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"researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1703a87b2e3444d8ba917253d25d5556.json"}}, {"family": "van der Hooft", "given": "Justin J J", "initials": "JJJ", "orcid": "0000-0002-9340-5511", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c3918b083fe4b31bfe49c2e2e7fcd07.json"}}, {"family": "Vicini", "given": "Andrea", "initials": "A"}, {"family": "Walter", "given": "Axel", "initials": "A"}, {"family": "Weber", "given": "Tilmann", "initials": "T", "orcid": "0000-0002-8260-5120", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd1d6e8b8a81479aac38273ab6da62a2.json"}}, {"family": "Xiong", "given": "Quanbo", "initials": "Q"}, {"family": "Xu", "given": "Tao", "initials": "T"}, {"family": "Pluskal", "given": "Tom\u00e1\u0161", "initials": "T", "orcid": "0000-0002-6940-3006", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0e73806a9bb8490c88dd6344f1da57aa.json"}}, {"family": "Dorrestein", "given": "Pieter C", "initials": "PC", "orcid": "0000-0002-3003-1030", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aab670a610074d7787adc1b56fa4cb47.json"}}, {"family": "Wang", "given": "Mingxun", "initials": "M", "orcid": "0000-0001-7647-6097", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a42a021d871489e97768fbd48fd3f7f.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "22", "issue": "6", "pages": "1247-1254", "issn-l": "1548-7091"}, "abstract": "Despite being information rich, the vast majority of untargeted mass spectrometry data are underutilized; most analytes are not used for downstream interpretation or reanalysis after publication. The inability to dive into these rich raw mass spectrometry datasets is due to the limited flexibility and scalability of existing software tools. Here we introduce a new language, the Mass Spectrometry Query Language (MassQL), and an accompanying software ecosystem that addresses these issues by enabling the community to directly query mass spectrometry data with an expressive set of user-defined mass spectrometry patterns. Illustrated by real-world examples, MassQL provides a data-driven definition of chemical diversity by enabling the reanalysis of all public untargeted metabolomics data, empowering scientists across many disciplines to make new discoveries. MassQL has been widely implemented in multiple open-source and commercial mass spectrometry analysis tools, which enhances the ability, interoperability and reproducibility of mining of mass spectrometry data for the research community.", "doi": "10.1038/s41592-025-02660-z", "pmid": "40355727", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS2097565"}, {"db": "pmc", "key": "PMC12334354"}, {"db": "pii", "key": "10.1038/s41592-025-02660-z"}], "notes": [], "created": "2026-08-20T09:03:29.583Z", "modified": "2026-08-20T09:03:30.387Z"}, {"entity": "publication", "iuid": "ed86cc02c63e46d09350d9ba3702350b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ed86cc02c63e46d09350d9ba3702350b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ed86cc02c63e46d09350d9ba3702350b"}}, "title": "Open-Source and FAIR Research Software for Proteomics.", "authors": [{"family": "Perez-Riverol", "given": "Yasset", "initials": "Y", "orcid": "0000-0001-6579-6941", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb4449bad29741b195a7593fc39a769d.json"}}, {"family": "Bittremieux", "given": "Wout", "initials": "W", "orcid": "0000-0002-3105-1359", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07e740b95ac84bb6ad8f3ff159aece03.json"}}, {"family": "Noble", "given": "William S", "initials": "WS", "orcid": "0000-0001-7283-4715", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/77bfbf9a1a8242b8955c8dd9f5642a8b.json"}}, {"family": "Martens", "given": "Lennart", "initials": "L", "orcid": "0000-0003-4277-658X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/df9a736ba6d04cbdb881a040480bf6f0.json"}}, {"family": "Bilbao", "given": "Aivett", "initials": "A", "orcid": "0000-0003-2985-8249", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2939469149284dee8f3b20bf40c9e2e9.json"}}, {"family": "Lazear", "given": "Michael