{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Katsavelis D"],"funding":["Dutch Research Council (NWO)","European Commission"],"pagination":["4792-4803"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12418494"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["24(9)"],"pubmed_abstract":["Serum proteomics plays a crucial role in biomarker discovery and disease research, yet the selection of an optimal sample preparation method remains challenging. Evaluating the accuracy of protein quantitation is of major importance and a vital part of a benchmarking study in proteomics, since clinical studies are based on the differential expression of certain proteins that can be used as biomarkers or be indicative of a pathological state. In this study, we performed a direct comparison of 6 widely used serum proteomic sample preparation workflows: In-gel digestion (IGD), Single-Pot Solid-Phase-enhanced Sample Preparation (SP3), Top 14 Abundant Protein Depletion (Top 14), Isopropanol/Trichloroacetic Acid (IPA/TCA) precipitation, PreOmics ENRICH-iST (PreOmics), and Seer Proteograph XT (Se"],"journal":["Journal of proteome research"],"pubmed_title":["Impact of Sample Preparation Strategies on the Quantitative Accuracy of Low-Abundance Serum Proteins in Shotgun Proteomics."],"pmcid":["PMC12418494"],"funding_grant_id":["184.034.019","JTFN-00102"],"pubmed_authors":["Permentier HP","Horvatovich P","Katsavelis D","van der Hart MGC","Wolters JC","Cremers TIFH"],"additional_accession":[]},"is_claimable":false,"name":"Impact of Sample Preparation Strategies on the Quantitative Accuracy of Low-Abundance Serum Proteins in Shotgun Proteomics.","description":"Serum proteomics plays a crucial role in biomarker discovery and disease research, yet the selection of an optimal sample preparation method remains challenging. Evaluating the accuracy of protein quantitation is of major importance and a vital part of a benchmarking study in proteomics, since clinical studies are based on the differential expression of certain proteins that can be used as biomarkers or be indicative of a pathological state. In this study, we performed a direct comparison of 6 widely used serum proteomic sample preparation workflows: In-gel digestion (IGD), Single-Pot Solid-Phase-enhanced Sample Preparation (SP3), Top 14 Abundant Protein Depletion (Top 14), Isopropanol/Trichloroacetic Acid (IPA/TCA) precipitation, PreOmics ENRICH-iST (PreOmics), and Seer Proteograph XT (Se","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Sep","modification":"2026-05-26T20:15:52.486Z","creation":"2026-05-24T03:07:44.201Z"},"accession":"S-EPMC12418494","cross_references":{"pubmed":["40857585"],"doi":["10.1021/acs.jproteome.5c00572"]}}