{"doi":"10.1021/acs.jproteome.3c00135","title":"ProtView: A Versatile Tool for\n                    <i>In Silico</i>\n                    Protease Evaluation and Selection in a Proteomic and Proteogenomic Context","abstract":null,"journal":"Journal of Proteome Research","year":2023,"id":592823,"datarank":0.24625421187475582,"base_score":1.3862943611198906,"endowment":1.3862943611198906,"self_citation_contribution":0.20794415416798362,"citation_network_contribution":0.0383100577067722,"self_endowment_contribution":0.20794415416798362,"citer_contribution":0.0383100577067722,"corpus_percentile":null,"corpus_rank":null,"citation_count":3,"citer_count":3,"citers_with_citation_signal":3,"citers_with_endowment":3,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1517087,"name":"Dominika Lewandowska","orcid":"0000-0002-4734-2791","position":1,"is_corresponding":false},{"id":1517088,"name":"Piers A. Hemsley","orcid":"0000-0003-2950-0634","position":2,"is_corresponding":false},{"id":809019,"name":"Runxuan Zhang","orcid":"0000-0001-7558-765X","position":3,"is_corresponding":false},{"id":1517085,"name":"Sophia S. Puliasis","orcid":"0000-0002-6688-8095","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"ProtView: A Versatile Tool for\n                    <i>In Silico</i>\n                    Protease Evaluation and Selection in a Proteomic and Proteogenomic Context","abstract":"High Resolution Image Download MS PowerPoint Slide Many tools have been created to generate in silico proteome digests with different protease enzymes and provide useful information for selecting optimal digest schemes for specific needs. This can save on time and resources and generate insights on the observable proteome. However, there remains a need for a tool that evaluates digest schemes beyond protein and amino acid coverages in the proteomic domain. Here, we present ProtView, a versatile in silico protease combination digest evaluation workflow that maps in silico -digested peptides to both protein and genome references, so that the potential observable portions of the proteome, transcriptome, and genome can be identified. The proteomic identification and quantification of evidence for transcriptional, co-transcriptional, post-transcriptional, translational, and post-translational regulation can all be examined in silico with ProtView prior to an experiment. Benchmarking against biological data comparing multiple proteases shows that ProtView can correctly estimate performances among the digest schemes. ProtView provides this information in a way that is easy to interpret, allowing for digest schemes to be evaluated before carrying out an experiment, in context that can optimize both proteomic and proteogenomic experiments. ProtView is available at https://github.com/SSPuliasis/ProtView .","is_dataset_classified":null,"base_score":1.3862943611198906,"endowment":1.3862943611198906,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"37248202","pmcid":"PMC10337256","openalex_id":"https://openalex.org/W4378672831","authors":[],"funders":[{"funder_name":"Biotechnology and Biological Sciences Research Council","grant_id":"BB/M010996/1","title":"East of Scotland Bioscience Doctoral Training Partnership"},{"funder_name":"Biotechnology and Biological Sciences Research Council","grant_id":"BB/P007902/1","title":"Control of dynamic palmitoylation: Identification of de-palmitoylating enzymes and their substrates in plants"},{"funder_name":"Biotechnology and Biological Sciences Research Council","grant_id":"BB/V018906/1","title":null},{"funder_name":"RESAS","grant_id":"JHI-B1-2","title":null},{"funder_name":"Rural and Environment Science and Analytical Services Division","grant_id":"","title":null}],"total_grants":5,"fwci":0.3276,"citation_percentile":0.46141732,"influential_citations":0,"citation_trend":[{"year":2025,"count":1},{"year":2026,"count":2}],"oa_status":"hybrid","license":"cc-by","oa_locations":[{"url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jproteome.3c00135","host_type":"journal"},{"url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jproteome.3c00135","host_type":"publisher"},{"url":"https://doi.org/10.1021/acs.jproteome.3c00135","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/37248202","host_type":"repository"},{"url":"https://discovery.dundee.ac.uk/en/publications/96f5e575-bc25-424f-a053-8c0e5223322c","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10337256","host_type":"repository"},{"url":"https://discovery.dundee.ac.uk/ws/files/104274502/acs.jproteome.3c00135.pdf","host_type":"repository"},{"url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10337256/pdf/pr3c00135.pdf","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC10337256","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC10337256?pdf=render","host_type":"Europe_PMC"},{"url":"https://doi.org/10.1101/2021.09.02.458698","host_type":""},{"url":"https://www.biorxiv.org/content/biorxiv/early/2021/09/06/2021.09.02.458698.full.pdf","host_type":""},{"url":"http://dx.doi.org/10.1021/acs.jproteome.3c00135","host_type":""},{"url":"https://dx.doi.org/10.1101/2021.09.02.458698","host_type":""},{"url":"https://doi.org/https://doi.org/10.1021/acs.jproteome.3c00135","host_type":""}],"fields_of_study":["Advanced Proteomics Techniques and Applications","Genomics and Phylogenetic Studies","Peptidase Inhibition and Analysis","0301 basic medicine","0303 health sciences","03 medical and health sciences"],"mesh_terms":["Proteogenomics","Peptide Hydrolases","Endopeptidases","Peptides","Proteome","Proteomics"],"keywords":["In silico","Proteome","Computational biology","Context (archaeology)","Workflow","Proteomics","Biology","Proteogenomics","Identification (biology)","UniProt","Computer science","Genome","Bioinformatics","Genomics","Genetics","Gene","Database","Protease","Enzyme","In Silico Digestion","Digest","576","Endopeptidases","Peptides","Peptide Hydrolases"],"sdg_mappings":[{"sdg_number":2,"sdg_label":"2. 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