title: Evaluation of SDS depletion using an affinity spin column and IMS-MS detection.
abstract: While the use of detergents is necessary for a variety of protein isolation preparation protocols, they are not compatible with mass spectral analysis due to ion suppression and adduct formation. This manuscript describes optimization of detergent removal, using commercially available SDS depletion spin columns containing an affinity resin, providing for both increased protein recovery and thorough SDS removal. Ion mobility spectrometry coupled with mass spectrometry (IMS-MS) allowed for a concurrent analysis of both analyte and detergent. In the case of both proteins and peptides, higher detergent concentrations than previously reported provided an increase of sample recovery; however there was a limit as SDS was detected by IMS-MS at higher levels of SDS indicating incomplete detergent depletion. The results also suggest that optimal conditions for SDS removal are dependent on the sample concentration. Overall, this study provides a useful guide for proteomic studies where SDS is required for efficient sample preparation.
authors.affiliation: Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
authors.forename: Shawna M
authors.initials: SM
authors.lastname: Hengel
authors.forename: Erica
authors.initials: E
authors.lastname: Floyd
authors.forename: Erin S
authors.initials: ES
authors.lastname: Baker
authors.forename: Rui
authors.initials: R
authors.lastname: Zhao
authors.forename: Si
authors.initials: S
authors.lastname: Wu
authors.forename: Ljiljana
authors.initials: L
authors.lastname: Paša-Tolić
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry; D008956:Models, Chemical; D010446:Peptide Fragments / Q000032:analysis / Q000737:chemistry / Q000302:isolation & purification; D040901:Proteomics / Q000379:methods*; D020592:Shewanella / Q000737:chemistry; D012967:Sodium Dodecyl Sulfate / Q000032:analysis / Q000737:chemistry* / Q000302:isolation & purification; D053719:Tandem Mass Spectrometry / Q000379:methods*; D025801:Ubiquitin / Q000737:chemistry
chemical_list: D001426:Bacterial Proteins; D010446:Peptide Fragments; D025801:Ubiquitin; D012967:Sodium Dodecyl Sulfate