ArticleAnalytical chemistry2014
Applying label-free quantitation to top down proteomics.
Article in Analytical chemistry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed.
- Proteoform medicine: characterizing and targeting protein forms in human disease.Nature reviews. Genetics · 2026Review
- Top-Down Proteomics for the Characterization and Quantification of Calreticulin Arginylation.Analytical chemistry · 2025Article
- Quantitative Top-down Proteomics Revealed Kinase Inhibitor-Induced Proteoform-Level Changes in Cancer Cells.Journal of proteome research · 2025Article
- FLASHQuant: A Fast Algorithm for Proteoform Quantification in Top-Down Proteomics.Analytical chemistry · 2024Article
- Top-down Proteomics for the Characterization and Quantification of Calreticulin Arginylation.bioRxiv : the preprint server for biology · 2024Article
- Mass spectrometry-intensive top-down proteomics: an update on technology advancements and biomedical applications.Analytical methods : advancing methods and applications · 2024Review
- Targeted Quantification of Proteoforms in Complex Samples by Proteoform Reaction Monitoring.Analytical chemistry · 2024Article
- Top-down proteomics.Nature reviews. Methods primers · 2024Article
- Global Proteomics for Identifying the Alteration Pathway of Niemann-Pick Disease Type C Using Hepatic Cell Models.International journal of molecular sciences · 2023Article
- Preparative Electrophoresis for HDL Particle Size Separation and Intact-Mass Apolipoprotein Proteoform Analysis.Journal of proteome research · 2023Article
- Proteoforms expand the world of microproteins and short open reading frame-encoded peptides.iScience · 2023Review
- Middle-Down Mass Spectrometry Reveals Activity-Modifying Phosphorylation Barcode in a Class C G Protein-Coupled Receptor.Journal of the American Chemical Society · 2022Article
- Spectrum of Apolipoprotein AI and Apolipoprotein AII Proteoforms and Their Associations With Indices of Cardiometabolic Health: The CARDIA Study.Journal of the American Heart Association · 2021Article
- New Interface for Faster Proteoform Analysis: Immunoprecipitation Coupled with SampleStream-Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2021Article
- An Improved Top-Down Mass Spectrometry Characterization ofJournal of the American Society for Mass Spectrometry · 2021Article
- Robustness and Ruggedness of Isoelectric Focusing and Superficially Porous Liquid Chromatography with Fourier Transform Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2021Article
- High-throughput quantitative top-down proteomics.Molecular omics · 2020Review
- Multidimensional Top-Down Proteomics of Brain-Region-Specific Mouse Brain Proteoforms Responsive to Cocaine and Estradiol.Journal of proteome research · 2019Article
- Proteomic Insights into Phycobilisome Degradation, A Selective and Tightly Controlled Process in The Fast-Growing CyanobacteriumBiomolecules · 2019Article
- Best practices and benchmarks for intact protein analysis for top-down mass spectrometry.Nature methods · 2019Review
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
With the prospect of resolving whole protein molecules into their myriad proteoforms on a proteomic scale, the question of their quantitative analysis in discovery mode comes to the fore. Here, we demonstrate a robust pipeline for the identification and stringent scoring of abundance changes of whole protein forms <30 kDa in a complex system. The input is ~100-400 μg of total protein for each biological replicate, and the outputs are graphical displays depicting statistical confidence metrics for each proteoform (i.e., a volcano plot and representations of the technical and biological variation). A key part of the pipeline is the hierarchical linear model that is tailored to the original design of the study. Here, we apply this new pipeline to measure the proteoform-level effects of deleting a histone deacetylase (rpd3) in S. cerevisiae. Over 100 proteoform changes were detected above a 5% false positive threshold in WT vs the Δrpd3 mutant, including the validating observation of hyperacetylation of histone H4 and both H2B isoforms. Ultimately, this approach to label-free top down proteomics in discovery mode is a critical technical advance for testing the hypothesis that whole proteoforms can link more tightly to complex phenotypes in cell and disease biology than do peptides created in shotgun proteomics.
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Registered trials
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