R", "initials": "MR", "orcid": "0000-0001-5313-4262", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ebe2629197bf4b53a53a06244b7f1302.json"}}, {"family": "Gr\u00fcning", "given": "Bjorn", "initials": "B", "orcid": "0000-0002-3079-6586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b2539c92f7e2437782cf04c0c9a23fc8.json"}}, {"family": "Katz", "given": "Daniel S", "initials": "DS", "orcid": "0000-0001-5934-7525", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b3f98d2fb8384d4684bd7e9e93dc3ef1.json"}}, {"family": "MacCoss", "given": "Michael J", "initials": "MJ", "orcid": "0000-0003-1853-0256", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b57b50e580b940cba50310ac37e89603.json"}}, {"family": "Dai", "given": "Chengxin", "initials": "C"}, {"family": "Eng", "given": "Jimmy K", "initials": "JK", "orcid": "0000-0001-6352-6737", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d748f8f4b03940ac81712a0910415b8b.json"}}, {"family": "Bouwmeester", "given": "Robbin", "initials": "R", "orcid": "0000-0001-6807-7029", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cd945733eeaf46d895f9d8799b430d66.json"}}, {"family": "Shortreed", "given": "Michael R", "initials": "MR", "orcid": "0000-0003-4626-0863", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cf4bd1d3f2ed44bf94983b952500e04d.json"}}, {"family": "Audain", "given": "Enrique", "initials": "E"}, {"family": "Sachsenberg", "given": "Timo", "initials": "T", "orcid": "0000-0002-2833-6070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d5425fd7b0434642b4c6f7aef67b5f23.json"}}, {"family": "Van Goey", "given": "Jeroen", "initials": "J"}, {"family": "Wallmann", "given": "Georg", "initials": "G"}, {"family": "Wen", "given": "Bo", "initials": "B"}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}, {"family": "Fondrie", "given": "William E", "initials": "WE", "orcid": "0000-0002-1554-3716", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0605055453fc4d54b057471ae964ca3f.json"}}], "type": "journal article", "published": "2025-05-02", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "24", "issue": "5", "pages": "2222-2234", "issn-l": "1535-3893"}, "abstract": "Scientific discovery relies on innovative software as much as experimental methods, especially in proteomics, where computational tools are essential for mass spectrometer setup, data analysis, and interpretation. Since the introduction of SEQUEST, proteomics software has grown into a complex ecosystem of algorithms, predictive models, and workflows, but the field faces challenges, including the increasing complexity of mass spectrometry data, limited reproducibility due to proprietary software, and difficulties integrating with other omics disciplines. Closed-source, platform-specific tools exacerbate these issues by restricting innovation, creating inefficiencies, and imposing hidden costs on the community. Open-source software (OSS), aligned with the FAIR Principles (Findable, Accessible, Interoperable, Reusable), offers a solution by promoting transparency, reproducibility, and community-driven development, which fosters collaboration and continuous improvement. In this manuscript, we explore the role of OSS in computational proteomics, its alignment with FAIR principles, and its potential to address challenges related to licensing, distribution, and standardization. Drawing on lessons from other omics fields, we present a vision for a future where OSS and FAIR principles underpin a transparent, accessible, and innovative proteomics community.", "doi": "10.1021/acs.jproteome.4c01079", "pmid": "40267229", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12053954"}], "notes": [], "created": "2026-08-20T08:12:01.116Z", "modified": "2026-08-20T08:12:01.507Z"}, {"entity": "publication", "iuid": "a4ffb040e494401da0c4f28f101292d0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a4ffb040e494401da0c4f28f101292d0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a4ffb040e494401da0c4f28f101292d0"}}, "title": "quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data.", "authors": [{"family": "Dai", "given": "Chengxin", "initials": "C"}, {"family": "Pfeuffer", "given": "Julianus", "initials": "J"}, {"family": "Wang", "given": "Hong", "initials": "H"}, {"family": "Zheng", "given": "Ping", "initials": "P"}