{"entity": "researcher", "timestamp": "2026-08-13T18:45:28.049Z", "family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "affiliations": ["Science for Life Laboratory, KTH-Royal Institute of Technology, 171 65 Stockholm, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/9c9f4444f83e43d79c4772a430ca3969.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/9c9f4444f83e43d79c4772a430ca3969"}}, "publications": [{"entity": "publication", "iuid": "6072fdc2c2a64ec5ad2b7aa1a93ddf0b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6072fdc2c2a64ec5ad2b7aa1a93ddf0b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6072fdc2c2a64ec5ad2b7aa1a93ddf0b"}}, "title": "Met-ID: An Open-Source Software for Comprehensive Annotation of Multiple On-Tissue Chemical Modifications in MALDI-MSI.", "authors": [{"family": "Bj\u00e4rterot", "given": "Patrik", "initials": "P"}, {"family": "Nilsson", "given": "Anna", "initials": "A"}, {"family": "Shariatgorji", "given": "Reza", "initials": "R"}, {"family": "Vallianatou", "given": "Theodosia", "initials": "T", "orcid": "0000-0002-1477-7756", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae610b7669754328a119654fdfcd6af4.json"}}, {"family": "Kaya", "given": "Ibrahim", "initials": "I"}, {"family": "Svenningsson", "given": "Per", "initials": "P"}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c9f4444f83e43d79c4772a430ca3969.json"}}, {"family": "Andr\u00e9n", "given": "Per E", "initials": "PE", "orcid": "0000-0002-4062-7743", "researcher": {"href": "https://publications.scilifelab.se/researcher/64f6381de42949db8d30b56b526f3e26.json"}}], "type": "journal article", "published": "2025-04-29", "journal": {"title": "Anal. Chem.", "issn": "1520-6882", "volume": "97", "issue": "16", "pages": "9033-9041", "issn-l": "0003-2700"}, "abstract": "Here, we introduce Met-ID, a graphical user interface software designed to efficiently identify metabolites from MALDI-MSI data sets. Met-ID enables annotation of m/z features from any type of MALDI-MSI experiment, involving either derivatizing or conventional matrices. It utilizes structural information for derivatizing matrices to generate a subset of targets that contain only functional groups specific to the derivatization agent. The software is able to identify multiple derivatization sites on the same molecule, facilitating identification of the derivatized compound. This ability is exemplified by FMP-10, a reactive matrix that assists the covalent charge-tagging of molecules containing phenolic hydroxyl and/or primary or secondary amine groups. Met-ID also permits users to recalibrate data with known m/z ratios, boosting confidence in mass match results. Furthermore, Met-ID includes a database featuring MS2 spectra of numerous chemical standards, consisting of neurotransmitters and metabolites derivatized with FMP-10, alongside peaks for FMP-10 itself, all accessible directly through the software. The MS2 spectral database supports user-uploaded spectra and enables comparison of these spectra with user-provided tissue MS2 spectra for similarity assessment. Although initially installed with basic data, Met-ID is designed to be customizable, encouraging users to tailor the software to their specific needs. While several MSI-oriented software solutions exist, Met-ID combines both MS1 and MS2 functionalities. Developed in alignment with the FAIR Guiding Principles for scientific software, Met-ID is freely available as an open-source tool on GitHub, ensuring wide accessibility and collaboration.", "doi": "10.1021/acs.analchem.5c00633", "pmid": "40253716", "labels": {"Spatial Mass Spectrometry": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC12044586"}], "notes": [], "created": "2025-11-21T09:59:55.456Z", "modified": "2025-11-21T09:59:55.515Z"}, {"entity": "publication", "iuid": "7b5ab99938d64b0bade39da0944a1982", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7b5ab99938d64b0bade39da0944a1982.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7b5ab99938d64b0bade39da0944a1982"}}, "title": "Spatial multimodal analysis of transcriptomes and metabolomes in tissues.", "authors": [{"family": "Vicari", "given": "Marco", "initials": "M", "orcid": "0000-0002-3042-6278", "researcher": {"href": "https://publications.scilifelab.se/researcher/6348d0901b3e44cd80bde25cecd0205b.json"}}, {"family": "Mirzazadeh", "given": "Reza", "initials": "R"}, {"family": "Nilsson", "given": "Anna", "initials": "A"}, {"family": "Shariatgorji", "given": "Reza", "initials": "R"}, {"family": "Bj\u00e4rterot", "given": "Patrik", "initials": "P", "orcid": "0000-0002-4350-5530", "researcher": {"href": "https://publications.scilifelab.se/researcher/bea1b606a9e149c8846bf0e155c80c6c.json"}}, {"family": "Larsson", "given": "Ludvig", "initials": "L"}, {"family": "Lee", "given": "Hower", "initials": "H", "orcid": "0000-0002-8781-3623", "researcher": {"href": "https://publications.scilifelab.se/researcher/640e45f19416457c8f447f2d9321dc95.