Proteomics, yeast + UPS1 label-free benchmark, Wave 3 run (2026-06-11)
phalaena:run:PA-R-6-5-wave3-2026-06-11
Wave 3 gap-fill run of paper 6.5 (Ramus 2016, the yeast + UPS1 spiked label-free standard). Two LC-MS runs end-to-end through the OpenMS plus Comet shotgun chain: mzML stats, reversed-decoy database, peak picking, Comet search, FDR filter at 1 percent, PSM export, plots, summary. SUCCESS at 06:59:49Z on 2026-06-10, 15.7 min wall clock (run id 038a88dd). This is the spike-in benchmark proteomics slot, where the UPS1 human-protein standard is the quantitative ground truth. The run reported 42,204 PSMs, 30,467 unique peptides, and 15,463 unique target proteins aggregated across the two samples; the protein count is far above the dataset's expected search space and is flagged below.
- kind
- run
- pipeline
- Proteomics pipeline, release p1.1
- status
- draft
- phalaena:run:038a88dd
- pride.project:PXD001819
View Proteomics, yeast + UPS1 label-free benchmark, Wave 3 run (2026-06-11) on the Phalaena Wiki