The success of bottom-up proteomic analysis frequently depends on the efficient removal of contaminants from protein or peptide samples before LC-MS/MS. For a peptide clean-up workflow, single-pot solid-phase-enhanced peptide sample preparation on carboxylate-modified paramagnetic beads (termed SP2) was evaluated for sodium dodecyl sulfate or polyethylene glycol removal from Arabidopsis thaliana tryptic peptides. The robust and efficient 40-min SP2 protocol, tested for 10-ng, 250-ng, and 10-µg peptide samples, was proposed and benchmarked thoroughly against the ethyl acetate extraction protocol. The SP2 protocol on carboxylated magnetic beads proved to be the most robust approach, even for the simultaneous removal of massive sodium dodecyl sulfate (SDS) and polyethylene glycol (PEG) contaminations from AT peptide samples in respect of the LC-MS/MS data outperforming ethyl acetate extraction.

• Keywords
• Arabidopsis thaliana, LC-MS/MS, SP2, detergent, ethyl acetate extraction, magnetic beads, peptide clean-up, polyethylene glycol, sodium dodecyl sulfate,
• MeSH
• Chromatography, Liquid methods   MeSH
• Sodium Dodecyl Sulfate MeSH
• Liquid Chromatography-Mass Spectrometry * MeSH
• Peptides analysis   MeSH
• Polyethylene Glycols * MeSH
• Proteomics methods   MeSH
• Tandem Mass Spectrometry methods   MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Sodium Dodecyl Sulfate MeSH
• ethyl acetate MeSH Browser
• Peptides MeSH
• Polyethylene Glycols * MeSH