ArticleJournal of proteome research2020
PEPPI-MS: Polyacrylamide-Gel-Based Prefractionation for Analysis of Intact Proteoforms and Protein Complexes by Mass Spectrometry.
Article in Journal of proteome research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
45 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Properties, Origin, and Consistency of Truncated Proteoforms Across Top-Down Proteomic Studies.Molecular & cellular proteomics : MCP · 2025Pooled it
- A Novel Protein Recovery Method via Gel Separation and Silica Columns Capable of Rapid Antigen Purification and Deep Proteomic Identification.Molecules (Basel, Switzerland) · 2026Article
- Covalent modification and liposomal delivery of hydroxytyrosol-soy protein complexes: A strategy to improve stability, functionality, and bioavailability.Food chemistry: X · 2026Article
- Mass spectrometry-based top-down proteomics for proteoform profiling of protein coronas.Nature protocols · 2026Review
- PEPPI-SP3: A Gel-Based High-Resolution Sample Preparation Workflow for In-Depth Top-Down Analysis of Intact Proteoforms by Mass Spectrometry.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Combining SDS-PAGE with Capillary Zone Electrophoresis-Tandem Mass Spectrometry for Top-Down Proteomics Analysis of Intact Histone Proteoforms.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Quantitative Top-Down Proteomics Reveals Significant Differences in Histone Proteoforms Between Metastatic and Nonmetastatic Colorectal Cancer Cells.Proteomics · 2025Article
- Comparative Analysis of Proteoform Clean-Up Methods for In-Depth Top-Down Proteomics.Proteomics · 2025Article
- Single-cell western blotting of cytoplasmic cytokeratin 8 proteoforms.The Analyst · 2025Article
- Sample preparation and cleanup methods for clinical top-down proteomics.Expert review of proteomics · 2025Review
- Single-cell western blotting of cytoplasmic cytokeratin 8 proteoforms.bioRxiv : the preprint server for biology · 2025Article
- PEPPI-MS: gel-based sample pre-fractionation for deep top-down and middle-down proteomics.Nature protocols · 2025Review
- Proteoform-predictor: Increasing the Phylogenetic Reach of Top-Down Proteomics.Journal of proteome research · 2025Article
- Cysteine-Directed Isobaric Labeling Combined with GeLC-FAIMS-MS for Quantitative Top-Down Proteomics.Journal of proteome research · 2025Article
- Gel-Based Sample Fractionation with SP3-Purification for Top-Down Proteomics.Journal of proteome research · 2025Article
- Intact Mass Proteomics Using a Proteoform Atlas.Journal of proteome research · 2025Article
- Top-Down Stability of Proteins from Rates of Oxidation (TD-SPROX) Approach for Measuring Proteoform-Specific Folding Stability.Analytical chemistry · 2024Article
- Top-Down Proteomics Identifies Plasma Proteoform Signatures of Liver Cirrhosis Progression.Molecular & cellular proteomics : MCP · 2024Article
- Influence of different sample preparation approaches on proteoform identification by top-down proteomics.Nature methods · 2024Article
- Deep Profiling of Plasma Proteoforms with Engineered Nanoparticles for Top-Down Proteomics.Journal of proteome research · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors.
Funding
Abstract
Prefractionation of complex mixtures of proteins derived from biological samples is indispensable for proteome analysis via top-down mass spectrometry (MS). Polyacrylamide gel electrophoresis (PAGE), which enables high-resolution protein separation based on molecular size, is a widely used technique in biochemical experiments and has the potential to be useful in sample fractionation for top-down MS analysis. However, the lack of a means to efficiently recover the separated proteins in-gel has always been a barrier to its use in sample prefractionation. In this study, we present a novel experimental workflow, called Passively Eluting Proteins from Polyacrylamide gels as Intact species for MS ("PEPPI-MS"), which allows top-down MS of PAGE-separated proteins. The optimization of Coomassie brilliant blue staining followed by the passive extraction step in the PEPPI-MS workflow enabled the efficient recovery of proteins, separated on commercial precast gels, from a wide range of molecular weight regions in under 10 min. Two-dimensional separation combining offline PEPPI-MS with online reversed-phase liquid chromatographic separation resulted in identification of over 1000 proteoforms recovered from the target region of the gel (≤50 kDa). Given the widespread availability and relatively low cost of traditional sodium dodecyl sulfate (SDS)-PAGE equipment, the PEPPI-MS workflow will be a powerful prefractionation strategy for top-down proteomics.
Indexed as
Identifiers
What OpenQuestion holds
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.