3 posts
A plasma proteomics report measures the relative abundance of hundreds to thousands of circulating proteins. Here is what the numbers mean, how the three main platforms differ, and how to analyze your own data without fooling yourself.
A working guide to taking personal proteomics data from raw instrument files or NPX tables to a quantitative matrix, QC'd and normalized, and then to within-person statistics you can defend.
A working guide to the Bioconductor DEP and DEP2 packages applied to a single person's mass-spectrometry proteomics: importing MaxQuant or DIA-NN output, handling left-censored missingness, choosing a design that survives n-of-1 sampling, and reading the result table without overclaiming.