Targeted Quantitative Mass Spectrometric Identification of Differentially Expressed Proteins between Bax-Expressing and Deficient Colorectal Carcinoma Cells
Bibliographic record
Abstract
Bax, a Bcl-2 interacting protein, plays a central role in several stimuli-induced apoptosis pathways through its functional and physical interactions with various biologically important proteins. Identification of the Bax-modulating protein network should be useful to further our understanding of Bax-mediated apoptosis. For the first time, we performed proteome-wide quantification and identification of differentially expressed proteins between Bax+/- and Bax-/- HCT116 clones using a newly developed quantitative mass spectrometric analysis strategy. This strategy is based on forward and reverse differential isotope labeling of the proteome digests of two comparative cells, followed by two-dimensional liquid chromatography separation and automated peptide deposition to matrix-assisted laser desorption ionization sample plates for MS quantification and MS/MS peptide sequence identification. We quantified and identified 200 differentially expressed proteins involved in various cellular processes. Through bioinformatic analysis, four groups of differentially expressed proteins were highlighted for the association with Bax: mitochondria permeability transition channel proteins, Bax regulator proteins, heat shock protein family members, and oxidative stress-triggered proteins. These results indicate the functional diversity of Bax and provide new research directions to study the biology of Bax-regulated apoptosis.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 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 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 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 source (direct Gemma or distilled Codex), 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".