ArticleJournal of proteome research2018
ProteomeGenerator: A Framework for Comprehensive Proteomics Based on de Novo Transcriptome Assembly and High-Accuracy Peptide Mass Spectral Matching.
Article in Journal of proteome research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 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.
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.
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Who cites it
18 citing papers in PubMed, 34 citations in OpenAlex.
- Computational identification and characterization of noncoding RNA-encoded peptides: tools, databases, and in silico strategies.Amino acids · 2026Review
- Identification of non-canonical peptides with moPepGen.Nature biotechnology · 2026Article
- High Dynamic Range Peptide Mass Spectrometry Using Segmented Precursor Ion Accumulation.Analytical chemistry · 2025Article
- Identification of non-canonical peptides with moPepGen.bioRxiv : the preprint server for biology · 2025Article
- Integration of proteomics profiling data to facilitate discovery of cancer neoantigens: a survey.Briefings in bioinformatics · 2025Review
- The role and application of bioinformatics techniques and tools in drug discovery.Frontiers in pharmacology · 2025Review
- Integrative Proteogenomics Using ProteomeGenerator2.Journal of proteome research · 2023Article
- A Drug Repurposing Pipeline Based on Bladder Cancer Integrated Proteotranscriptomics Signatures.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Proteogenomic Analysis of Breast Cancer Transcriptomic and Proteomic Data, Using De Novo Transcript Assembly: Genome-Wide Identification of Novel Peptides and Clinical Implications.Molecular & cellular proteomics : MCP · 2022Article
- Proteotranscriptomics - A facilitator in omics research.Computational and structural biotechnology journal · 2022Review
- Discovery of Protein Modifications Using Differential Tandem Mass Spectrometry Proteomics.Journal of proteome research · 2021Article
- Spritz: A Proteogenomic Database Engine.Journal of proteome research · 2021Article
- Immunopeptidogenomics: Harnessing RNA-Seq to Illuminate the Dark Immunopeptidome.Molecular & cellular proteomics : MCP · 2021Article
- CCPRD: A Novel Analytical Framework for the Comprehensive Proteomic Reference Database Construction of NonModel Organisms.ACS omega · 2020Article
- Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis.International journal of molecular sciences · 2020Review
- Splice-Junction-Based Mapping of Alternative Isoforms in the Human Proteome.Cell reports · 2019Article
- Exploiting Interdata Relationships in Next-generation Proteomics Analysis.Molecular & cellular proteomics : MCP · 2019Review
- Review
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
Modern mass spectrometry now permits genome-scale and quantitative measurements of biological proteomes. However, analysis of specific specimens is currently hindered by the incomplete representation of biological variability of protein sequences in canonical reference proteomes and the technical demands for their construction. Here, we report ProteomeGenerator, a framework for de novo and reference-assisted proteogenomic database construction and analysis based on sample-specific transcriptome sequencing and high-accuracy mass spectrometry proteomics. This enables the assembly of proteomes encoded by actively transcribed genes, including sample-specific protein isoforms resulting from non-canonical mRNA transcription, splicing, or editing. To improve the accuracy of protein isoform identification in non-canonical proteomes, ProteomeGenerator relies on statistical target-decoy database matching calibrated using sample-specific controls. Its current implementation includes automatic integration with MaxQuant mass spectrometry proteomics algorithms. We applied this method for the proteogenomic analysis of splicing factor SRSF2 mutant leukemia cells, demonstrating high-confidence identification of non-canonical protein isoforms arising from alternative transcriptional start sites, intron retention, and cryptic exon splicing as well as improved accuracy of genome-scale proteome discovery. Additionally, we report proteogenomic performance metrics for current state-of-the-art implementations of SEQUEST HT, MaxQuant, Byonic, and PEAKS mass spectral analysis algorithms. Finally, ProteomeGenerator is implemented as a Snakemake workflow within a Singularity container for one-step installation in diverse computing environments, thereby enabling open, scalable, and facile discovery of sample-specific, non-canonical, and neomorphic biological proteomes.
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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.