Formation of (b<sub><i>n</i>−1</sub> + H<sub>2</sub>O) ions by collisional activation of maldi-formed peptide [M + H]<sup>+</sup> ions in a QqTOF mass spectrometer
Bibliographic record
Abstract
Collisional activation of [M + H](+) parent ions from peptides of n amino acid residues may yield a rearrangement that involves loss of the C-terminal amino acid residue to produce (b(n-1) + H(2)O) daughters. We have studied this reaction by a retrospective examination of the m/z spectra of two collections of data. The first set comprised 398 peptides from coat protein digests of a number of plant viruses by various enzymes, where conditions in the tryptic digests were chosen so as to produce many missed cleavages. In this case, a large effect was observed-323 (b(n-1) + H(2)O) daughter ions (approximately 81%), including 185 (approximately 46%) "strong" decays with ratios (b(n-1) + H(2)O)/(b(n-1)) > 1. The second set comprised 1200 peptides, all from tryptic digests, which were carried out under more stringent conditions, resulting in relatively few missed cleavages. Even here, 190 (b(n-1) + H(2)O) ions (approximately 16%) were observed, including 87 (> 7%) "strong" decays, so the effect is still appreciable. The results suggest that the tendency for (b(n-1) + H(2)O) ion formation is promoted by the protonated side chain of a non-C-terminal basic amino acid residue, in the order arginine >> lysine > or = histidine, and that its (non-C-terminal) position is not critical. The results can be interpreted by a mechanism in which hydrogen bonding between the protonated side chain and the (n - 1) carbonyl oxygen facilitates loss of the C-terminal amino acid residue to give a product ion having a carboxyl group at the new C-terminus.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.002 |
| Bibliometrics | 0.001 | 0.003 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.001 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".