Efficient, Low-Cost,\nand High-Throughput Sodium Dodecyl\nSulfate (SDS) Removal from Protein Digests Using Weak-Anion Exchange

Sodium dodecyl sulfate (SDS) plays a pivotal role in\nprotein denaturation,\ntissue extraction, and protein mass-based electrophoretic separations.\nHowever, even modest concentrations of SDS can cause column overpressure,\nretention time shifts, and ionization signal suppression during liquid\nchromatography-tandem mass spectrometry (LC-MS/MS) analyses. Thus,\nSDS removal is a critical step for LC-MS/MS analysis of protein digests\ncontaining SDS. This study describes an inexpensive and high-throughput\nmethod to remove SDS from protein digests using weak-anion exchange\n(WAX) resins in 96-well filter plates. Requiring less than 3 min,\nthis method can reduce SDS concentrations from 0.1–0.4% to\nless than 5 ppm and from 0.6–1% to less than 100 ppm. After\nSDS removal, the recoveries of unmodified tryptic peptides and phosphorylated\npeptides (at 94.3 nM) were ∼90% and ∼70%, respectively.\nAdditionally, when using aqueous 1% SDS to solubilize trastuzumab-spiked\nmouse serum and subsequently removing the SDS using the WAX resin,\nquantitation of trastuzumab exhibited excellent linearity (<i>R</i><sup>2</sup> = 0.9996) together with a low coefficient\nof variation (<10%). Calculated concentrations were within 20%\nof the expected value for spiked standard samples (0.5, 1, and 2 μg/mL\ntrastuzumab in mouse serum). The method is about 20× more cost-effective\nversus commercialized SDS removal kits and both the resin and filter\nplate are readily available, so the method should easily transfer\nto other laboratories.