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}, {"family": "Sachsenberg", "given": "Timo", "initials": "T", "orcid": "0000-0002-2833-6070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d5425fd7b0434642b4c6f7aef67b5f23.json"}}, {"family": "Demichev", "given": "Vadim", "initials": "V", "orcid": "0000-0002-2424-9412", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2be8ed6154cd48a0a6de55d75ed3ad52.json"}}, {"family": "Bai", "given": "Mingze", "initials": "M"}, {"family": "Kohlbacher", "given": "Oliver", "initials": "O", "orcid": "0000-0003-1739-4598", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9317a8da5d9d4df782158d7555f229eb.json"}}, {"family": "Perez-Riverol", "given": "Yasset", "initials": "Y", "orcid": "0000-0001-6579-6941", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb4449bad29741b195a7593fc39a769d.json"}}], "type": "journal article", "published": "2024-09-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "21", "issue": "9", "pages": "1603-1607", "issn-l": "1548-7091"}, "abstract": "The volume of public proteomics data is rapidly increasing, causing a computational challenge for large-scale reanalysis. Here, we introduce quantms ( https://quant,ms.org/ ), an open-source cloud-based pipeline for massively parallel proteomics data analysis. We used quantms to reanalyze 83 public ProteomeXchange datasets, comprising 29,354 instrument files from 13,132 human samples, to quantify 16,599 proteins based on 1.03 million unique peptides. quantms is based on standard file formats improving the reproducibility, submission and dissemination of the data to ProteomeXchange.", "doi": "10.1038/s41592-024-02343-1", "pmid": "38965444", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11399091"}, {"db": "pii", "key": "10.1038/s41592-024-02343-1"}], "notes": [], "created": "2026-08-20T09:03:06.217Z", "modified": "2026-08-20T09:03:06.356Z"}, {"entity": "publication", "iuid": "cf131f18e0054b35903421a1b0de6f39", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cf131f18e0054b35903421a1b0de6f39.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cf131f18e0054b35903421a1b0de6f39"}}, "title": "A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics.", "authors": [{"family": "Luo", "given": "Xiyang", "initials": "X"}, {"family": "Bittremieux", "given": "Wout", "initials": "W", "orcid": "0000-0002-3105-1359", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07e740b95ac84bb6ad8f3ff159aece03.json"}}, {"family": "Griss", "given": "Johannes", "initials": "J", "orcid": "0000-0003-2206-9511", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b001048c5a5148bdb9bd16ff46e067db.json"}}, {"family": "Deutsch", "given": "Eric W", "initials": "EW", "orcid": "0000-0001-8732-0928", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2463c206245a4dbb979cad9d201d73c4.json"}}, {"family": "Sachsenberg", "given": "Timo", "initials": "T", "orcid": "0000-0002-2833-6070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d5425fd7b0434642b4c6f7aef67b5f23.json"}}, {"family": "Levitsky", "given": "Lev I", "initials": "LI", "orcid": "0000-0002-4048-0876", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d992ceb2e30945529ee9200b4fe306c9.json"}}, {"family": "Ivanov", "given": "Mark V", "initials": "MV", "orcid": "0000-0003-4762-2846", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cd0d8592597c43eea8a122dd2ac128b5.json"}}, {"family": "Bubis", "given": "Julia A", "initials": "JA", "orcid": "0000-0002-4895-6146", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1face4f1b57e4bddafffb09013e3e07c.json"}}, {"family": "Gabriels", "given": "Ralf", "initials": "R", "orcid": "0000-0002-1679-1711", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/30094adc291549c28c6c74cbeb9aacd2.json"}}, {"family": "Webel", "given": "Henry", "initials": "H"}, {"family": "Sanchez", "given": "Aniel", "initials": "A"}, {"family": "Bai", "given": "Mingze", "initials": "M"}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L"}, {"family": "Perez-Riverol", "given": "Yasset", "initials": "Y", "orcid": "0000-0001-6579-6941", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb4449bad29741b195a7593fc39a769d.json"}}], "type": "journal