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#31 · Proteomics

Reproducible proteomics via narrow-window DIA, error control and modular software

4 preprints
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The common thread is engineering reproducibility into the decision and analysis layers of proteomics rather than into a single measurement. The narrow-window DIA/DDA benchmark compares pipelines and reports that the new Tesorai Search engine yields the highest protein coverage with rigorous FDR control. The Atlas of Proteomic Technologies is an open curated resource with decision tools that rank six commercial platforms and complementary options. stably applies error-controlled stability selection, contrasting Shah-Samworth and Meinshausen-Buhlmann variants, to DIA proteomics for stable biomarker panel discovery. AlphaPeptTools provides a scverse/AnnData-based Python framework for ingestion, QC, preprocessing and statistical analysis. What is new is that error control and standardized data structures are built into the software and selection workflows themselves, though the benchmark addresses pipeline performance and the atlas addresses platform selection rather than analysis code.

Preprints

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