{"entity": "researcher", "timestamp": "2026-08-17T02:18:03.282Z", "family": "Fuchs", "given": "Johannes", "initials": "J", "orcid": "0000-0001-9317-6969", "affiliations": [], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/65bf045dd14e45a4b61b4eb36e979bc0.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/65bf045dd14e45a4b61b4eb36e979bc0"}}, "publications": [{"entity": "publication", "iuid": "3b583a77d8b3461e8235d388087a4736", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3b583a77d8b3461e8235d388087a4736.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3b583a77d8b3461e8235d388087a4736"}}, "title": "Proteomic analysis of Down syndrome cerebrospinal fluid compared to late-onset and autosomal dominant Alzheimer\u00b4s disease.", "authors": [{"family": "Montoliu-Gaya", "given": "Laia", "initials": "L", "orcid": "0000-0001-7684-6318", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddcfba9a14f14ba7ad912dcfd5fe92d9.json"}}, {"family": "Bian", "given": "Shijia", "initials": "S"}, {"family": "Dammer", "given": "Eric B", "initials": "EB", "orcid": "0000-0003-2947-7606", "researcher": {"href": "https://publications.scilifelab.se/researcher/026547f280c8451586bf92ab028090f7.json"}}, {"family": "Alcolea", "given": "Daniel", "initials": "D", "orcid": "0000-0002-3819-3245", "researcher": {"href": "https://publications.scilifelab.se/researcher/57c67b243f6a4ea38023ea8ae4f35e88.json"}}, {"family": "Sauer", "given": "Mathias", "initials": "M"}, {"family": "Mart\u00e1-Ariza", "given": "Mitchell", "initials": "M", "orcid": "0000-0002-2121-7685", "researcher": {"href": "https://publications.scilifelab.se/researcher/cbbcf516eead45b0999f29a79d94afe1.json"}}, {"family": "Ashton", "given": "Nicholas J", "initials": "NJ"}, {"family": "Belbin", "given": "Olivia", "initials": "O", "orcid": "0000-0002-6109-6371", "researcher": {"href": "https://publications.scilifelab.se/researcher/24e4b78f7fe8416596794fd2da2d3b4b.json"}}, {"family": "Fuchs", "given": "Johannes", "initials": "J", "orcid": "0000-0001-9317-6969", "researcher": {"href": "https://publications.scilifelab.se/researcher/65bf045dd14e45a4b61b4eb36e979bc0.json"}}, {"family": "Watson", "given": "Caroline M", "initials": "CM", "orcid": "0000-0001-6574-0833", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab9107bdd4b246718df18654ffa1f67e.json"}}, {"family": "Ping", "given": "Lingyan", "initials": "L"}, {"family": "Duong", "given": "Duc M", "initials": "DM"}, {"family": "Nilsson", "given": "Johanna", "initials": "J", "orcid": "0000-0002-2856-6060", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbfa9ce69cde46568cc315f0af089d2b.json"}}, {"family": "Barroeta", "given": "Isabel", "initials": "I"}, {"family": "Lantero-Rodriguez", "given": "Juan", "initials": "J", "orcid": "0000-0002-7426-678X", "researcher": {"href": "https://publications.scilifelab.se/researcher/492e19dc85914831bad0cefe5b7eb613.json"}}, {"family": "Videla", "given": "Laura", "initials": "L", "orcid": "0000-0002-9748-8465", "researcher": {"href": "https://publications.scilifelab.se/researcher/be25e716385448deb9741619b60b91bd.json"}}, {"family": "Benejam", "given": "Bessy", "initials": "B"}, {"family": "Roberts", "given": "Blaine R", "initials": "BR", "orcid": "0000-0001-5466-0053", "researcher": {"href": "https://publications.scilifelab.se/researcher/558f53068f1e45f1a828e9fcf8d905c6.json"}}, {"family": "Blennow", "given": "Kaj", "initials": "K", "orcid": "0000-0002-1890-4193", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e646be026ce42ecbfd4d62eca3f9bce.json"}}, {"family": "Seyfried", "given": "Nicholas T", "initials": "NT", "orcid": "0000-0002-4507-624X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c940f8678724c38b1c6e98ea1b335e4.json"}}, {"family": "Levey", "given": "Allan I", "initials": "AI", "orcid": "0000-0002-3153-502X", "researcher": {"href": "https://publications.scilifelab.se/researcher/290c68791bfe4999b7a68ec208ea952b.json"}}, {"family": "Carmona-Iragui", "given": "Mar\u00eda", "initials": "M"}, {"family": "Gobom", "given": "Johan", "initials": "J", "orcid": "0000-0001-6193-6193", "researcher": {"href": "https://publications.scilifelab.se/researcher/add4c0c68cff447383c1f0184e2be943.json"}}, {"family": "Lle\u00f3", "given": "Alberto", "initials": "A", "orcid": "0000-0002-2568-5478", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f93b0e1f2b0458ea41339b0935e892b.json"}}, {"family": "Wisniewski", "given": "Thomas", "initials": "T", "orcid": "0000-0002-3379-8966", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c220af79d5a424f8bfe4e8d7c294276.json"}}, {"family": "Zetterberg", "given": "Henrik", "initials": "H", "orcid": "0000-0003-3930-4354", "researcher": {"href": "https://publications.scilifelab.se/researcher/85efee74eb4a4b38b63cf2823d204529.json"}}, {"family": "Fortea", "given": "Juan", "initials": "J", "orcid": "0000-0002-1340-638X", "researcher": {"href": "https://publications.scilifelab.se/researcher/339f94b3044b4d8b82167c6968085be2.json"}}, {"family": "Johnson", "given": "Erik C B", "initials": "ECB", "orcid": "0000-0002-0604-2944", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e9903bd257a439b9a8072f0d478a558.json"}}], "type": "journal article", "published": "2025-07-01", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "6003", "issn-l": "2041-1723"}, "abstract": "Almost all individuals with Down Syndrome (DS) develop Alzheimer's disease (AD) by mid to late life. However, the degree to which AD in DS shares pathological changes with sporadic late-onset AD (LOAD) and autosomal