ArticleCells2023
A Practical and Analytical Comparative Study of Gel-Based Top-Down and Gel-Free Bottom-Up Proteomics Including Unbiased Proteoform Detection.
Article in Cells, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
What it found
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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.
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Who cites it
14 citing papers in PubMed.
- Platelets mirror changes in the frontal lobe antioxidant system in Alzheimer's disease.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2025Article
- Honeybee proteins in Saudi honeys: A shotgun gel-free proteomic study.Food chemistry: X · 2025Article
- Leveraging multi-omics tools to comprehend responses and tolerance mechanisms of heavy metals in crop plants.Functional & integrative genomics · 2024Review
- Proteomic reference map for sarcopenia research: mass spectrometric identification of key muscle proteins of organelles, cellular signaling, bioenergetic metabolism and molecular chaperoning.European journal of translational myology · 2024Article
- Proteomic reference map for sarcopenia research: mass spectrometric identification of key muscle proteins located in the sarcomere, cytoskeleton and the extracellular matrix.European journal of translational myology · 2024Article
- Proteomic Insights into Osteoporosis: Unraveling Diagnostic Markers of and Therapeutic Targets for the Metabolic Bone Disease.Biomolecules · 2024Review
- Proteomics-The State of the Field: The Definition and Analysis of Proteomes Should Be Based in Reality, Not Convenience.Proteomes · 2024Article
- How Can Proteomics Help to Elucidate the Pathophysiological Crosstalk in Muscular Dystrophy and Associated Multi-System Dysfunction?Proteomes · 2024Article
- Exploring the secretome ofFrontiers in bioengineering and biotechnology · 2024Article
- Proteomic Approaches to Unravel the Molecular Dynamics of Early Pregnancy in Farm Animals: An In-Depth Review.Journal of developmental biology · 2023Review
- Proteomic methods for the study of porcine acute phase proteins - anything new to detect?Veterinary research communications · 2023Review
- Mass Spectrometry-Based Proteomic Technology and Its Application to Study Skeletal Muscle Cell Biology.Cells · 2023Review
- Proteomics in Childhood Acute Lymphoblastic Leukemia: Challenges and Opportunities.Diagnostics (Basel, Switzerland) · 2023Review
- Extracellular Matrix Proteomics: TheBiomolecules · 2023Review
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Proteomics is an indispensable analytical technique to study the dynamic functioning of biological systems via different proteins and their proteoforms. In recent years, bottom-up shotgun has become more popular than gel-based top-down proteomics. The current study examined the qualitative and quantitative performance of these two fundamentally different methodologies by the parallel measurement of six technical and three biological replicates of the human prostate carcinoma cell line DU145 using its two most common standard techniques, label-free shotgun and two-dimensional differential gel electrophoresis (2D-DIGE). The analytical strengths and limitations were explored, finally focusing on the unbiased detection of proteoforms, exemplified by discovering a prostate cancer-related cleavage product of pyruvate kinase M2. Label-free shotgun proteomics quickly yields an annotated proteome but with reduced robustness, as determined by three times higher technical variation compared to 2D-DIGE. At a glance, only 2D-DIGE top-down analysis provided valuable, direct stoichiometric qualitative and quantitative information from proteins to their proteoforms, even with unexpected post-translational modifications, such as proteolytic cleavage and phosphorylation. However, the 2D-DIGE technology required almost 20 times as much time per protein/proteoform characterization with more manual work. Ultimately, this work should expose both techniques' orthogonality with their different contents of data output to elucidate biological questions.
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Registered trials
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