ArticleJournal of proteome research2011
Improvements in proteomic metrics of low abundance proteins through proteome equalization using ProteoMiner prior to MudPIT.
Article in Journal of proteome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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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
29 citing papers in PubMed.
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- Metabolomic and proteomic stratification of equine osteoarthritis.Equine veterinary journal · 2025Article
- Low-Abundance Protein Enrichment for Medical Applications: The Involvement of Combinatorial Peptide Library Technique.International journal of molecular sciences · 2023Review
- Proteomics and disease network associations evaluation of environmentally relevant Bisphenol A concentrations in a human 3D neural stem cell model.Frontiers in cell and developmental biology · 2023Article
- Subcellular Fractionation for DIGE-Based Proteomics.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Localization of EccABMC microbiology · 2022Article
- LC-MS/MS-Based Serum Protein Profiling for Identification of Candidate Biomarkers in Pakistani Rheumatoid Arthritis Patients.Life (Basel, Switzerland) · 2022Article
- Optimization of Synovial Fluid Collection and Processing for NMR Metabolomics and LC-MS/MS Proteomics.Journal of proteome research · 2020Article
- Extracellular Matrix Disparities in anFrontiers in cardiovascular medicine · 2020Article
- Comparative Proteomics of Ostreid Herpesvirus 1 and Pacific Oyster Interactions With Two Families Exhibiting Contrasted Susceptibility to Viral Infection.Frontiers in immunology · 2020Article
- Irreversible oxidative post-translational modifications in heart disease.Expert review of proteomics · 2019Review
- Drought-Induced Leaf Proteome Changes in Switchgrass Seedlings.International journal of molecular sciences · 2016Article
- Current state of the art for enhancing urine biomarker discovery.Expert review of proteomics · 2016Review
- Contributions of immunoaffinity chromatography to deep proteome profiling of human biofluids.Journal of chromatography. B, Analytical technologies in the biomedical and life sciences · 2016Review
- Oxyntomodulin Identified as a Marker of Type 2 Diabetes and Gastric Bypass Surgery by Mass-spectrometry Based Profiling of Human Plasma.EBioMedicine · 2016Article
- MS for investigation of time-dependent protein adsorption on surfaces in complex biological samples.Future science OA · 2015Article
- Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome.Genome research · 2013Article
- Deep proteome coverage based on ribosome profiling aids mass spectrometry-based protein and peptide discovery and provides evidence of alternative translation products and near-cognate translation initiation events.Molecular & cellular proteomics : MCP · 2013Article
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8 authors.
Funding
Abstract
Ideally, shotgun proteomics would facilitate the identification of an entire proteome with 100% protein sequence coverage. In reality, the large dynamic range and complexity of cellular proteomes results in oversampling of abundant proteins, while peptides from low abundance proteins are undersampled or remain undetected. We tested the proteome equalization technology, ProteoMiner, in conjunction with Multidimensional Protein Identification Technology (MudPIT) to determine how the equalization of protein dynamic range could improve shotgun proteomics methods for the analysis of cellular proteomes. Our results suggest low abundance protein identifications were improved by two mechanisms: (1) depletion of high abundance proteins freed ion trap sampling space usually occupied by high abundance peptides and (2) enrichment of low abundance proteins increased the probability of sampling their corresponding more abundant peptides. Both mechanisms also contributed to dramatic increases in the quantity of peptides identified and the quality of MS/MS spectra acquired due to increases in precursor intensity of peptides from low abundance proteins. From our large data set of identified proteins, we categorized the dominant physicochemical factors that facilitate proteome equalization with a hexapeptide library. These results illustrate that equalization of the dynamic range of the cellular proteome is a promising methodology to improve low abundance protein identification confidence, reproducibility, and sequence coverage in shotgun proteomics experiments, opening a new avenue of research for improving proteome coverage.
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Registered trials
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