paramounter
Measures LC–MS processing parameters directly from the data, rather than tuning them by hand.
Resources
Software and data from the lab. Analysis code for individual papers is released as a research compendium alongside the paper; general-purpose tools are separate R packages.
Software
mzrtools
Turns molecular formulas into the values mass spectrometry needs: monoisotopic masses, targeted libraries, isotope enumeration and probability distributions, and correction for natural isotope abundance.
Data and analysis
Lactate transport inhibition in pulmonary fibrosis
Everything behind the Science Translational Medicine paper, deposited in five places. All are CC BY 4.0.
- Raw data and figure code — Zenodo
- RNA-seq reads — NIH SRA, PRJNA1011992
- RNA-seq pipeline and summarised data — Zenodo, archived from GitHub
- Xenium spatial data — NIH GEO, GSE325253
- Xenium pipeline and summarised data — Zenodo
MYC and proliferating cell metabolism in hypoxia
Everything behind the eLife paper: metabolic flux analysis, RNA-seq, and the analysis code.
- Raw data and figure code — research compendium, archived at Software Heritage
- RNA-seq reads — NIH SRA, PRJNA721596
- Prolyl hydroxylase inhibition RNA-seq — molidustat-treated lung fibroblasts
Endothelial immunometabolic phenotypes
LC–MS data and analysis supporting the endothelial immunometabolism paper.
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