Tag: mass-spectrometry

A practical survey of proteomics applications, the main measurement methods, and what you can do with your own plasma protein data once you have the files.

A practical comparison of mass spectrometry, affinity panels, and aptamer arrays as purchasable proteomics services, with the file formats, tools, and failure modes you should expect if you plan to analyze the data yourself.

A practical pipeline for turning vendor raw files from a plasma proteomics run into an FDR-controlled protein quantification matrix you can model, with the tools, flags, and failure modes named.

A step-by-step guide to processing personal plasma proteomics data, from raw mass spectrometry files or affinity panel exports through quantification, quality control, normalization, and longitudinal modeling in R.

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 for one person's mass-spectrometry proteomics. Covers import, missing values and design.