{"entity": "researcher", "timestamp": "2026-08-20T20:49:46.723Z", "family": "Kuster", "given": "Bernhard", "initials": "B", "orcid": "0000-0002-9094-1677", "affiliations": ["Proteomics and Bioanalytics , Technical University of Munich , Freising 85354 , Germany.", "Bavarian Biomolecular Mass Spectrometry Center , Technical University of Munich , Freising 85354 , Germany."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/5196477f29b345ccb3f4a8fc32c9fac4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/5196477f29b345ccb3f4a8fc32c9fac4"}}, "publications": [{"entity": "publication", "iuid": "bfb0fab4d8ad45d8bdecde9050e90dd6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bfb0fab4d8ad45d8bdecde9050e90dd6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bfb0fab4d8ad45d8bdecde9050e90dd6"}}, "title": "Quantification and discovery of sequence determinants of protein-per-mRNA amount in 29 human tissues.", "authors": [{"family": "Eraslan", "given": "Basak", "initials": "B"}, {"family": "Wang", "given": "Dongxue", "initials": "D", "orcid": "0000-0002-4402-0690", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2a04ae502b9c44cab6bd9f7e98d69cd5.json"}}, {"family": "Gusic", "given": "Mirjana", "initials": "M"}, {"family": "Prokisch", "given": "Holger", "initials": "H", "orcid": "0000-0003-2379-6286", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/96a24b7cb49f4fb59bd330d36636c8b9.json"}}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Pont\u00e9n", "given": "Frederik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f5294424542413c9ba4432c839c2b63.json"}}, {"family": "Wieland", "given": "Thomas", "initials": "T"}, {"family": "Hopf", "given": "Thomas", "initials": "T"}, {"family": "Hahne", "given": "Hannes", "initials": "H", "orcid": "0000-0003-3601-0051", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/826c1633eb59412192a78bd0a622a4c1.json"}}, {"family": "Kuster", "given": "Bernhard", "initials": "B", "orcid": "0000-0002-9094-1677", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5196477f29b345ccb3f4a8fc32c9fac4.json"}}, {"family": "Gagneur", "given": "Julien", "initials": "J", "orcid": "0000-0002-8924-8365", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d003f1d4e07f407b9c2ce0f40db1d53d.json"}}], "type": "journal article", "published": "2019-02-18", "journal": {"title": "Mol Syst Biol", "issn": "1744-4292", "volume": "15", "issue": "2", "pages": "e8513", "issn-l": "1744-4292"}, "abstract": "Despite their importance in determining protein abundance, a comprehensive catalogue of sequence features controlling protein-to-mRNA (PTR) ratios and a quantification of their effects are still lacking. Here, we quantified PTR ratios for 11,575 proteins across 29 human tissues using matched transcriptomes and proteomes. We estimated by regression the contribution of known sequence determinants of protein synthesis and degradation in addition to 45 mRNA and 3 protein sequence motifs that we found by association testing. While PTR ratios span more than 2 orders of magnitude, our integrative model predicts PTR ratios at a median precision of 3.2-fold. A reporter assay provided functional support for two novel UTR motifs, and an immobilized mRNA affinity competition-binding assay identified motif-specific bound proteins for one motif. Moreover, our integrative model led to a new metric of codon optimality that captures the effects of codon frequency on protein synthesis and degradation. Altogether, this study shows that a large fraction of PTR ratio variation in human tissues can be predicted from sequence, and it identifies many new candidate post-transcriptional regulatory elements.", "doi": "10.15252/msb.20188513", "pmid": "30777893", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6379048"}], "notes": [], "created": "2026-08-20T12:51:51.104Z", "modified": "2026-08-20T12:51:51.281Z"}, {"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": "https://publications-affiliated.scilifelab.se/researcher/5196477f29b345ccb3f4a8fc32c9fac4.json"}}, {"family": "Volders", "given": "Pieter-Jan", "initials": "PJ", "orcid": "0000-0002-2685-2637", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6fac44563b164dae90052b9764a8f9ab.json"}}, {"family": "Jehmlich", "given": "Nico", "initials": "N", "orcid": "0000-0002-5638-6868", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b1c3e5702c6740c6a4d553b60eee62e3.json"}}, {"family": "Vissers", "given": "Johannes P C", "initials": "JPC", "orcid": "0000-0001-6283-8456", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3cde55fba2234534a8ce709f13478e42.json"}}, {"family": "Wolan", "given": "Dennis W", "initials": "DW", "orcid": "0000-0001-9879-8353", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/635cea76374a4c90a9514aa845b7f59c.json"}}, {"family": "Wang", "given": "Ana 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"}]}