l-alanine modification.
Notably, a histone H2B peptide, PEPTK+104.0268SAPAPK, was identified with a mass shift of +104.0268 Da at the lysine residue position H2BK5 (Fig. 1).
In case of batch B, only 3 spots were visible on the 2D gel: (i) spot 1 with the correct mass of 17417.2 Da containing 72.5% and (ii) spot 2 with a mass shift of +1 Da (17418.2 Da) containing 22.6% of Bet v 1.0401.
We show the percentages of random PBNs with stationary mass shift Δ = π U - ≥ 0 in Table 4 for different control policies and different p b 's.
Table 2 gives the percentages of random BNps with stationary mass shift Δ = π U - ≥ 0 for different control policies and different values of p b.
Although a deuterated acetyl group is transferred to the lysine side chains, the corresponding mass shift still results in ambiguity with endogenous acetylation or trimethylation PTMs, which have the same nominal mass of 42 Da.
Many of them show no mass shift in product ions, compared with their matched library spectra (see Supplementary Figure S5), indicating that their precursor ion masses might have been incorrectly judged.
For the homozygous variant C sample, the measured MW was 15 857.4033 Da (MWcalc 15 857.3094, Δ 5.9 ppm), suggesting the presence of a variant with a mass shift of −1 Da.
