{"entity": "researcher", "timestamp": "2026-08-20T20:40:34.116Z", "family": "Skiadopoulou", "given": "Dafni", "initials": "D", "orcid": "0000-0001-5572-0070", "affiliations": ["Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, NO-5020 Bergen, Norway.", "Computational Biology Unit, Department of Informatics, University of Bergen, NO-5020 Bergen, Norway."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/1875dd41dae84e64813089daa83138c6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/1875dd41dae84e64813089daa83138c6"}}, "publications": [{"entity": "publication", "iuid": "44870a114cd24900baccd4796b422a86", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/44870a114cd24900baccd4796b422a86.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/44870a114cd24900baccd4796b422a86"}}, "title": "ProHap enables human proteomic database generation accounting for population diversity.", "authors": [{"family": "Va\u0161\u00ed\u010dek", "given": "Jakub", "initials": "J", "orcid": "0000-0003-2340-0560", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da1faf367e5c42028b5ecdde0f346b46.json"}}, {"family": "Kuznetsova", "given": "Ksenia G", "initials": "KG", "orcid": "0000-0001-7447-4047", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8a07e1c078c64e019aaac124b238877c.json"}}, {"family": "Skiadopoulou", "given": "Dafni", "initials": "D", "orcid": "0000-0001-5572-0070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1875dd41dae84e64813089daa83138c6.json"}}, {"family": "Unger", "given": "Lucas", "initials": "L"}, {"family": "Chera", "given": "Simona", "initials": "S", "orcid": "0000-0001-6310-3486", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2bbfcb7c2c8545ef923a005dd39ac44f.json"}}, {"family": "Ghila", "given": "Luiza M", "initials": "LM", "orcid": "0000-0001-7173-6312", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ad5fb83952714f2c9ee454a34af3270f.json"}}, {"family": "Bandeira", "given": "Nuno", "initials": "N", "orcid": "0000-0001-8385-3655", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6ef3073f45c14b7291348f2257d503b8.json"}}, {"family": "Nj\u00f8lstad", "given": "P\u00e5l R", "initials": "PR", "orcid": "0000-0003-0304-6728", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0f9b2ded531b4e728c808c7dad460489.json"}}, {"family": "Johansson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-2298-7008", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0e5286d7375241e685d8eab789a3c1de.json"}}, {"family": "Bruckner", "given": "Stefan", "initials": "S", "orcid": "0000-0002-0885-8402", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6985e8b619de452d8022809ef7c7df6a.json"}}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}, {"family": "Vaudel", "given": "Marc", "initials": "M", "orcid": "0000-0003-1179-9578", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2596035e48ab48c6a100c6ef81757b4f.json"}}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "22", "issue": "2", "pages": "273-277", "issn-l": "1548-7091"}, "abstract": "Amid the advances in genomics, the availability of large reference panels of human haplotypes is key to account for human diversity within and across populations. However, mass spectrometry-based proteomics does not benefit from this information. To address this gap, we introduce ProHap, a Python-based tool that constructs protein sequence databases from phased genotypes of reference panels. ProHap enables researchers to account for haplotype diversity in proteomic searches.", "doi": "10.1038/s41592-024-02506-0", "pmid": "39653819", "labels": [], "xrefs": [{"db": "pii", "key": "10.1038/s41592-024-02506-0"}], "notes": [], "created": "2026-08-20T09:03:16.989Z", "modified": "2026-08-20T09:03:17.367Z"}, {"entity": "publication", "iuid": "f5131ad6484247fd9eb5ae3ed7addc96", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f5131ad6484247fd9eb5ae3ed7addc96.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f5131ad6484247fd9eb5ae3ed7addc96"}}, "title": "ProHap enables proteomic database generation accounting for population diversity", "authors": [{"family": "Va\u0161\u00ed\u010dek", "given": "Jakub", "initials": "J", "orcid": "0000-0003-2340-0560", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da1faf367e5c42028b5ecdde0f346b46.json"}}, {"family": "Kuznetsova", "given": "Ksenia G", "initials": "KG", "orcid": "0000-0001-7447-4047", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8a07e1c078c64e019aaac124b238877c.json"}}, {"family": "Skiadopoulou", "given": "Dafni", "initials": "D", "orcid": "0000-0001-5572-0070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1875dd41dae84e64813089daa83138c6.json"}}, {"family": "Nj\u00f8lstad", "given": "P\u00e5l