ArticleJournal of proteome research2021
Spritz: A Proteogenomic Database Engine.
Article in Journal of proteome research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- LRP2: A proteogenomics pipeline for long-read informed protein isoform analysis and discovery.bioRxiv : the preprint server for biology · 2026Article
- Identification of non-canonical peptides with moPepGen.Nature biotechnology · 2026Article
- Sample-specific haplotype-resolved protein isoform characterization via long-read RNA-seq-based proteogenomics.bioRxiv : the preprint server for biology · 2026Article
- Identification of non-canonical peptides with moPepGen.bioRxiv : the preprint server for biology · 2025Article
- Chemoproteogenomic stratification of the missense variant cysteinome.Nature communications · 2024Article
- Multi-omic stratification of the missense variant cysteinome.bioRxiv : the preprint server for biology · 2023Article
- Identification of Splice Variants and Isoforms in Transcriptomics and Proteomics.Annual review of biomedical data science · 2023Review
- Integrative Proteogenomics Using ProteomeGenerator2.Journal of proteome research · 2023Article
- Comparing Top-Down Proteoform Identification: Deconvolution, PrSM Overlap, and PTM Detection.Journal of proteome research · 2023Article
- OpenCustomDB: Integration of Unannotated Open Reading Frames and Genetic Variants to Generate More Comprehensive Customized Protein Databases.Journal of proteome research · 2023Article
- Overview and considerations in bottom-up proteomics.The Analyst · 2023Review
- Enhanced Proteomic Data Analysis with MetaMorpheus.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Enhanced protein isoform characterization through long-read proteogenomics.Genome biology · 2022Article
- An overview of technologies for MS-based proteomics-centric multi-omics.Expert review of proteomics · 2022Article
- Prospects and challenges of cancer systems medicine: from genes to disease networks.Briefings in bioinformatics · 2022Review
- Proteoforms and Proteoform Families: Past, Present, and Future.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Personalized Proteome: Comparing Proteogenomics and Open Variant Search Approaches for Single Amino Acid Variant Detection.Journal of proteome research · 2021Article
- Cloudy with a Chance of Peptides: Accessibility, Scalability, and Reproducibility with Cloud-Hosted Environments.Journal of proteome research · 2021Article
- Binary Classifier for Computing Posterior Error Probabilities in MetaMorpheus.Journal of proteome research · 2021Article
- ProteaseGuru: A Tool for Protease Selection in Bottom-Up Proteomics.Journal of proteome research · 2021Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Proteoforms are the workhorses of the cell, and subtle differences between their amino acid sequences or post-translational modifications (PTMs) can change their biological function. To most effectively identify and quantify proteoforms in genetically diverse samples by mass spectrometry (MS), it is advantageous to search the MS data against a sample-specific protein database that is tailored to the sample being analyzed, in that it contains the correct amino acid sequences and relevant PTMs for that sample. To this end, we have developed Spritz (https://smith-chem-wisc.github.io/Spritz/), an open-source software tool for generating protein databases annotated with sequence variations and PTMs. We provide a simple graphical user interface for Windows and scripts that can be run on any operating system. Spritz automatically sets up and executes approximately 20 tools, which enable the construction of a proteogenomic database from only raw RNA sequencing data. Sequence variations that are discovered in RNA sequencing data upon comparison to the Ensembl reference genome are annotated on proteins in these databases, and PTM annotations are transferred from UniProt. Modifications can also be discovered and added to the database using bottom-up mass spectrometry data and global PTM discovery in MetaMorpheus. We demonstrate that such sample-specific databases allow the identification of variant peptides, modified variant peptides, and variant proteoforms by searching bottom-up and top-down proteomic data from the Jurkat human T lymphocyte cell line and demonstrate the identification of phosphorylated variant sites with phosphoproteomic data from the U2OS human osteosarcoma cell line.
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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.