ArticleBioinformatics (Oxford, England)2015
MSProGene: integrative proteogenomics beyond six-frames and single nucleotide polymorphisms.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Integrative transcriptomics and peptidomics approach reveals unexpectedly diverse endogenous secretory peptides in Odorrana grahami frog skin.BMC biology · 2025Article
- Proteomic Profiling Towards a Better Understanding of Genetic Based Muscular Diseases: The Current Picture and a Look to the Future.Biomolecules · 2025Review
- Proteogenomic Approaches for Diseasome Studies.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Deep Proteogenomics of a Photosynthetic Cyanobacterium.Journal of proteome research · 2023Article
- Article
- An analysis of proteogenomics and how and when transcriptome-informed reduction of protein databases can enhance eukaryotic proteomics.Genome biology · 2022Article
- A Practical Guide to Small Protein Discovery and Characterization Using Mass Spectrometry.Journal of bacteriology · 2022Article
- Comprehensive Pan-Cancer Analysis of GINS2 for Human Tumour Prognosis and as an Immunological Biomarker.Computational and mathematical methods in medicine · 2022Article
- Personalized Proteome: Comparing Proteogenomics and Open Variant Search Approaches for Single Amino Acid Variant Detection.Journal of proteome research · 2021Article
- Methods for Proteogenomics Data Analysis, Challenges, and Scalability Bottlenecks: A Survey.IEEE access : practical innovations, open solutions · 2021Article
- Proteoform Identification by Combining RNA-Seq and Top-Down Mass Spectrometry.Journal of proteome research · 2021Article
- Immunopeptidogenomics: Harnessing RNA-Seq to Illuminate the Dark Immunopeptidome.Molecular & cellular proteomics : MCP · 2021Article
- Identification of Non-Canonical Translation Products inFrontiers in genetics · 2021Article
- CCPRD: A Novel Analytical Framework for the Comprehensive Proteomic Reference Database Construction of NonModel Organisms.ACS omega · 2020Article
- Splice-Junction-Based Mapping of Alternative Isoforms in the Human Proteome.Cell reports · 2019Article
- ProteomeGenerator: A Framework for Comprehensive Proteomics Based on de Novo Transcriptome Assembly and High-Accuracy Peptide Mass Spectral Matching.Journal of proteome research · 2018Article
- An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics.Genome research · 2017Article
- Integrating Next-Generation Genomic Sequencing and Mass Spectrometry To Estimate Allele-Specific Protein Abundance in Human Brain.Journal of proteome research · 2017Article
- Detecting protein variants by mass spectrometry: a comprehensive study in cancer cell-lines.Genome medicine · 2017Article
- Methods, Tools and Current Perspectives in Proteogenomics.Molecular & cellular proteomics : MCP · 2017Review
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
unlabelledOngoing advances in high-throughput technologies have facilitated accurate proteomic measurements and provide a wealth of information on genomic and transcript level. In proteogenomics, this multi-omics data is combined to analyze unannotated organisms and to allow more accurate sample-specific predictions. Existing analysis methods still mainly depend on six-frame translations or reference protein databases that are extended by transcriptomic information or known single nucleotide polymorphisms (SNPs). However, six-frames introduce an artificial sixfold increase of the target database and SNP integration requires a suitable database summarizing results from previous experiments. We overcome these limitations by introducing MSProGene, a new method for integrative proteogenomic analysis based on customized RNA-Seq driven transcript databases. MSProGene is independent from existing reference databases or annotated SNPs and avoids large six-frame translated databases by constructing sample-specific transcripts. In addition, it creates a network combining RNA-Seq and peptide information that is optimized by a maximum-flow algorithm. It thereby also allows resolving the ambiguity of shared peptides for protein inference. We applied MSProGene on three datasets and show that it facilitates a database-independent reliable yet accurate prediction on gene and protein level and additionally identifies novel genes. AVAILABILITY AND IMPLEMENTATION: MSProGene is written in Java and Python. It is open source and available at http://sourceforge.net/projects/msprogene/.
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