ReviewNature methods2014
Proteogenomics: concepts, applications and computational strategies.
Review in Nature methods, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 379 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
379 citing papers in PubMed.
- ProteoRift Protocols: A Deep Learning Filtering Workflow for Peptide Identification in Mass Spectrometry Data.Methods in molecular biology (Clifton, N.J.) · 2027Article
- LRP2: A proteogenomics pipeline for long-read informed protein isoform analysis and discovery.bioRxiv : the preprint server for biology · 2026Article
- Beyond Protein Abundance: Proteoform Diversity and Phosphoproteome Remodeling in Maize (Proteomes · 2026Review
- Application of Proteogenomic Approaches for Refinement of the Entamoeba histolytica Reference Genome Using High Resolution Mass-Spectrometry Data.Acta parasitologica · 2026Article
- Pipettes and Pipelines: The Weapons of Omics Sciences for a New Age of Clinical Studies.Current issues in molecular biology · 2026Review
- Advances in delivery technologies-powered cancer vaccines.Bioactive materials · 2026Review
- Review
- A One Health Framework for Proteomics Across the Tree of Life to Advance Food Security, Animal Health, and Ecosystem Resilience.Proteomes · 2026Review
- SPAID: a comprehensive database for disease-specific autoantigens in autoimmune disorders.Advanced biotechnology · 2026Article
- pAnno: a comprehensive, precise, and fast proteogenomic workflow for the discovery of novel coding regions.Genome biology · 2026Article
- Computational identification and characterization of noncoding RNA-encoded peptides: tools, databases, and in silico strategies.Amino acids · 2026Review
- Antioxidant Protein Hydrolysates and Peptides from Catfish: Enzymatic Production, In Vitro Bioactivity, and Translational Gaps for Functional Foods.Antioxidants (Basel, Switzerland) · 2026Review
- Article
- Brownotate, a Comprehensive Solution to Generate Protein Sequence Databases for Any Species.Proteomics · 2026Article
- A Framework for Database Search with AI Models in Mass Spectrometry-Based Proteomics.Journal of proteome research · 2026Review
- Integrated peptidogenomics decoding yak non-conventional peptides: functional mapping and biopotential mining of genetic resources.Animal bioscience · 2026Article
- Harnessing Proteogenomics to Advance Precision Oncology: From Melanoma and Hepatocellular Carcinoma Perspective.Current oncology reports · 2026Review
- Proteoform medicine: characterizing and targeting protein forms in human disease.Nature reviews. Genetics · 2026Review
- Benchmarking Software for DDA-PASEF Immunopeptidomics.Molecular & cellular proteomics : MCP · 2026Article
- Identification of non-canonical peptides with moPepGen.Nature biotechnology · 2026Article
319 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
1 author.
Funding
Abstract
Proteogenomics is an area of research at the interface of proteomics and genomics. In this approach, customized protein sequence databases generated using genomic and transcriptomic information are used to help identify novel peptides (not present in reference protein sequence databases) from mass spectrometry-based proteomic data; in turn, the proteomic data can be used to provide protein-level evidence of gene expression and to help refine gene models. In recent years, owing to the emergence of new sequencing technologies such as RNA-seq and dramatic improvements in the depth and throughput of mass spectrometry-based proteomics, the pace of proteogenomic research has greatly accelerated. Here I review the current state of proteogenomic methods and applications, including computational strategies for building and using customized protein sequence databases. I also draw attention to the challenge of false positive identifications in proteogenomics and provide guidelines for analyzing the data and reporting the results of proteogenomic studies.
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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.