ReviewJournal of proteomics2010
Proteogenomics to discover the full coding content of genomes: a computational perspective.
Review in Journal of proteomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 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
68 citing papers in PubMed, 155 citations in OpenAlex.
- Proteogenomic investigation of plant constituents in herbal beverages.NPJ science of food · 2026Article
- Combined NGS and proteomics improves viral diagnostics in wildlife: coronaviruses confirmed in hedgehogs.Frontiers in cellular and infection microbiology · 2026Article
- Metagenomic Assembly and Gene Prediction.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Comprehensive Peptide Mapping Is Crucial for Proteogenomics and Proteomics.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Micropeptides: potential treatment strategies for cancer.Cancer cell international · 2024Review
- Micropeptides translated from putative long non-coding RNAs.Acta biochimica et biophysica Sinica · 2022Review
- Characterization of protein isoform diversity in human umbilical vein endothelial cells via long-read proteogenomics.RNA biology · 2022Article
- Mirror proteases of Ac-Trypsin and Ac-LysargiNase precisely improve novel event identifications inFrontiers in microbiology · 2022Article
- Large-scale discovery of non-conventional peptides in grape (Horticulture research · 2022Article
- Improved methods for RNAseq-based alternative splicing analysis.Scientific reports · 2021Article
- Proteogenomic Analysis Unveils the HLA Class I-Presented Immunopeptidome in Melanoma and EGFR-Mutant Lung Adenocarcinoma.Molecular & cellular proteomics : MCP · 2021Article
- The genetic proteome: Using genetics to inform the proteome of mycobacterial pathogens.PLoS pathogens · 2021Review
- Proteogenomic Annotation of Chinese Hamsters Reveals Extensive Novel Translation Events and Endogenous Retroviral Elements.Journal of proteome research · 2019Article
- Terminomics Methodologies and the Completeness of Reductive Dimethylation: A Meta-Analysis of Publicly Available Datasets.Proteomes · 2019Article
- Detection of Proteome Diversity Resulted from Alternative Splicing is Limited by Trypsin Cleavage Specificity.Molecular & cellular proteomics : MCP · 2018Article
- Proteogenomic Analysis ofFrontiers in microbiology · 2018Article
- An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics.Genome research · 2017Article
- Mining for Micropeptides.Trends in cell biology · 2017Review
- Detecting protein variants by mass spectrometry: a comprehensive study in cancer cell-lines.Genome medicine · 2017Article
- A systematic approach for peptide characterization of B-cell receptor in chronic lymphocytic leukemia cells.Oncotarget · 2017Article
8 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Proteogenomics has emerged as a field at the junction of genomics and proteomics. It is a loose collection of technologies that allow the search of tandem mass spectra against genomic databases to identify and characterize protein-coding genes. Proteogenomic peptides provide invaluable information for gene annotation, which is difficult or impossible to ascertain using standard annotation methods. Examples include confirmation of translation, reading-frame determination, identification of gene and exon boundaries, evidence for post-translational processing, identification of splice-forms including alternative splicing, and also, prediction of completely novel genes. For proteogenomics to deliver on its promise, however, it must overcome a number of technological hurdles, including speed and accuracy of peptide identification, construction and search of specialized databases, correction of sampling bias, and others. This article reviews the state of the art of the field, focusing on the current successes, and the role of computation in overcoming these challenges. We describe how technological and algorithmic advances have already enabled large-scale proteogenomic studies in many model organisms, including arabidopsis, yeast, fly, and human. We also provide a preview of the field going forward, describing early efforts in tackling the problems of complex gene structures, searching against genomes of related species, and immunoglobulin gene reconstruction.
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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.