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ProteomicsSP3 protocol for proteomic plant sample preparation prior LC-MS/MS
Quantitative protein extraction from biological samples, as well as contaminants removal before LC-MS/MS, is fundamental for the successful bottom-up proteomic analysis. Four sample preparation methods, including the filter-aided sample preparation (FASP), two single-pot solid-phase-enhanced sample p...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2021-02-26 | PXD022688 | Pride
Protein cleanup Arabidopsis thaliana Bottom-up Mass spectrometry Sds removal Sp3 Fasp Carboxylated magnetic beads 
ProteomicsInfluence of bead chemistry and protein-to-bead ratio on the efficiency of solid-phase proteolysis
Optimization of an SP3 digestion workflow on human plasma samples. The performance of the SP3 workflow using beads with different surface chemistries (SpeedBeads and MagReSyn beads) was evaluated.
ORGANISM(S): Homo sapiens (Human) 
2026-02-24 | PXD065651 | Pride
Sp3 Plasma Digestion 
ProteomicsComparison of In-Gel and SP3 Mass Spectrometry Sample Preparation Protocols
Sensitivity, robustness, and reproducibility of sample preparation are main determinants of data quality in bottom-up mass spectrometry-based proteomics. To this end, in-gel protein clean-up and digestion has been used for decades and is characterized by its robustness and compatibility with harsh l...
ORGANISM(S): Homo sapiens (Human) 
2026-08-24 | PXD064954 | Pride
ProteomicsSolvent Precipitation SP3 (SP4) enhances recovery for proteomics sample preparation without magnetic beads
Complete, reproducible extraction of protein material is essential for comprehensive and unbiased proteome analyses. A current gold standard is single-pot, solid-phase-enhanced sample preparation (SP3), in which organic solvent and magnetic beads are used to denature and capture proteins, with subse...
ORGANISM(S): Mus musculus (Mouse) 
2022-08-03 | PXD028768 | Pride
Microparticles Protein aggregation Contaminant removal Lc−ms/ms Protein precipitation Sample preparation 
ProteomicsSolvent Precipitation SP3 (SP4) enhances recovery for proteomics sample preparation without magnetic beads
Complete, reproducible extraction of protein material is essential for comprehensive and unbiased proteome analyses. A current gold standard is single-pot, solid-phase-enhanced sample preparation (SP3), in which organic solvent and magnetic beads are used to denature and capture protein aggregates, ...
ORGANISM(S): Mus musculus (Mouse) Homo sapiens (Human) Drosophila melanogaster (Fruit fly) 
2022-08-01 | PXD032095 | Pride
Microparticles Proteomics Sample preparation Protein aggregation Contaminant removal Lc−ms/ms Protein precipitation 
ProteomicsAutomated sample preparation with SP3 for low-input clinical proteomics
High-throughput and streamlined workflows are essential in clinical proteomics for standardized processing of samples originating from a variety of sources, including frozen tissue, FFPE tissue, or blood. To reach this goal, we have implemented single-pot solid-phase-enhanced sample preparation (SP3...
ORGANISM(S): Homo sapiens (Human) 
2020-01-10 | PXD014556 | Pride
Sp3 Clinical proteomics Pulmonary adenocarcinoma Sample preparation Low-input High-throughput Automation 
ProteomicsAutomated sample preparation with SP3 for low-input clinical proteomics
High-throughput and streamlined workflows are essential in clinical proteomics for standardized processing of samples originating from a variety of sources, including frozen tissue, FFPE tissue, or blood. To reach this goal, we have implemented single-pot solid-phase-enhanced sample preparation (SP3...
ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse) Sus scrofa domesticus (domestic pig) 
2020-03-27 | PXD015840 | Pride
Fresh-frozen tissue Proteomics Sp3 Cells Sample preparation 
ProteomicsMultiplexed Proteome Profiling of Carbon Source Perturbations in Two Yeast Species with SL-SP3-TMT
Saccharomyces cerevisiae and Schizosaccharomyces pombe are the most commonly studied yeast model systems, yet comparisons of global proteome remodeling between these yeast species are scarce. Here, we profile the proteomes of S. cerevisiae and S. pombe cultured with either glucose or pyruvate as the...
ORGANISM(S): Homo sapiens (Human) 
2021-05-11 | PXD014546 | Pride
Sps-ms3 Cerevisiae Pombe Tmt Isobaric Pyruvate 
ProteomicsRefinement of paramagnetic bead–based digestion protocol for automatic sample preparation using an artificial neural network
Despite technological advances in the proteomics field, sample preparation still represents the main bottleneck in mass spectrometry (MS) analysis. Bead-based protein aggregation techniques have recently emerged as an efficient, reproducible, and high-throughput alternative for protein extraction an...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) Mus musculus (Mouse) Homo sapiens (Human) Escherichia coli Rattus norvegicus (Rat) 
2024-05-31 | PXD048358 | Pride
Bile Magnetic beads Protein aggregation Sp3 protein digestion Artificial neural network 
ProteomicsDevelopment of an Adaptive, Economical, and Easy-to-Use SP3-TMT Automated Sample Preparation Workflow for Quantitative Proteomics
Liquid handling robots have been developed to automate various steps of the bottom-up proteomics workflow, however, protocols for the generation of isobarically labeled peptides remain limited. Existing methods often require costly specialty devices and are constrained by fixed workflows. To address...
ORGANISM(S): Homo sapiens (Human) 
2025-06-16 | PXD060786 | Pride
Automation Sample preperation Unfolded protein response and tandem mass tags 
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