ReviewMass spectrometry reviews2017
Proteogenomics from a bioinformatics angle: A growing field.
Review in Mass spectrometry reviews, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 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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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.
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Who cites it
44 citing papers in PubMed.
- Review
- An Overview of Advancements in Proteomic Approaches to Enhance Livestock Production and Aquaculture.Animals : an open access journal from MDPI · 2025Review
- Review
- PepCentric Enables Fast Repository-Scale Proteogenomics Searches.bioRxiv : the preprint server for biology · 2025Article
- ProHap enables human proteomic database generation accounting for population diversity.Nature methods · 2025Article
- Investigating proteogenomic divergence in patient-derived xenograft models of ovarian cancer.Scientific reports · 2025Article
- Discovering Novel Proteoforms Using Proteogenomic Workflows Within the Galaxy Bioinformatics Platform.Methods in molecular biology (Clifton, N.J.) · 2025Article
- From Gene to Whole Cell: Modeling, Visualization, and Analysis.Methods in molecular biology (Clifton, N.J.) · 2025Article
- PgxSAVy: A tool for comprehensive evaluation of variant peptide quality in proteogenomics - catching the (un)usual suspects.Computational and structural biotechnology journal · 2024Article
- Phenotyping Tumor Heterogeneity through Proteogenomics: Study Models and Challenges.International journal of molecular sciences · 2024Review
- Unveiling the power of proteomics in advancing tropical animal health and production.Tropical animal health and production · 2024Article
- Disclosing the molecular basis of salinity priming in olive trees using proteogenomic model discovery.Plant physiology · 2023Article
- Finding haplotypic signatures in proteins.GigaScience · 2022Article
- Mass spectrometry-based draft of the mouse proteome.Nature methods · 2022Article
- Computational methods and translational applications for targeted next-generation sequencing platforms.Genes, chromosomes & cancer · 2022Review
- Cancer proteogenomics: current impact and future prospects.Nature reviews. Cancer · 2022Review
- A Practical Guide to Small Protein Discovery and Characterization Using Mass Spectrometry.Journal of bacteriology · 2022Article
- Mirror proteases of Ac-Trypsin and Ac-LysargiNase precisely improve novel event identifications inFrontiers in microbiology · 2022Article
- Leveraging orthogonal mass spectrometry based strategies for comprehensive sequencing and characterization of ribosomal antimicrobial peptide natural products.Natural product reports · 2021Review
- Identification of a Novel Protein-Based Signature to Improve Prognosis Prediction in Renal Clear Cell Carcinoma.Frontiers in molecular biosciences · 2021Article
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.
Funding
Abstract
Proteogenomics is a research area that combines areas as proteomics and genomics in a multi-omics setup using both mass spectrometry and high-throughput sequencing technologies. Currently, the main goals of the field are to aid genome annotation or to unravel the proteome complexity. Mass spectrometry based identifications of matching or homologues peptides can further refine gene models. Also, the identification of novel proteoforms is also made possible based on detection of novel translation initiation sites (cognate or near-cognate), novel transcript isoforms, sequence variation or novel (small) open reading frames in intergenic or un-translated genic regions by analyzing high-throughput sequencing data from RNAseq or ribosome profiling experiments. Other proteogenomics studies using a combination of proteomics and genomics techniques focus on antibody sequencing, the identification of immunogenic peptides or venom peptides. Over the years, a growing amount of bioinformatics tools and databases became available to help streamlining these cross-omics studies. Some of these solutions only help in specific steps of the proteogenomics studies, e.g. building custom sequence databases (based on next generation sequencing output) for mass spectrometry fragmentation spectrum matching. Over the last few years a handful integrative tools also became available that can execute complete proteogenomics analyses. Some of these are presented as stand-alone solutions, whereas others are implemented in a web-based framework such as Galaxy. In this review we aimed at sketching a comprehensive overview of all the bioinformatics solutions that are available for this growing research area. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:584-599, 2017.
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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.