A method for filamentous fungal growth and sample preparation aimed at more consistent MALDI-TOF MS spectra despite variations in growth rates and/or incubation times
Why this work is in the frame
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Bibliographic record
Abstract
Matrix-assisted laser-desorption and ionization time-of-flight mass spectrometry can be used for the characterization and identification of filamentous fungi, for which it is desirable to have a means of growth in which the resulting spectra remain as consistent as possible over time. To this end, we initially opted for growth in oil-overlaid small-volume liquid culture, using a medium (Czapek Dox) not containing significant amount of proteins or peptides, and with protein extraction from the entire culture volume. For both 3-week and 10-day time courses, however, we observed marked spectral changes over growth time, along with lower peak richness compared to agar-plate controls. Guided by the above, we next employed a more nutrient-rich MALDI-TOF MS-compatible liquid-culture medium, now used without an oil overlay. For a 10-day time course, we again observed marked spectral changes over growth time, along with lower peak richness compared to agar-plate controls. Finally, we opted for a method employing filter-paper-supported growth in the same MALDI-TOF MS-compatible rich medium within sealed 1.5 ml Eppendorf tubes, again with protein extraction from the entire culture volume. Using this final method, while we observed significant spectral changes between 2 days and 3 days, from 3 days to 10 days the spectra remained very consistent, with comparable peak richness to agar-plate controls. This method gave slightly better identifications and lower spectral variance compared to agar-plate controls, and the use of this method for the construction of growth-time-point-specific databases for fungal identification is discussed.
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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 | 0.001 |
| 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 | 0.000 |
| 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 it