• Alex Kentsis

  • Jul 22, 2020

Three extraction methods for mass spectrometry proteomics of frozen mammalian tissues

Sample preparation remains essential for high-quality mass spectrometry proteomics. Here, we compared three commonly used methods for protein extraction of frozen mammalian tissues: 1) extraction using SDS buffer followed by FASP purification, 2) extraction using SDS buffer followed by S-Trap purification, and 3) extraction using a guanidine hydrochloride buffer followed by in-solution digestion.

Based on bicinchoninic acid assay, all three methods display similar recovery of total protein content. However, proteomics-based analysis identified far fewer proteins from the extraction guanidine hydrochloride. SDS-FASP identifies as many proteins as the SDS-STrap method with good coverage of proteins from different cellular compartments.

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