ArticleProteomics2010
Investigating protein isoforms via proteomics: a feasibility study.
Article in Proteomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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
25 citing papers in PubMed.
- Advances in Mass Spectrometry Instrumentation and Methodology for Analysis of Alternative Protein Isoforms.Journal of mass spectrometry : JMS · 2026Review
- Integrative Multi-Omics Characterization and Structural Insights into the Poorly Annotated IntegrinGenes · 2025Article
- IS-PRM-Based Peptide Targeting Informed by Long-Read Sequencing for Alternative Proteome Detection.Journal of the American Society for Mass Spectrometry · 2024Article
- Tissue Usage Preference and Intrinsically Disordered Region Remodeling of Alternative Splicing Derived Proteoforms in the Heart.Journal of proteome research · 2024Article
- APOER2 splicing repertoire in Alzheimer's disease: Insights from long-read RNA sequencing.PLoS genetics · 2024Article
- IS-PRM-based peptide targeting informed by long-read sequencing for alternative proteome detection.bioRxiv : the preprint server for biology · 2024Article
- Transcription factors and splice factors - interconnected regulators of stem cell differentiation.Current stem cell reports · 2023Article
- Transcriptional and proteomic analysis of the innate immune response to microbial stimuli in a model invertebrate chordate.Frontiers in immunology · 2023Article
- Re-evaluating the impact of alternative RNA splicing on proteomic diversity.Frontiers in genetics · 2023Review
- Uncovering the impacts of alternative splicing on the proteome with current omics techniques.Wiley interdisciplinary reviews. RNA · 2022Review
- Enhanced protein isoform characterization through long-read proteogenomics.Genome biology · 2022Article
- Characterization of protein isoform diversity in human umbilical vein endothelial cells via long-read proteogenomics.RNA biology · 2022Article
- Understanding small ORF diversity through a comprehensive transcription feature classification.DNA research : an international journal for rapid publication of reports on genes and genomes · 2021Review
- Analysis of Protein-Protein Interactions by Protein Microarrays.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Alternatively Splicing Interactomes Identify Novel Isoform-Specific Partners for NSD2.Frontiers in cell and developmental biology · 2021Article
- FAM136A immunoreactivity is associated with nodal involvement and survival in lung adenocarcinoma in a Chinese case series.Bioengineered · 2020Article
- Protein interaction network of alternatively spliced NudCD1 isoforms.Scientific reports · 2017Article
- Impact of Alternative Splicing on the Human Proteome.Cell reports · 2017Article
- Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation.Annual review of analytical chemistry (Palo Alto, Calif.) · 2016Review
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Alternative splicing (AS) and processing of pre-messenger RNAs explains the discrepancy between the number of genes and proteome complexity in multicellular eukaryotic organisms. However, relatively few alternative protein isoforms have been experimentally identified, particularly at the protein level. In this study, we assess the ability of proteomics to inform on differently spliced protein isoforms in human and four other model eukaryotes. The number of Ensembl-annotated genes for which proteomic data exists that informs on AS exceeds 33% of the alternately spliced genes in the human and worm genomes. Examining AS in chicken via proteomics for the first time, we find support for over 600 AS genes. However, although peptide identifications support only a small fraction of alternative protein isoforms that are annotated in Ensembl, many more variants are amenable to proteomic identification. There remains a sizeable gap between these existing identifications (10-52% of AS genes) and those that are theoretically feasible (90-99%). We also compare annotations between Swiss-Prot and Ensembl, recommending use of both to maximize coverage of AS. We propose that targeted proteomic experiments using selected reactions and standards are essential to uncover further alternative isoforms and discuss the issues surrounding these strategies.
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.