dominant AD (ADAD) beyond core AD biomarkers such as amyloid-\u03b2 (A\u03b2) and tau is unknown. Here, we used proteomics of cerebrospinal fluid from individuals with DS (n = 229) in the Down Alzheimer Barcelona Neuroimaging Initiative (DABNI) cohort to assess the evolution of AD pathophysiology from asymptomatic to dementia stages and compared the proteomic biomarker changes in DS to those observed in LOAD and ADAD. Although many proteomic alterations were shared across DS, LOAD, and ADAD, DS demonstrated more severe changes in immune-related proteins, extracellular matrix pathways, and plasma proteins likely related to blood-brain barrier dysfunction compared to LOAD. These changes were present in young adults with DS prior to the onset of A\u03b2 or tau pathology, suggesting they are associated with trisomy 21 and may serve as risk factors for DSAD. DSAD showed an earlier increase in markers of axonal and white matter pathology and earlier changes in markers potentially associated with cerebral amyloid angiopathy compared to ADAD. The unique features of DSAD may have important implications for treatment strategies in this population.", "doi": "10.1038/s41467-025-61054-z", "pmid": "40595720", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12214755"}, {"db": "pii", "key": "10.1038/s41467-025-61054-z"}], "notes": [], "created": "2025-10-23T13:09:26.368Z", "modified": "2025-10-23T13:09:27.449Z"}, {"entity": "publication", "iuid": "f603d9d298dc4c11ab66784e73e88159", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f603d9d298dc4c11ab66784e73e88159.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f603d9d298dc4c11ab66784e73e88159"}}, "title": "Discovery of Species-unique Peptide Biomarkers of Bacterial Pathogens by Tandem Mass Spectrometry-based Proteotyping.", "authors": [{"family": "Karlsson", "given": "Roger", "initials": "R", "orcid": "0000-0002-5919-2639", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd9b10fd0fa34dd9a3de96f3c4860e32.json"}}, {"family": "Thorsell", "given": "Annika", "initials": "A"}, {"family": "Gomila", "given": "Margarita", "initials": "M"}, {"family": "Salv\u00e0-Serra", "given": "Francisco", "initials": "F"}, {"family": "Jakobsson", "given": "Hedvig E", "initials": "HE"}, {"family": "Gonzales-Siles", "given": "Lucia", "initials": "L"}, {"family": "Ja\u00e9n-Luchoro", "given": "Daniel", "initials": "D"}, {"family": "Skovbjerg", "given": "Susann", "initials": "S"}, {"family": "Fuchs", "given": "Johannes", "initials": "J", "orcid": "0000-0001-9317-6969", "researcher": {"href": "https://publications.scilifelab.se/researcher/65bf045dd14e45a4b61b4eb36e979bc0.json"}}, {"family": "Karlsson", "given": "Anders", "initials": "A"}, {"family": "Boulund", "given": "Fredrik", "initials": "F"}, {"family": "Johnning", "given": "Anna", "initials": "A"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Moore", "given": "Edward R B", "initials": "ERB"}], "type": "journal article", "published": "2020-03-00", "journal": {"title": "Mol. Cell Proteomics", "issn": "1535-9484", "volume": "19", "issue": "3", "pages": "518-528", "issn-l": "1535-9476"}, "abstract": "Mass spectrometry (MS) and proteomics offer comprehensive characterization and identification of microorganisms and discovery of protein biomarkers that are applicable for diagnostics of infectious diseases. The use of biomarkers for diagnostics is widely applied in the clinic and the use of peptide biomarkers is increasingly being investigated for applications in the clinical laboratory. Respiratory-tract infections are a predominant cause for medical treatment, although, clinical assessments and standard clinical laboratory protocols are time-consuming and often inadequate for reliable diagnoses. Novel methods, preferably applied directly to clinical samples, excluding cultivation steps, are needed to improve diagnostics of infectious diseases, provide adequate treatment and reduce the use of antibiotics and associated development of antibiotic resistance. This study applied nano-liquid chromatography (LC) coupled with tandem MS, with a bioinformatics pipeline and an in-house database of curated high-quality reference genome sequences to identify species-unique peptides as potential biomarkers for four bacterial pathogens commonly found in respiratory tract infections (RTIs): Staphylococcus aureus; Moraxella catarrhalis; Haemophilus influenzae and Streptococcus pneumoniae The species-unique peptides were initially identified in pure cultures of bacterial reference strains, reflecting the genomic variation in the four species and, furthermore, in clinical respiratory tract samples, without prior cultivation, elucidating proteins expressed in clinical conditions of infection. For each of the four bacterial pathogens, the peptide biomarker candidates most predominantly found in clinical samples, are presented. Data are available via ProteomeXchange with identifier PXD014522. As proof-of-principle, the most promising species-unique peptides were applied in targeted tandem MS-analyses of clinical samples and their relevance for identifications of the pathogens, i.e. proteotyping, was validated, thus demonstrating their potential as peptide biomarker candidates for diagnostics of infectious diseases.", "doi": "10.1074/mcp.RA119.001667", "pmid": "31941798", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1535-9476(20)35038-6"}, {"db": "pmc", "key": "PMC7050107"}], "notes": [], "created": "2020-01-30T15:57:23.467Z", "modified": "2024-01-16T13:46:30.972Z"}]}