Enhanced Identifications and Quantification through Retention Time Down-Sampling in Fast-Cycling diagonal-PASEF Methods
Bibliographic record
Abstract
Abstract Data-independent acquisition mass spectrometry is essential for comprehensive quantification of proteomes, enabling deeper insights into cellular processes and disease mechanisms. On the timsTOF platform, diagonal-PASEF acquisition methods have recently been introduced to directly and continuously cover the observed diagonal shape of the peptide precursor ion distributions. Although diagonal-PASEF has shown great promise, its broad adoption as a routine workflow has been hampered by a lack of available algorithmic solutions and a paucity of demonstrated real-world applications. Here, we conducted a systematic and comprehensive optimization of diagonal-PASEF for 17-minute gradients on the timsTOF HT in conjunction to Spectronaut 19. We demonstrate that Spectronaut 19 fully supports all tested diagonal-PASEF methods independent of the number of slices or overlaps and with minimal user intervention required. Using our optimized analysis strategy we coupled diagonal-PASEF acquisitions to retention time down-sampling by summation (RTsum), thereby providing a novel mode of analysis of this data that exploits the fast-cycling nature of diagonal-PASEF methods. Through the combination of RTsum with diagonal-PASEF, we demonstrate that this strategy yields higher signal-to-noise ratios while retaining the peak shape for analytes of interest. Importantly, combining RTsum with diagonal-PASEF improved overall identifications and quantitative precision when compared to dia-PASEF with static or variable quadrupole isolation widths and across different input amounts for cell line injections. We also tested the performance of diagonal-PASEF in controlled quantitative experiments where diagonal-PASEF outperformed dia-PASEF in the overall number of retained candidates, quantitative precision and identifications on peptide level. These data indicate that RTsum demonstrates a positive use case of the high sampling rate of diagonal-PASEF. Collectively, our findings imply that diagonal-PASEF methods are superior for peptide and protein level analyses especially at lower input amounts.
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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 | 0.002 | 0.003 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| 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".