{"entity": "researcher", "timestamp": "2026-08-20T21:24:30.319Z", "family": "MacCoss", "given": "Michael J", "initials": "MJ", "orcid": "0000-0003-1853-0256", "affiliations": ["Department of Genome Sciences, University of Washington, Seattle, Washington 98195 United States."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/b57b50e580b940cba50310ac37e89603.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/b57b50e580b940cba50310ac37e89603"}}, "publications": [{"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": "0f57550e021d409b9b359cb41520fee2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0f57550e021d409b9b359cb41520fee2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0f57550e021d409b9b359cb41520fee2"}}, "title": "Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics?", "authors": [{"family": "Plubell", "given": "Deanna L", "initials": "DL", "orcid": "0000-0002-6580-8073", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c353f24426604d199be325edcde06be7.json"}}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}, {"family": "Webb-Robertson", "given": "Bobbie-Jo", "initials": "BJ"}, {"family": "Bramer", "given": "Lisa M", "initials": "LM", "orcid": "0000-0002-8384-1926", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e214d736fc5d44d3be3baff22c478df2.json"}}, {"family": "Ives", "given": "Ashley", "initials": "A", "orcid": "0000-0002-1318-5732", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f27079ba95934664ab1fc288fa121cbf.json"}}, {"family": "Kelleher", "given": "Neil L", "initials": "NL", "orcid": "0000-0002-8815-3372", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/db299d87427049b8972eabe2d9f453a8.json"}}, {"family": "Smith", "given": "Lloyd M", "initials": "LM"}, {"family": "Montine", "given": "Thomas J", "initials": "TJ", "orcid": "0000-0002-1346-2728", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4a2c2ba8b0d49ccb31bceea9e11206b.json"}}, {"family": "Wu", "given": "Christine C", "initials": "CC"}, {"family": "MacCoss", "given": "Michael J", "initials": "MJ", "orcid": "0000-0003-1853-0256", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b57b50e580b940cba50310ac37e89603.json"}}], "type": "journal article", "published": "2022-04-01", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "21", "issue": "4", "pages": "891-898", "issn-l": "1535-3893"}, "abstract": "Bottom-up proteomics provides peptide measurements and has been invaluable for moving proteomics into large-scale analyses. Commonly, a single quantitative value is reported for each protein-coding gene by aggregating peptide quantities into protein groups following protein inference or parsimony. However, given the complexity of both RNA splicing and post-translational protein modification, it is overly simplistic to assume that all peptides that map to a singular protein-coding gene will demonstrate the same quantitative response. By assuming that all peptides from a protein-coding sequence are representative of the same protein, we may miss the discovery of important biological differences. To capture the contributions of existing proteoforms, we need to reconsider the practice of aggregating protein values to a single quantity per protein-coding gene.", "doi": "10.1021/acs.jproteome.1c00894", "pmid": "35220718", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS1789966"}, {"db": "pmc", "key": "PMC8976764"}], "notes": [], "created": "2026-08-20T08:11:26.625Z", "modified": "2026-08-20T08:11:26.897Z"}, {"entity": "publication", "iuid": "9b67e9b516cb40128033ab972207b9fa", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9b67e9b516cb40128033ab972207b9fa.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9b67e9b516cb40128033ab972207b9fa"}}, "title": "Can we put Humpty Dumpty back together again? What does protein quantification mean in bottom-up proteomics?", "authors": [{"family": "Plubell", "given": "Deanna L", "initials": "DL", "orcid": "0000-0002-6580-8073", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c353f24426604d199be325edcde06be7.json"}}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}, {"family": "Webb-Robertson", "given": "Bobbie Jo", "initials": "BJ", "orcid": "0000-0002-4744-2397", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b6a368f002a24dd996fecb43b53a6a2c.json"}}, {"family": "Bramer", "given": "Lisa", "initials": "L"}, {"family": "Ives", "given": "Ashley", "initials": "A"}, {"family": "Kelleher", "given": "Neil L", "initials": "NL", "orcid": "0000-0002-8815-3372", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/db299d87427049b8972eabe2d9f453a8.json"}}, {"family": "Smith", "given": "Lloyd M", "initials": "LM"}, {"family": "Montine", "given": "Thomas J", "initials": "TJ"}, {"family": "Wu", "given": "Christine C", "initials": "CC"}, {"family": "MacCoss", "given": "Michael J", "initials": "MJ", "orcid": "0000-0003-1853-0256", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b57b50e580b940cba50310ac37e89603.json"}}], "type": "posted-content", "published": "2021-01-27", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.01.25.428175", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:01:15.591Z", "modified": "2026-08-20T10:01:15.707Z"}]}