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Foyer", "given": "Julia", "initials": "J"}, {"family": "Ekvall", "given": "Markus", "initials": "M"}, {"family": "Czarnewski", "given": "Paulo", "initials": "P"}, {"family": "Zhang", "given": "Xiaoqun", "initials": "X"}, {"family": "Svenningsson", "given": "Per", "initials": "P"}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c9f4444f83e43d79c4772a430ca3969.json"}}, {"family": "Andr\u00e9n", "given": "Per E", "initials": "PE", "orcid": "0000-0002-4062-7743", "researcher": {"href": "https://publications.scilifelab.se/researcher/64f6381de42949db8d30b56b526f3e26.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2023-09-04", "journal": {"title": "Nat. Biotechnol.", "issn": "1546-1696", "issn-l": "1087-0156", "volume": null, "issue": null, "pages": null}, "abstract": "We present a spatial omics approach that combines histology, mass spectrometry imaging and spatial transcriptomics to facilitate precise measurements of mRNA transcripts and low-molecular-weight metabolites across tissue regions. The workflow is compatible with commercially available Visium glass slides. We demonstrate the potential of our method using mouse and human brain samples in the context of dopamine and Parkinson's disease.", "doi": "10.1038/s41587-023-01937-y", "pmid": "37667091", "labels": {"Spatial Mass Spectrometry": "Collaborative", "In Situ Sequencing": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41587-023-01937-y"}], "notes": [], "created": "2023-11-30T10:50:43.055Z", "modified": "2025-10-17T13:02:16.919Z"}, {"entity": "publication", "iuid": "131283b276484c18b504aa4dc0115f19", "links": {"self": {"href": "https://publications.scilifelab.se/publication/131283b276484c18b504aa4dc0115f19.json"}, "display": {"href": "https://publications.scilifelab.se/publication/131283b276484c18b504aa4dc0115f19"}}, "title": "The one-carbon pool controls mitochondrial energy metabolism via complex I and iron-sulfur clusters.", "authors": [{"family": "Schober", "given": "Florian A", "initials": "FA", "orcid": "0000-0003-4604-6170", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e9cd9d0742d40e3b5dc1abfde64d5c4.json"}}, {"family": "Moore", "given": "David", "initials": "D"}, {"family": "Atanassov", "given": "Ilian", "initials": "I", "orcid": "0000-0001-8259-2545", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8d22eab41e44364be8966abaf693de1.json"}}, {"family": "Moedas", "given": "Marco F", "initials": "MF", "orcid": "0000-0001-5461-0320", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a9cd9caaa014f4280544a243520e18c.json"}}, {"family": "Clemente", "given": "Paula", "initials": "P"}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}}, {"family": "Fissi", "given": "Najla El", "initials": "NE", "orcid": "0000-0002-6631-4630", "researcher": {"href": "https://publications.scilifelab.se/researcher/dec87cba920947028856aadb5892f7a6.json"}}, {"family": "Filograna", "given": "Roberta", "initials": "R"}, {"family": "Bucher", "given": "Anna-Lena", "initials": "AL", "orcid": "0000-0002-9391-4850", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ec4467fb36b44f0a0b1dfa056ec964d.json"}}, {"family": "Hinze", "given": "Yvonne", "initials": "Y", "orcid": "0000-0002-2966-9862", "researcher": {"href": "https://publications.scilifelab.se/researcher/a922a71f2fde43908945980353ed595a.json"}}, {"family": "The", "given": "Matthew", "initials": "M", "orcid": "0000-0002-5401-5553", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e90cde879dc41eaade439bcf951a646.json"}}, {"family": "Hedman", "given": "Erik", "initials": "E", "orcid": "0000-0003-4017-9749", "researcher": {"href": "https://publications.scilifelab.se/researcher/ffc752d50a6649248c6809ea5aec803d.json"}}, {"family": "Chernogubova", "given": "Ekaterina", "initials": "E"}, {"family": "Begzati", "given": "Arjana", "initials": "A", "orcid": "0000-0002-8770-8022", "researcher": {"href": "https://publications.scilifelab.se/researcher/a15af0dbd68445538bd92c89f6d901df.json"}}, {"family": "Wibom", "given": "Rolf", "initials": "R", "orcid": "0000-0001-6721-4642", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7d5fc666ef84a8784d8b