article", "published": "2022-06-03", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "21", "issue": "6", "pages": "1566-1574", "issn-l": "1535-3893"}, "abstract": "Spectrum clustering is a powerful strategy to minimize redundant mass spectra by grouping them based on similarity, with the aim of forming groups of mass spectra from the same repeatedly measured analytes. Each such group of near-identical spectra can be represented by its so-called consensus spectrum for downstream processing. Although several algorithms for spectrum clustering have been adequately benchmarked and tested, the influence of the consensus spectrum generation step is rarely evaluated. Here, we present an implementation and benchmark of common consensus spectrum algorithms, including spectrum averaging, spectrum binning, the most similar spectrum, and the best-identified spectrum. We have analyzed diverse public data sets using two different clustering algorithms (spectra-cluster and MaRaCluster) to evaluate how the consensus spectrum generation procedure influences downstream peptide identification. The BEST and BIN methods were found the most reliable methods for consensus spectrum generation, including for data sets with post-translational modifications (PTM) such as phosphorylation. All source code and data of the present study are freely available on GitHub at https://github.com/statisticalbiotechnology/representative-spectra-benchmark.", "doi": "10.1021/acs.jproteome.2c00069", "pmid": "35549218", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9171829"}], "notes": [], "created": "2026-08-20T08:11:35.592Z", "modified": "2026-08-20T08:11:35.948Z"}, {"entity": "publication", "iuid": "245bd5639e1f4d64ac139e92715c8495", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/245bd5639e1f4d64ac139e92715c8495.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/245bd5639e1f4d64ac139e92715c8495"}}, "title": "A comprehensive evaluation of consensus spectrum generation methods in proteomics", "authors": [{"family": "Luo", "given": "Xiyang", "initials": "X"}, {"family": "Bittremieux", "given": "Wout", "initials": "W", "orcid": "0000-0002-3105-1359", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07e740b95ac84bb6ad8f3ff159aece03.json"}}, {"family": "Griss", "given": "Johannes", "initials": "J", "orcid": "0000-0003-2206-9511", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b001048c5a5148bdb9bd16ff46e067db.json"}}, {"family": "Deutsch", "given": "Eric W", "initials": "EW", "orcid": "0000-0001-8732-0928", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2463c206245a4dbb979cad9d201d73c4.json"}}, {"family": "Sachsenberg", "given": "Timo", "initials": "T", "orcid": "0000-0002-2833-6070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d5425fd7b0434642b4c6f7aef67b5f23.json"}}, {"family": "Levitsky", "given": "Lev I", "initials": "LI", "orcid": "0000-0002-4048-0876", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d992ceb2e30945529ee9200b4fe306c9.json"}}, {"family": "Ivanov", "given": "Mark V", "initials": "MV", "orcid": "0000-0003-4762-2846", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cd0d8592597c43eea8a122dd2ac128b5.json"}}, {"family": "Bubis", "given": "Julia A", "initials": "JA", "orcid": "0000-0002-4895-6146", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1face4f1b57e4bddafffb09013e3e07c.json"}}, {"family": "Gabriels", "given": "Ralf", "initials": "R", "orcid": "0000-0002-1679-1711", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/30094adc291549c28c6c74cbeb9aacd2.json"}}, {"family": "Webel", "given": "Henry", "initials": "H", "orcid": "0000-0001-8833-7617", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b16b0288b71a4c37a9d3c0cee30a16bf.json"}}, {"family": "Sanchez", "given": "Aniel", "initials": "A", "orcid": "0000-0002-0278-8802", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e38a8f60ffc14ab18499396cbf8595a8.json"}}, {"family": "Bai", "given": "Mingze", "initials": "M", "orcid": "0000-0002-9782-2056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb01c19bbd9c4a96950d782fc71db8b9.json"}}, {"family": "Kall", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}, {"family": "Perez-Riverol", "given": "Yasset", "initials": "Y", "orcid": "0000-0001-6579-6941", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb4449bad29741b195a7593fc39a769d.json"}}], "type": "posted-content", "published": "2022-01-27", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.01.25.477699", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:09:16.755Z", "modified": "2026-08-20T10:09:17.065Z"}, {"entity": "publication", "iuid": "a7ce02e60546456c9e91f0cbfc6f4e73", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a7ce02e60546456c9e91f0cbfc6f4e73.