Comparing Machine Learning Architectures for the Prediction of Peptide Collisional Cross Section
Bibliographic record
Abstract
1 Abstract Mass spectrometry is the method of choice in large-scale proteomics studies. One common method is data-independent acquisition (DIA), which allows for high-throughput analysis of biological samples, but also produces complex data. Methods of peptide separation, in addition to retention time, improve data analysis and there has been increasing interest in separating peptides based on collisional cross section (CCS), which is a measure of the size of a peptide. However, existing libraries that are used during data analysis lack CCS measurements, and this data is expensive and time-consuming to acquire. This has led to the desire to predict library values for mass spectrometry analysis. Here we compare three deep learning architectures, LSTM, CNN, and transformer, for the tasks of retention time and collisional cross section prediction. We show that the LSTM and CNN models perform similarly and that the transformer has a lower performance than expected.
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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 | 0.003 | 0.005 |
| Meta-epidemiology (narrow) | 0.002 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.002 | 0.001 |
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".