ArticleBMC bioinformatics2016
PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq.
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- MassNet: billion-scale AI-ready mass spectral corpus empowering scalable deep learning in proteomics.Nature methods · 2026Article
- 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
- ProteoformDB: A Built-In Application to Generate Proteoform Database.Journal of proteome research · 2026Article
- DeepMVP: deep learning models trained on high-quality data accurately predict PTM sites and variant-induced alterations.Nature methods · 2025Article
- Identification of non-canonical peptides with moPepGen.bioRxiv : the preprint server for biology · 2025Article
- Assessment of Data-Independent Acquisition Mass Spectrometry (DIA-MS) for the Identification of Single Amino Acid Variants.Proteomes · 2024Article
- Deep Learning Prediction Boosts Phosphoproteomics-Based Discoveries Through Improved Phosphopeptide Identification.Molecular & cellular proteomics : MCP · 2024Article
- Improving the genome and proteome annotations of the marine model diatomMarine life science & technology · 2023Article
- Variant biomarker discovery using mass spectrometry-based proteogenomics.Frontiers in aging · 2023Review
- 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
- Prospects and challenges of cancer systems medicine: from genes to disease networks.Briefings in bioinformatics · 2022Review
- Improving the Genome Annotation ofCurrent genomics · 2021Article
- caAtlas: An immunopeptidome atlas of human cancer.iScience · 2021Article
- Systematic functional interrogation of human pseudogenes using CRISPRi.Genome biology · 2021Article
- Personalized Proteome: Comparing Proteogenomics and Open Variant Search Approaches for Single Amino Acid Variant Detection.Journal of proteome research · 2021Article
- Immunopeptidogenomics: Harnessing RNA-Seq to Illuminate the Dark Immunopeptidome.Molecular & cellular proteomics : MCP · 2021Article
- Proteoform Identification by Combining RNA-Seq and Top-Down Mass Spectrometry.Journal of proteome research · 2021Article
- Methods for Proteogenomics Data Analysis, Challenges, and Scalability Bottlenecks: A Survey.IEEE access : practical innovations, open solutions · 2021Article
- DeepRescore: Leveraging Deep Learning to Improve Peptide Identification in Immunopeptidomics.Proteomics · 2020Article
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPeptide identification based upon mass spectrometry (MS) is generally achieved by comparison of the experimental mass spectra with the theoretically digested peptides derived from a reference protein database. Obviously, this strategy could not identify peptide and protein sequences that are absent from a reference database. A customized protein database on the basis of RNA-Seq data is thus proposed to assist with and improve the identification of novel peptides. Correspondingly, development of a comprehensive pipeline, which provides an end-to-end solution for novel peptide detection with the customized protein database, is necessary.
resultsA pipeline with an R package, assigned as a PGA utility, was developed that enables automated treatment to the tandem mass spectrometry (MS/MS) data acquired from different MS platforms and construction of customized protein databases based on RNA-Seq data with or without a reference genome guide. Hence, PGA can identify novel peptides and generate an HTML-based report with a visualized interface. On the basis of a published dataset, PGA was employed to identify peptides, resulting in 636 novel peptides, including 510 single amino acid polymorphism (SAP) peptides, 2 INDEL peptides, 49 splice junction peptides, and 75 novel transcript-derived peptides. The software is freely available from http://bioconductor.org/packages/PGA/ , and the example reports are available at http://wenbostar.github.io/PGA/ .
conclusionsThe pipeline of PGA, aimed at being platform-independent and easy-to-use, was successfully developed and shown to be capable of identifying novel peptides by searching the customized protein database derived from RNA-Seq data.
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