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a7ce02e60546456c9e91f0cbfc6f4e73"}}, "title": "Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides", "authors": [{"family": "Umer", "given": "Husen M", "initials": "HM", "orcid": "0000-0003-3971-2462", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/922625c410444833a263244d0313980e.json"}}, {"family": "Zhu", "given": "Yafeng", "initials": "Y", "orcid": "0000-0003-1947-9026", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/377403d2493c4176984da3bf8802aebd.json"}}, {"family": "Pfeuffer", "given": "Julianus", "initials": "J", "orcid": "0000-0001-8948-9209", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b52fcbdb2ad745aeb6b3f06f16908e41.json"}}, {"family": "Sachsenberg", "given": "Timo", "initials": "T", "orcid": "0000-0002-2833-6070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d5425fd7b0434642b4c6f7aef67b5f23.json"}}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/561efcf32e2648c8a10fee692fc4e908.json"}}, {"family": "Branca", "given": "Rui", "initials": "R", "orcid": "0000-0003-3890-6476", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7f557cf4f7ed402c8843173ab0bbef04.json"}}, {"family": "Perez-Riverol", "given": "Yasset", "initials": "Y", "orcid": "0000-0001-6579-6941", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb4449bad29741b195a7593fc39a769d.json"}}], "type": "posted-content", "published": "2021-06-09", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.06.08.447496", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:04:43.925Z", "modified": "2026-08-20T10:04:44.093Z"}, {"entity": "publication", "iuid": "ea525cca041145b7bdfe210040715780", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ea525cca041145b7bdfe210040715780.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ea525cca041145b7bdfe210040715780"}}, "title": "Expanding the Use of Spectral Libraries in Proteomics.", "authors": [{"family": "Deutsch", "given": "Eric W", "initials": "EW", "orcid": "0000-0001-8732-0928", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2463c206245a4dbb979cad9d201d73c4.json"}}, {"family": "Perez-Riverol", "given": "Yasset", "initials": "Y", "orcid": "0000-0001-6579-6941", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb4449bad29741b195a7593fc39a769d.json"}}, {"family": "Chalkley", "given": "Robert J", "initials": "RJ"}, {"family": "Wilhelm", "given": "Mathias", "initials": "M", "orcid": "0000-0002-9224-3258", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2eda8473072c48639cbd09676ed17cfe.json"}}, {"family": "Tate", "given": "Stephen", "initials": "S"}, {"family": "Sachsenberg", "given": "Timo", "initials": "T", "orcid": "0000-0002-2833-6070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d5425fd7b0434642b4c6f7aef67b5f23.json"}}, {"family": "Walzer", "given": "Mathias", "initials": "M"}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}, {"family": "Delanghe", "given": "Bernard", "initials": "B"}, {"family": "B\u00f6cker", "given": "Sebastian", "initials": "S", "orcid": "0000-0002-9304-8091", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c71ab14b72a540f3be202f873d6c7dea.json"}}, {"family": "Schymanski", "given": "Emma L", "initials": "EL", "orcid": "0000-0001-6868-8145", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc533a4744624b80960f4cf28cabdd64.json"}}, {"family": "Wilmes", "given": "Paul", "initials": "P", "orcid": "0000-0002-6478-2924", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e169727cc0f9482baf98944388a77b24.json"}}, {"family": "Dorfer", "given": "Viktoria", "initials": "V", "orcid": "0000-0002-5332-5701", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b2a0a15b0b2945238e7a39343b5c2a29.json"}}, {"family": "Kuster", "given": "Bernhard", "initials": "B", "orcid": "0000-0002-9094-1677", "researcher": {"href": 