R", "initials": "PR", "orcid": "0000-0003-0304-6728", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0f9b2ded531b4e728c808c7dad460489.json"}}, {"family": "Johansson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-2298-7008", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0e5286d7375241e685d8eab789a3c1de.json"}}, {"family": "Bruckner", "given": "Stefan", "initials": "S", "orcid": "0000-0002-0885-8402", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6985e8b619de452d8022809ef7c7df6a.json"}}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}, {"family": "Vaudel", "given": "Marc", "initials": "M", "orcid": "0000-0003-1179-9578", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2596035e48ab48c6a100c6ef81757b4f.json"}}], "type": "posted-content", "published": "2023-12-24", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2023.12.24.572591", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:51:19.244Z", "modified": "2026-08-20T10:51:19.346Z"}, {"entity": "publication", "iuid": "3ac9d6f4c7f747bcb5eb79b3b456ce7e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3ac9d6f4c7f747bcb5eb79b3b456ce7e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3ac9d6f4c7f747bcb5eb79b3b456ce7e"}}, "title": "Retention Time and Fragmentation Predictors Increase Confidence in Identification of Common Variant Peptides.", "authors": [{"family": "Skiadopoulou", "given": "Dafni", "initials": "D", "orcid": "0000-0001-5572-0070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1875dd41dae84e64813089daa83138c6.json"}}, {"family": "Va\u0161\u00ed\u010dek", "given": "Jakub", "initials": "J"}, {"family": "Kuznetsova", "given": "Ksenia", "initials": "K"}, {"family": "Bouyssi\u00e9", "given": "David", "initials": "D", "orcid": "0000-0002-0847-4759", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/877b0a0677fb463b829241dc4fc52203.json"}}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}, {"family": "Vaudel", "given": "Marc", "initials": "M", "orcid": "0000-0003-1179-9578", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2596035e48ab48c6a100c6ef81757b4f.json"}}], "type": "journal article", "published": "2023-10-06", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "22", "issue": "10", "pages": "3190-3199", "issn-l": "1535-3893"}, "abstract": "Precision medicine focuses on adapting care to the individual profile of patients, for example, accounting for their unique genetic makeup. Being able to account for the effect of genetic variation on the proteome holds great promise toward this goal. However, identifying the protein products of genetic variation using mass spectrometry has proven very challenging. Here we show that the identification of variant peptides can be improved by the integration of retention time and fragmentation predictors into a unified proteogenomic pipeline. By combining these intrinsic peptide characteristics using the search-engine post-processor Percolator, we demonstrate improved discrimination power between correct and incorrect peptide-spectrum matches. Our results demonstrate that the drop in performance that is induced when expanding a protein sequence database can be compensated, hence enabling efficient identification of genetic variation products in proteomics data. We anticipate that this enhancement of proteogenomic pipelines can provide a more refined picture of the unique proteome of patients and thereby contribute to improving patient care.", "doi": "10.1021/acs.jproteome.3c00243", "pmid": "37656829", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10563157"}], "notes": [], "created": "2026-08-20T08:11:48.966Z", "modified": "2026-08-20T08:11:49.136Z"}, {"entity": "publication", "iuid": "772681df37b54f1e84504f3cc0fd0e98", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/772681df37b54f1e84504f3cc0fd0e98.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/772681df37b54f1e84504f3cc0fd0e98"}}, "title": "Retention time and fragmentation predictors increase confidence in variant peptide identification", "authors": [{"family": "Skiadopoulou", "given": "Dafni", "initials": "D", "orcid": "0000-0001-5572-0070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1875dd41dae84e64813089daa83138c6.json"}}, {"family": "Va\u0161\u00ed\u010dek", "given": "Jakub", "initials": "J", "orcid": "0000-0003-2340-0560", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da1faf367e5c42028b5ecdde0f346b46.json"}}, {"family": "Kuznetsova", "given": "Ksenia", "initials": "K", "orcid": "0000-0001-7447-4047", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8a07e1c078c64e019aaac124b238877c.json"}}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}, {"family": "Vaudel", "given": "Marc", "initials": "M", "orcid": "0000-0003-1179-9578", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2596035e48ab48c6a100c6ef81757b4f.json"}}], "type": "posted-content", "published": "2023-04-01", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2023.03.29.534843", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:45:05.589Z", "modified": "2026-08-20T10:45:05.665Z"}, {"entity": "publication", "iuid": "75c6fd13095a4c8490df8c472f6f2b35", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/75c6fd13095a4c8490df8c472f6f2b35.