Journal of the American Society for Mass Spectrometry [J Am Soc Mass Spectrom] 2025 Apr 02; Vol. 36 (4), pp. 680-687. Date of Electronic Publication: 2024 Dec 09.

Publisher: ACS Publications Country of Publication: United States NLM ID: 9010412 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1879-1123 (Electronic) Linking ISSN: 10440305 NLM ISO Abbreviation: J Am Soc Mass Spectrom Subsets: MEDLINE

Sodium Dodecyl Sulfate*/isolation & purification , Sodium Dodecyl Sulfate*/chemistry , Tandem Mass Spectrometry*/methods , High-Throughput Screening Assays*/methods , High-Throughput Screening Assays*/economics , Proteins*/chemistry , Proteins*/analysis , Anion Exchange Resins*/chemistry, Animals ; Mice ; Chromatography, Ion Exchange/methods ; Chromatography, Ion Exchange/economics ; Trastuzumab/chemistry ; Trastuzumab/blood ; Chromatography, Liquid/methods

Sodium dodecyl sulfate (SDS) plays a pivotal role in protein denaturation, tissue extraction, and protein mass-based electrophoretic separations. However, even modest concentrations of SDS can cause column overpressure, retention time shifts, and ionization signal suppression during liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses. Thus, SDS removal is a critical step for LC-MS/MS analysis of protein digests containing SDS. This study describes an inexpensive and high-throughput method to remove SDS from protein digests using weak-anion exchange (WAX) resins in 96-well filter plates. Requiring less than 3 min, this method can reduce SDS concentrations from 0.1-0.4% to less than 5 ppm and from 0.6-1% to less than 100 ppm. After SDS removal, the recoveries of unmodified tryptic peptides and phosphorylated peptides (at 94.3 nM) were ∼90% and ∼70%, respectively. Additionally, when using aqueous 1% SDS to solubilize trastuzumab-spiked mouse serum and subsequently removing the SDS using the WAX resin, quantitation of trastuzumab exhibited excellent linearity ( R² = 0.9996) together with a low coefficient of variation (<10%). Calculated concentrations were within 20% of the expected value for spiked standard samples (0.5, 1, and 2 μg/mL trastuzumab in mouse serum). The method is about 20× more cost-effective versus commercialized SDS removal kits and both the resin and filter plate are readily available, so the method should easily transfer to other laboratories.