{"entity": "researcher", "timestamp": "2026-08-20T20:50:29.204Z", "family": "The", "given": "Matthew", "initials": "M", "orcid": "0000-0002-5401-5553", "affiliations": ["Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising 85354, Germany."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/9d8d7d850ed24f92b9506b203ca63ed1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/9d8d7d850ed24f92b9506b203ca63ed1"}}, "publications": [{"entity": "publication", "iuid": "aab16dd656aa430cb47450fac81f6274", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/aab16dd656aa430cb47450fac81f6274.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/aab16dd656aa430cb47450fac81f6274"}}, "title": "Triqler for Protein Summarization of Data from Data-Independent Acquisition Mass Spectrometry.", "authors": [{"family": "Truong", "given": "Patrick", "initials": "P"}, {"family": "The", "given": "Matthew", "initials": "M", "orcid": "0000-0002-5401-5553", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9d8d7d850ed24f92b9506b203ca63ed1.json"}}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}], "type": "journal article", "published": "2023-04-07", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "22", "issue": "4", "pages": "1359-1366", "issn-l": "1535-3893"}, "abstract": "A frequent goal, or subgoal, when processing data from a quantitative shotgun proteomics experiment is a list of proteins that are differentially abundant under the examined experimental conditions. Unfortunately, obtaining such a list is a challenging process, as the mass spectrometer analyzes the proteolytic peptides of a protein rather than the proteins themselves. We have previously designed a Bayesian hierarchical probabilistic model, Triqler, for combining peptide identification and quantification errors into probabilities of proteins being differentially abundant. However, the model was developed for data from data-dependent acquisition. Here, we show that Triqler is also compatible with data-independent acquisition data after applying minor alterations for the missing value distribution. Furthermore, we find that it has better performance than a set of compared state-of-the-art protein summarization tools when evaluated on data-independent acquisition data.", "doi": "10.1021/acs.jproteome.2c00607", "pmid": "36988210", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10088044"}], "notes": [], "created": "2026-08-20T08:11:42.307Z", "modified": "2026-08-20T08:11:42.435Z"}, {"entity": "publication", "iuid": "2f9a4135ce9b472f857af9618ec81eda", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2f9a4135ce9b472f857af9618ec81eda.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2f9a4135ce9b472f857af9618ec81eda"}}, "title": "Integrating identification and quantification uncertainty for differential protein abundance analysis with Triqler", "authors": [{"family": "The", "given": "Matthew", "initials": "M", "orcid": "0000-0002-5401-5553", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9d8d7d850ed24f92b9506b203ca63ed1.json"}}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}], "type": "posted-content", "published": "2020-09-25", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2020.09.24.311605", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T09:59:15.777Z", "modified": "2026-08-20T09:59:15.842Z"}, {"entity": "publication", "iuid": "ae1e75a1bfa8462d90a2ca48c163aed2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ae1e75a1bfa8462d90a2ca48c163aed2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ae1e75a1bfa8462d90a2ca48c163aed2"}}, "title": "Integrated Identification and Quantification Error Probabilities for Shotgun Proteomics.", "authors": [{"family": "The", "given": "Matthew", "initials": "M", "orcid": "0000-0002-5401-5553", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9d8d7d850ed24f92b9506b203ca63ed1.json"}}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}], "type": "journal article", "published": "2019-03-00", "journal": {"title": "Mol. Cell Proteomics", "issn": "1535-9484", "volume": "18", "issue": "3", "pages": "561-570", "issn-l": "1535-9476"}, "abstract": "Protein quantification by label-free shotgun proteomics experiments is plagued by a multitude of error sources. Typical pipelines for identifying differential proteins use intermediate filters to control the error rate. However, they often ignore certain error sources and, moreover, regard filtered lists as completely correct in subsequent steps. These two indiscretions can easily lead to a loss of control of the false discovery rate (FDR). We propose a probabilistic graphical model, Triqler, that propagates error information through all steps, employing distributions in favor of point estimates, most notably for missing value imputation. The model outputs posterior probabilities for fold changes between treatment groups, highlighting uncertainty rather than hiding it. We analyzed 3 engineered data sets and achieved FDR control and high sensitivity, even for truly absent proteins. In a bladder cancer clinical data set we discovered 35 proteins at 5% FDR, whereas the original study discovered 1 and MaxQuant/Perseus 4 proteins at this threshold. Compellingly, these 35 proteins showed enrichment for functional annotation terms, whereas the top ranked proteins reported by MaxQuant/Perseus showed no enrichment. The model executes in minutes and is freely available at https://pypi.org/project/triqler/.", "doi": "10.1074/mcp.RA118.001018", "pmid": "30482846", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6398204"}, {"db": "pii", "key": "S1535-9476(20)31858-2"}], "notes": [], "created": "2026-08-20T09:32:41.376Z", "modified": "2026-08-20T09:32:41.462Z"}, {"entity": "publication", "iuid": "143a7d8eb97041e0b96883f663e3c04b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/143a7d8eb97041e0b96883f663e3c04b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/143a7d8eb97041e0b96883f663e3c04b"}}, "title": "Focus on the spectra that matter by clustering of quantification data in shotgun proteomics", "authors": [{"family": "The", "given": "Matthew", "initials": "M", "orcid": "0000-0002-5401-5553", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9d8d7d850ed24f92b9506b203ca63ed1.json"}}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}], "type": "posted-content", "published": "2018-12-06", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/488015", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:11:45.176Z", "modified": "2026-08-20T11:11:45.233Z"}, {"entity": "publication", "iuid": "cc6bf32e36184d888661f18dd3303c43", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cc6bf32e36184d888661f18dd3303c43.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cc6bf32e36184d888661f18dd3303c43"}}, "title": "Integrated identification and quantification error probabilities for shotgun proteomics", "authors": [{"family": "The", "given": "Matthew", "initials": "M", "orcid": "0000-0002-5401-5553", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9d8d7d850ed24f92b9506b203ca63ed1.json"}}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}], "type": "posted-content", "published": "2018-06-28", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/357285", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:10:34.829Z", "modified": "2026-08-20T11:10:34.853Z"}, {"entity": "publication", "iuid": "bcc3ce0b92d346ef938cd492f9ee633e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bcc3ce0b92d346ef938cd492f9ee633e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bcc3ce0b92d346ef938cd492f9ee633e"}}, "title": "A protein standard that emulates homology for the characterization of protein inference algorithms", "authors": [{"family": "The", "given": "Matthew", "initials": "M", "orcid": "0000-0002-5401-5553", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9d8d7d850ed24f92b9506b203ca63ed1.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e213b04f8984c8eb00c68f5bc2f6a36.json"}}, {"family": "Perez-Riverol", "given": "Yasset", "initials": "Y", "orcid": "0000-0001-6579-6941", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb4449bad29741b195a7593fc39a769d.json"}}, {"family": "Payne", "given": "Samuel H", "initials": "SH", "orcid": "0000-0002-8351-1994", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe701ec4cf24456980c1902ec61a0ab1.json"}}, {"family": "Hoopmann", "given": "Michael R", "initials": "MR", "orcid": "0000-0001-7029-7792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/04f75056428f499d9806d2fd85d50e9a.json"}}, {"family": "Palmblad", "given": "Magnus", "initials": "M", "orcid": "0000-0002-5865-8994", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/80053e2256cd4e55afc7ba916821602c.json"}}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}], "type": "posted-content", "published": "2017-12-19", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/236471", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:08:00.975Z", "modified": "2026-08-20T11:08:01.125Z"}]}