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/75c6fd13095a4c8490df8c472f6f2b35"}}, "title": "Finding haplotypic signatures in proteins.", "authors": [{"family": "Va\u0161\u00ed\u010dek", "given": "Jakub", "initials": "J", "orcid": "0000-0003-2340-0560", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da1faf367e5c42028b5ecdde0f346b46.json"}}, {"family": "Skiadopoulou", "given": "Dafni", "initials": "D", "orcid": "0000-0001-5572-0070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1875dd41dae84e64813089daa83138c6.json"}}, {"family": "Kuznetsova", "given": "Ksenia G", "initials": "KG", "orcid": "0000-0001-7447-4047", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8a07e1c078c64e019aaac124b238877c.json"}}, {"family": "Wen", "given": "Bo", "initials": "B", "orcid": "0000-0003-2261-3150", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b6303720e4bd46ecbaddc0f1621c8fca.json"}}, {"family": "Johansson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-2298-7008", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0e5286d7375241e685d8eab789a3c1de.json"}}, {"family": "Nj\u00f8lstad", "given": "P\u00e5l R", "initials": "PR", "orcid": "0000-0003-0304-6728", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0f9b2ded531b4e728c808c7dad460489.json"}}, {"family": "Bruckner", "given": "Stefan", "initials": "S", "orcid": "0000-0002-0885-8402", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6985e8b619de452d8022809ef7c7df6a.json"}}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}, {"family": "Vaudel", "given": "Marc", "initials": "M", "orcid": "0000-0003-1179-9578", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2596035e48ab48c6a100c6ef81757b4f.json"}}], "type": "journal article", "published": "2022-12-28", "journal": {"title": "Gigascience", "issn": "2047-217X", "volume": "12", "issn-l": "2047-217X"}, "abstract": "The nonrandom distribution of alleles of common genomic variants produces haplotypes, which are fundamental in medical and population genetic studies. Consequently, protein-coding genes with different co-occurring sets of alleles can encode different amino acid sequences: protein haplotypes. These protein haplotypes are present in biological samples and detectable by mass spectrometry, but they are not accounted for in proteomic searches. Consequently, the impact of haplotypic variation on the results of proteomic searches and the discoverability of peptides specific to haplotypes remain unknown.\n\nHere, we study how common genetic haplotypes influence the proteomic search space and investigate the possibility to match peptides containing multiple amino acid substitutions to a publicly available data set of mass spectra. We found that for 12.42% of the discoverable amino acid substitutions encoded by common haplotypes, 2 or more substitutions may co-occur in the same peptide after tryptic digestion of the protein haplotypes. We identified 352 spectra that matched to such multivariant peptides, and out of the 4,582 amino acid substitutions identified, 6.37% were covered by multivariant peptides. However, the evaluation of the reliability of these matches remains challenging, suggesting that refined error rate estimation procedures are needed for such complex proteomic searches.\n\nAs these procedures become available and the ability to analyze protein haplotypes increases, we anticipate that proteomics will provide new information on the consequences of common variation, across tissues and time.", "doi": "10.1093/gigascience/giad093", "pmid": "37919975", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10622322"}, {"db": "pii", "key": "7334270"}], "notes": [], "created": "2026-08-20T09:41:38.734Z", "modified": "2026-08-20T09:41:38.884Z"}, {"entity": "publication", "iuid": "0c0378b720fc43d3b9d7ab06cd912cab", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0c0378b720fc43d3b9d7ab06cd912cab.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0c0378b720fc43d3b9d7ab06cd912cab"}}, "title": "Finding Haplotypic Signatures in Proteins", "authors": [{"family": "Va\u0161\u00ed\u010dek", "given": "Jakub", "initials": "J", "orcid": "0000-0003-2340-0560", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da1faf367e5c42028b5ecdde0f346b46.json"}}, {"family": "Skiadopoulou", "given": "Dafni", "initials": "D", "orcid": "0000-0001-5572-0070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1875dd41dae84e64813089daa83138c6.json"}}, {"family": "Kuznetsova", "given": "Ksenia G", "initials": "KG", "orcid": "0000-0001-7447-4047", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8a07e1c078c64e019aaac124b238877c.json"}}, {"family": "Wen", "given": "Bo", "initials": "B", "orcid": "0000-0003-2261-3150", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b6303720e4bd46ecbaddc0f1621c8fca.json"}}, {"family": "Johansson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-2298-7008", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0e5286d7375241e685d8eab789a3c1de.json"}}, {"family": "Nj\u00f8lstad", "given": "P\u00e5l R", "initials": "PR", "orcid": "0000-0003-0304-6728", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0f9b2ded531b4e728c808c7dad460489.json"}}, {"family": "Bruckner", "given": "Stefan", "initials": "S", "orcid": "0000-0002-0885-8402", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6985e8b619de452d8022809ef7c7df6a.json"}}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}, {"family": "Vaudel", "given": "Marc", "initials": "M", "orcid": "0000-0003-1179-9578", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2596035e48ab48c6a100c6ef81757b4f.json"}}], "type": "posted-content", "published": "2022-11-24", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.11.21.517096", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:42:20.368Z", "modified": "2026-08-20T10:42:20.511Z"}]}