{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Bortel P"],"funding":["European Commission Marie Sklodowska-Curie Actions","Osterreichische Forschungsgemeinschaft","University of Vienna","H2020","Novo Nordisk Foundation Center for Protein Research","European Commission","Novo Nordisk Fonden"],"pagination":["100754"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC11087715"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["23(5)"],"pubmed_abstract":["Improving coverage, robustness, and sensitivity is crucial for routine phosphoproteomics analysis by single-shot liquid chromatography-tandem mass spectrometry (LC-MS/MS) from minimal peptide inputs. Here, we systematically optimized key experimental parameters for automated on-bead phosphoproteomics sample preparation with a focus on low-input samples. Assessing the number of identified phosphopeptides, enrichment efficiency, site localization scores, and relative enrichment of multiply-phosphorylated peptides pinpointed critical variables influencing the resulting phosphoproteome. Optimizing glycolic acid concentration in the loading buffer, percentage of ammonium hydroxide in the elution buffer, peptide-to-beads ratio, binding time, sample, and loading buffer volumes allowed us to confi"],"journal":["Molecular & cellular proteomics : MCP"],"pubmed_title":["Systematic Optimization of Automated Phosphopeptide Enrichment for High-Sensitivity Phosphoproteomics."],"pmcid":["PMC11087715"],"funding_grant_id":["PI Jesper Velgaard Olsen"],"pubmed_authors":["Olsen JV","Gerner C","Martinez-Val A","Piga I","Koenig C","Bortel P"],"additional_accession":[]},"is_claimable":false,"name":"Systematic Optimization of Automated Phosphopeptide Enrichment for High-Sensitivity Phosphoproteomics.","description":"Improving coverage, robustness, and sensitivity is crucial for routine phosphoproteomics analysis by single-shot liquid chromatography-tandem mass spectrometry (LC-MS/MS) from minimal peptide inputs. Here, we systematically optimized key experimental parameters for automated on-bead phosphoproteomics sample preparation with a focus on low-input samples. Assessing the number of identified phosphopeptides, enrichment efficiency, site localization scores, and relative enrichment of multiply-phosphorylated peptides pinpointed critical variables influencing the resulting phosphoproteome. Optimizing glycolic acid concentration in the loading buffer, percentage of ammonium hydroxide in the elution buffer, peptide-to-beads ratio, binding time, sample, and loading buffer volumes allowed us to confi","dates":{"release":"2024-01-01T00:00:00Z","publication":"2024 May","modification":"2026-06-02T06:09:28.785Z","creation":"2026-04-15T03:10:08.827Z"},"accession":"S-EPMC11087715","cross_references":{"pubmed":["38548019"],"doi":["10.1016/j.mcpro.2024.100754"]}}