Displacement of N/Q-rich Peptides on TiO<sub>2</sub>Beads Enhances the Depth and Coverage of Yeast Phosphoproteome Analyses
Bibliographic record
Abstract
Phosphorylation is a reversible protein modification that regulates major cellular processes such as cell division, growth, and differentiation through highly dynamic and complex signaling pathways. Large-scale phosphoproteomics analyses have been greatly facilitated using affinity chromatography such as metal oxide affinity chromatography (e.g., TiO2), which in combination with mass spectrometry has enabled unbiased detection and quantification of thousands of phosphorylation sites in a single experiment. However, global phosphoproteome analyses do not provide comparable enrichment yields for different model organisms. While the proportion of phosphopeptides exceed 90% in mammalian cells using TiO2, similar levels have been notoriously difficult to achieve for yeast or dictylostelium cells. In a systematic study of TiO2 using cell extracts from different organisms, we determined that phosphopeptides are coenriched with peptides containing repetitive stretches of glutamine and asparagine residues. The proportion of these nonspecific binders can reach up to 50% in cell extracts from budding yeast and thus limit the depth and comprehensiveness of phosphoproteomics analyses. To address this limitation, we developed an effective method that used decoy amino acids to reduce the extent of nonspecific peptide binding and improve the recovery and detection of low abundance phosphopeptides that remained undetected by conventional TiO2 enrichment protocols.
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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) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 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".