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Random editing site assignment was used to produce coding sequences with randomly assigned editing sites.
Further, all spectra corresponding to phosphopeptides were manually inspected for correct sequence identification validation and site assignment based on the presence of site determining fragment ions.
In the MS/MS spectrum, its phosphorylation site is sandwiched by fragments still bearing the modification as well as the corresponding neutral loss (-98Da) fragments, i.e. y4, y5, y6, y7, y8-98, y8, y9-98, y9, y10, which validates the phosphorylation site assignment.
All the hurdles make accurate O-GlcNAc site assignment a challenging task.
Manual analysis of MS/MS patterns were performed to validate phosphorylation site assignment.
Citrullinated peptides were inspected for validity of site assignment (Additional file 2: Figures S1-S7).
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The calculated hyperfine constants related to the coupling of the unpaired electron spin to the N and C nuclei, for which the Fermi contact terms vary from over 200 MHz to less than 3 MHz, are generally in good agreement with the largest experimental values, both in terms of absolute magnitudes and site assignments.
Eventually we would like to hire and train a managing director for every one of the 10 states in South Sudan to oversee the training and site assignments of literacy tutors in their state.
This reflects the general problem of PTM site assignments.
However, despite these advances manual evaluation of the spectra is still essential for reliable site assignments.
The second sequence read from polyadenylation junction enables verification of polyadenylation site assignments of transcripts.
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