Affibody molecule-mediated depletion of HSA and IgG using different buffer compositions: a 15 min protocol for parallel processing of 1-48 samples

High‐abundant plasma proteins pose a challenge in a large number of proteomics‐based technologies. Depletion of these high‐abundant proteins has proven to be a fruitful strategy to circumvent masking of lower‐abundant proteins that could serve as valuable biomarker candidates. However, current strategies often do not meet the throughput requirements of large‐scale proteomic studies. In the present paper, a flexible and parallelized method for the depletion of high‐abundant proteins is described, allowing the removal of the two most abundant proteins from 48 blood‐derived samples in less than 15 min using Affibody molecules as affinity ligands. A sample‐processing platform like this should be suitable for a number of proteomics technologies; its flexibility in buffer composition allows for different types of downstream applications.