28ecf233146.json"}}, {"family": "Jain", "given": "Mohit", "initials": "M"}, {"family": "Nilsson", "given": "Roland", "initials": "R", "orcid": "0000-0002-6020-7498", "researcher": {"href": "https://publications.scilifelab.se/researcher/0667c6d082934d818445fe0187dbb23e.json"}}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c9f4444f83e43d79c4772a430ca3969.json"}}, {"family": "Wedell", "given": "Anna", "initials": "A"}, {"family": "Freyer", "given": "Christoph", "initials": "C", "orcid": "0000-0003-0418-1673", "researcher": {"href": "https://publications.scilifelab.se/researcher/888298d25fb94acca7639063d3592373.json"}}, {"family": "Wredenberg", "given": "Anna", "initials": "A", "orcid": "0000-0002-2500-6121", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ea9ee7305424cdb8c238ef569e5be03.json"}}], "type": "journal article", "published": "2021-02-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "7", "issue": "8", "issn-l": "2375-2548"}, "abstract": "Induction of the one-carbon cycle is an early hallmark of mitochondrial dysfunction and cancer metabolism. Vital intermediary steps are localized to mitochondria, but it remains unclear how one-carbon availability connects to mitochondrial function. Here, we show that the one-carbon metabolite and methyl group donor S-adenosylmethionine (SAM) is pivotal for energy metabolism. A gradual decline in mitochondrial SAM (mitoSAM) causes hierarchical defects in fly and mouse, comprising loss of mitoSAM-dependent metabolites and impaired assembly of the oxidative phosphorylation system. Complex I stability and iron-sulfur cluster biosynthesis are directly controlled by mitoSAM levels, while other protein targets are predominantly methylated outside of the organelle before import. The mitoSAM pool follows its cytosolic production, establishing mitochondria as responsive receivers of one-carbon units. Thus, we demonstrate that cellular methylation potential is required for energy metabolism, with direct relevance for pathophysiology, aging, and cancer.", "doi": "10.1126/sciadv.abf0717", "pmid": "33608280", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "7/8/eabf0717"}, {"db": "pmc", "key": "PMC7895438"}], "notes": [], "created": "2021-12-06T13:45:25.780Z", "modified": "2024-01-16T13:48:40.799Z"}, {"entity": "publication", "iuid": "f5ae0bcb00e84e21ab0bdf4d81044a0c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f5ae0bcb00e84e21ab0bdf4d81044a0c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f5ae0bcb00e84e21ab0bdf4d81044a0c"}}, "title": "HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics.", "authors": [{"family": "Branca", "given": "Rui M M", "initials": "RM", "orcid": "0000-0003-3890-6476", "researcher": {"href": "https://publications.scilifelab.se/researcher/87d6256540174d3da581d4572f9d182a.json"}}, {"family": "Orre", "given": "Lukas M", "initials": "LM", "orcid": "0000-0002-0384-1003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b4e49a93b0143db88059c4d1e9fdc59.json"}}, {"family": "Johansson", "given": "Henrik J", "initials": "HJ", "orcid": "0000-0003-4729-4205", "researcher": {"href": "https://publications.scilifelab.se/researcher/18aebf211fa640f48a7c8d860c168e5a.json"}}, {"family": "Granholm", "given": "Viktor", "initials": "V"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "P\u00e9rez-Bercoff", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Forshed", "given": "Jenny", "initials": "J"}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c9f4444f83e43d79c4772a430ca3969.json"}}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}], "type": "journal article", "published": "2014-01-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "11", "issue": "1", "pages": "59-62", "issn-l": "1548-7091"}, "abstract": "We present a liquid chromatography-mass spectrometry (LC-MS)-based method permitting unbiased (gene prediction-independent) genome-wide discovery of protein-coding loci in higher eukaryotes. Using high-resolution isoelectric focusing (HiRIEF) at the peptide level in the 3.7-5.0 pH range and accurate peptide isoelectric point (pI) prediction, we probed the six-reading-frame translation of the human and mouse genomes and identified 98 and 52 previously undiscovered protein-coding loci, respectively. The method also enabled deep proteome coverage, identifying 13,078 human and 10,637 mouse proteins.", "doi": "10.1038/nmeth.2732", "pmid": "24240322", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "nmeth.2732"}], "notes": [], "created": "2023-06-16T12:47:04.864Z", "modified": "2023-06-16T12:47:27.234Z"}]}