Comparison of In-Solution, FASP, and S-Trap Based Digestion Methods for Bottom-Up Proteomic Studies

Journal of Proteome Research
Katelyn R LudwigAmanda B Hummon

Abstract

Bottom-up proteomic strategies rely on efficient digestion of proteins into peptides for mass spectrometry analysis. In-solution and filter-based strategies are commonly used for proteomic analysis. In recent years, filter-aided sample preparation (FASP) has become the dominant filter-based method due to its ability to remove SDS prior to mass spectrometry analysis. However, the time-consuming nature of FASP protocols have led to the development of new filter-based strategies. Suspension traps (S-Traps) were recently reported as an alternative to FASP and in-solution strategies as they allow for high concentrations of SDS in a fraction of the time of a typical FASP protocol. In this study, we compare the yields from in-solution, FASP, and S-Trap based digestions of proteins extracted in SDS and urea-based lysis buffers. We performed label-free quantification to analyze the differences in the portions of the proteome identified using each method. Overall, our results show that each digestion method had a high degree of reproducibility within the method type. However, S-Traps outperformed FASP and in-solution digestions by providing the most efficient digestion with the greatest number of unique protein identifications. This is t...Continue Reading

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Citations

Aug 3, 2018·Expert Review of Proteomics·Tobias KronigerDörte Becher
Mar 6, 2019·Molecular & Cellular Proteomics : MCP·Tanveer S BatthJesper V Olsen
Jan 11, 2020·Rapid Communications in Mass Spectrometry : RCM·Omar Mendoza-PorrasGene Wijffels
Sep 27, 2019·Frontiers in Microbiology·Karim HayounBéatrice Alpha-Bazin
Mar 28, 2020·Analytical and Bioanalytical Chemistry·Naviya Schuster-LittleRebecca Whelan
Dec 22, 2019·Nature Protocols·Hillary Andaluz AguilarW Andy Tao
Mar 25, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Camille Lombard-Banek, John E Schiel
Jun 4, 2020·Clinical Proteomics·Andrew MacklinThomas Kislinger
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Jul 12, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Sadegh BalotfCalum R Wilson
Mar 5, 2020·Molecular Systems Biology·Torsten MüllerJeroen Krijgsveld
Aug 10, 2020·Journal of Lipid Research·Cerina ChhuonIda Chiara Guerrera
Sep 18, 2020·Molecular & Cellular Proteomics : MCP·Nicholas M RileySharon J Pitteri
Dec 7, 2020·Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences·Liting DengPaul A Haynes
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May 1, 2019·Molecular & Cellular Proteomics : MCP·Tanveer S BatthJesper V Olsen
Feb 16, 2021·Molecular & Cellular Proteomics : MCP·Nicholas M RileySharon J Pitteri
Mar 23, 2021·Current Protocols·Melinda WojtkiewiczRebekah L Gundry
Mar 30, 2021·Frontiers in Plant Science·Kamil MikulášekZbyněk Zdráhal
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May 30, 2019·Journal of the American Society for Mass Spectrometry·Thu T A NguyenStephanie M Cologna
Mar 9, 2019·Journal of Proteome Research·Yi-Han LinYanbao Yu
Aug 17, 2018·Journal of Proteome Research·Milkessa HaileMariamYanbao Yu
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Jan 15, 2020·Journal of Proteome Research·Dylan M MarchioneJohn B Wojcik
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Aug 27, 2021·Journal of Molecular and Cellular Cardiology·Melinda WojtkiewiczRebekah L Gundry
Sep 2, 2021·Expert Review of Proteomics·Jacqueline S Gerritsen, Forest M White
Sep 5, 2021·Journal of Proteomics·Maryam BaniasadMichael A Freitas

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