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Y", "initials": "AY"}, {"family": "Mendoza", "given": "Luis", "initials": "L", "orcid": "0000-0003-0128-8643", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b6e8a7feab0f481eaf6acd7ec097c5c5.json"}}, {"family": "Shofstahl", "given": "Jim", "initials": "J"}, {"family": "Dowsey", "given": "Andrew W", "initials": "AW", "orcid": "0000-0002-7404-9128", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a1cb70e527d84d32b1e995014007efb8.json"}}, {"family": "Griss", "given": "Johannes", "initials": "J", "orcid": "0000-0003-2206-9511", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b001048c5a5148bdb9bd16ff46e067db.json"}}, {"family": "Salek", "given": "Reza M", "initials": "RM", "orcid": "0000-0001-8604-1732", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/62799f5748ef484b816827380b723b2c.json"}}, {"family": "Neumann", "given": "Steffen", "initials": "S", "orcid": "0000-0002-7899-7192", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3fd85c99a6364305ba466010ed3012ec.json"}}, {"family": "Binz", "given": "Pierre-Alain", "initials": "PA", "orcid": "0000-0002-0045-7698", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f857e16ce82b4242ab0e780c8bec9539.json"}}, {"family": "Lam", "given": "Henry", "initials": "H", "orcid": "0000-0001-7928-0364", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5f27cfbc77fe4122977457e89968814c.json"}}, {"family": "Vizca\u00edno", "given": "Juan Antonio", "initials": "JA", "orcid": "0000-0002-3905-4335", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81245410f3234e658147bc94f6b3dad2.json"}}, {"family": "Bandeira", "given": "Nuno", "initials": "N"}, {"family": "R\u00f6st", "given": "Hannes", "initials": "H", "orcid": "0000-0003-0990-7488", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4579af772375404da76c447b23c658a3.json"}}], "type": "journal article", "published": "2018-12-07", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "17", "issue": "12", "pages": "4051-4060", "issn-l": "1535-3893"}, "abstract": "The 2017 Dagstuhl Seminar on Computational Proteomics provided an opportunity for a broad discussion on the current state and future directions of the generation and use of peptide tandem mass spectrometry spectral libraries. Their use in proteomics is growing slowly, but there are multiple challenges in the field that must be addressed to further increase the adoption of spectral libraries and related techniques. The primary bottlenecks are the paucity of high quality and comprehensive libraries and the general difficulty of adopting spectral library searching into existing workflows. There are several existing spectral library formats, but none captures a satisfactory level of metadata; therefore, a logical next improvement is to design a more advanced, Proteomics Standards Initiative-approved spectral library format that can encode all of the desired metadata. The group discussed a series of metadata requirements organized into three designations of completeness or quality, tentatively dubbed bronze, silver, and gold. The metadata can be organized at four different levels of granularity: at the collection (library) level, at the individual entry (peptide ion) level, at the peak (fragment ion) level, and at the peak annotation level. Strategies for encoding mass modifications in a consistent manner and the requirement for encoding high-quality and commonly seen but as-yet-unidentified spectra were discussed. The group also discussed related topics, including strategies for comparing two spectra, techniques for generating representative spectra for a library, approaches for selection of optimal signature ions for targeted workflows, and issues surrounding the merging of two or more libraries into one. We present here a review of this field and the challenges that the community must address in order to accelerate the adoption of spectral libraries in routine analysis of proteomics datasets.", "doi": "10.1021/acs.jproteome.8b00485", "pmid": "30270626", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS1015163"}, {"db": "pmc", "key": "PMC6443480"}], "notes": [], "created": "2026-08-20T08:12:14.655Z", "modified": "2026-08-20T08:12:15.306Z"}]}