Thus, spectra of peptides with unanticipated modifications cannot be identified.
The results showed that pMatch can effectively identify unanticipated modifications and significantly increase spectral identification rate.
It extends the existing library search algorithms in at least three aspects to support the identification of unanticipated modifications.
In the case of post-translational modifications, these differential levels could be the purpose of the experiment, such as in phosphorylation monitoring (Gruhler et al. 2005; Iwai et al. 2010) but, in general, they can also be artifacts, reflecting unanticipated modifications related to sample preparation, rather than real changes in the relative abundance of the parent proteins.
Also, Bandeira et al. (2007) developed a database-independent algorithm, named Spectral-Networks, to detect spectral pairs produced from modified and unmodified versions of the same peptide and identify the unanticipated modifications by propagating spectral annotations in the networks of related spectral pairs.
However, its potential in identification of unanticipated post-translational modifications has rarely been explored.
These analyses revealed several unanticipated problems, including thiaproline modification of the N-terminal cysteine, cleavage by a Kex2-like protease at a site near the N-terminus, proteolysis at sites near the hinge, addition of a hexose in the CH3 domain of the Fc region, and several sites of methionine oxidation.
Our findings demonstrate that modified U34 is an evolutionarily conserved accelerator of decoding and reveal an unanticipated role for tRNA modifications in maintaining proteome integrity.
Thus deficiencies in technical performance that arise from unanticipated demands and/or unintended consequences may be addressed not only by modification of the infrastructure but also by alternative strategies that obviate the need for such modification.
Markedly, however, none of the modification guide snoRNAs showed such strong alteration in any helicase mutant, suggesting that their binding and release involve unanticipated mechanisms.
This unanticipated observation is a consequence of the altered spatial electronic environment around the axial ligands of haem (in lieu of Met52 modification to SeMet52).
