SP2: Rapid and Automatable Contaminant Removal from Peptide Samples for Proteomic Analyses

Journal of Proteome Research
Matthew WaasRebekah L Gundry

Abstract

Peptide cleanup is essential for the removal of contaminating substances that may be introduced during sample preparation steps in bottom-up proteomic workflows. Recent studies have described benefits of carboxylate-modified paramagnetic particles over traditional reversed-phase methods for detergent and polymer removal, but challenges with reproducibility have limited the widespread implementation of this approach among laboratories. To overcome these challenges, the current study systematically evaluated key experimental parameters regarding the use of carboxylate-modified paramagnetic particles and determined those that are critical for maximum performance and peptide recovery and those for which the protocol is tolerant to deviation. These results supported the development of a detailed, easy-to-use standard operating protocol, termed SP2, which can be applied to remove detergents and polymers from peptide samples while concentrating the sample in solvent that is directly compatible with typical LC-MS workflows. We demonstrate that SP2 can be applied to phosphopeptides and glycopeptides and that the approach is compatible with robotic liquid handling for automated sample processing. Altogether, the results of this study and...Continue Reading

References

Apr 21, 2009·Nature Methods·Jacek R WiśniewskiMatthias Mann
Nov 2, 2014·Molecular Systems Biology·Christopher S HughesJeroen Krijgsveld
Mar 21, 2017·Data in Brief·Johan LarsbrinkLauren S McKee
Sep 28, 2017·Journal of Proteome Research·Malte SielaffUte Distler
Mar 23, 2018·Journal of Proteome Research·Sophie MoggridgeChristopher S Hughes
Apr 19, 2018·Journal of the American Society for Mass Spectrometry·Matthew J Rardin

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Citations

Mar 5, 2020·Molecular Systems Biology·Torsten MüllerJeroen Krijgsveld
Aug 11, 2020·Journal for Immunotherapy of Cancer·Robyn A A OldhamJeffrey A Medin
Sep 18, 2020·Molecular & Cellular Proteomics : MCP·Nicholas M RileySharon J Pitteri
Feb 16, 2021·Molecular & Cellular Proteomics : MCP·Nicholas M RileySharon J Pitteri
Mar 23, 2021·Current Protocols·Melinda WojtkiewiczRebekah L Gundry
May 6, 2021·Journal of the American Society for Mass Spectrometry·Xinyue LiuJoao A Paulo
May 7, 2021·Journal of Virology·Melissa L WhyteAmy W Hudson
Jul 23, 2020·Journal of Proteome Research·Matthew Waas, Thomas Kislinger
Dec 8, 2021·Translational Vision Science & Technology·Jonathon B YoungIris S Kassem

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