ArticleMolecular systems biology2020
Automated sample preparation with SP3 for low-input clinical proteomics.
Article in Molecular systems biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 170 papers.
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Who cites it
170 citing papers in PubMed, 287 citations in OpenAlex.
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- dia-PASEF Enables Rapid Profiling of the Human Secretome for Deeper Insights Into Cellular Dynamics and Inflammatory Mechanisms.Molecular & cellular proteomics : MCP · 2026Article
- Comparison of In-Gel and SP3 Based Sample Preparation Protocols for LC-MS/MS Based Proteomics.Proteomics · 2026Article
- Recent advancements in sample pretreatment methods for glycoproteomics.Biophysics reports · 2026Article
- Endothelial glycocalyx perturbation in obstructive sleep apnea is associated with repetitive hypoxemia and immunothrombotic endothelial dysfunction.Journal of translational medicine · 2026Article
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- Riboflavin metabolism shapes FSP1-driven ferroptosis resistance.Nature cell biology · 2026Article
- BAP1 dysregulation impairs trophoblast differentiation and contributes to placental dysfunction in preeclampsia.Cell death & disease · 2026Article
- Proteomic landscape of Ewing sarcoma primary tumors and metastases.Nature communications · 2026Article
- High-Throughput Proteomics Sample Preparation Using a 96-Channel Pipettor and Magnetic Pin Device.Journal of proteome research · 2026Article
- Article
110 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput and streamlined workflows are essential in clinical proteomics for standardized processing of samples from a variety of sources, including fresh-frozen tissue, FFPE tissue, or blood. To reach this goal, we have implemented single-pot solid-phase-enhanced sample preparation (SP3) on a liquid handling robot for automated processing (autoSP3) of tissue lysates in a 96-well format. AutoSP3 performs unbiased protein purification and digestion, and delivers peptides that can be directly analyzed by LCMS, thereby significantly reducing hands-on time, reducing variability in protein quantification, and improving longitudinal reproducibility. We demonstrate the distinguishing ability of autoSP3 to process low-input samples, reproducibly quantifying 500-1,000 proteins from 100 to 1,000 cells. Furthermore, we applied this approach to a cohort of clinical FFPE pulmonary adenocarcinoma (ADC) samples and recapitulated their separation into known histological growth patterns. Finally, we integrated autoSP3 with AFA ultrasonication for the automated end-to-end sample preparation and LCMS analysis of 96 intact tissue samples. Collectively, this constitutes a generic, scalable, and cost-effective workflow with minimal manual intervention, enabling reproducible tissue proteomics in a broad range of clinical and non-clinical applications.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.