Suspension Trapping (S-Trap) Is Compatible with Typical Protein Extraction Buffers and Detergents for Bottom-Up Proteomics

The analysis of cells and tissue by bottom-up proteomics starts with lysis, followed by in-solution digestion. Lysis buffers commonly used include detergents and other reagents for achieving efficient protein solubility. However, these reagents are, for the most part, incompatible with downstream analytical instrumentation. One method for in-solution digestion and cleanup, termed suspension trapping (S-Trap), has been recently introduced. We present an evaluation of the compatibility of commonly used lysis buffers with S-Trap: SDS, urea, NP-40, RIPA, and SDS with DTT (SDT). We show that S-Trap is compatible with all of the tested buffers, with SDS and SDT performing the best. On the basis of these data, we anticipate that the method will transform experimental planning for mass-spectrometry-based proteomics, making it far more flexible and tolerable of various lysis buffers. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD011665.