Development of specimen processing workflows for mass spectrometric detection and characterization of TDP-43
Bibliographic record
Abstract
Transactive response DNA-binding protein 43 kDa (TDP-43) is a highly conserved protein that regulates nucleic acid processing. In humans, TDP-43 is widely expressed across different tissues in the body. In frontotemporal dementia and amyotrophic lateral sclerosis, two progressive neurodegenerative diseases, TDP-43 forms insoluble aggregates in central nervous tissues. Unfortunately, there is no cure for these diseases and a definitive diagnosis can only be made upon autopsy. As such, there is great interest in detecting, characterizing and quantifying TDP-43 and its disease-related post-translational modifications to investigate pathogenesis and as a potential biomarker. Characteristic TDP-43 post-translational modifications of TDP-43 deposits in frontotemporal dementia and amyotrophic lateral sclerosis include ubiquitination, hyper-phosphorylation, and proteolytic fragmentation. These pathological deposits have been primarily characterized by immunometric methods, namely western blot analysis, and thus methods with greater structural resolution are needed to aid in our understanding of the pathological processes associated with TDP-43 misfolding and aggregation. Detailed analysis of TDP-43 in human tissues and biofluids is hindered by sample complexity and the relatively low abundance of TDP-43. The aims of this thesis were thus to (1) develop a selective and multiplex method for the detection and characterization of TDP-43 using liquid chromatography-tandem mass spectrometry (LC-MS/MS), and (2) develop protocols for enrichment of TDP-43 from human fluids, tissues and cells to improve analytical sensitivity. Application of the LC-MS/MS method enabled detection and characterization of TDP-43 in biological matrices including human cell lines and human brain tissue. In addition, aptamer enrichment of endogenous TDP-43 from these biological matrices led to improved signal-to-noise ratios and increased sequence coverage, when coupled to the LC-MS/MS method. This targeted multiplex mass spectrometric provides the opportunity for characterization of pathological forms of TDP-43 at higher resolution compared to ligand binding methods.
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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 | 0.005 | 0.006 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.003 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.002 | 0.002 |
| Research integrity | 0.001 | 0.003 |
| Insufficient payload (model declined to judge) | 0.006 | 0.009 |
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".