{"entity": "researcher", "timestamp": "2026-07-11T14:35:55.643Z", "family": "Karlsson", "given": "Roger", "initials": "R", "orcid": "0000-0002-5919-2639", "affiliations": [], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/bd9b10fd0fa34dd9a3de96f3c4860e32.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/bd9b10fd0fa34dd9a3de96f3c4860e32"}}, "publications": [{"entity": "publication", "iuid": "837fd5a3e240418a922a7efe0a36c863", "links": {"self": {"href": "https://publications.scilifelab.se/publication/837fd5a3e240418a922a7efe0a36c863.json"}, "display": {"href": "https://publications.scilifelab.se/publication/837fd5a3e240418a922a7efe0a36c863"}}, "title": "Identification of Streptococcus pneumoniae-Specific Proteins by Surface-Shaving Proteomics.", "authors": [{"family": "Acha Alarcon", "given": "Leonarda", "initials": "L", "orcid": "0000-0002-9453-7479", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fa254340a5b4ec39809654b54fd3481.json"}}, {"family": "Segu\u00ed", "given": "Guillem", "initials": "G"}, {"family": "Pi\u00f1eiro-Iglesias", "given": "Beatriz", "initials": "B"}, {"family": "Svetlicic", "given": "Ema", "initials": "E"}, {"family": "Kondori", "given": "Nahid", "initials": "N"}, {"family": "Gomila", "given": "Margarita", "initials": "M"}, {"family": "Moore", "given": "Edward R B", "initials": "ERB", "orcid": "0000-0001-7693-924X", "researcher": {"href": "https://publications.scilifelab.se/researcher/10b1c68436094391bfefd7de22757aba.json"}}, {"family": "Karlsson", "given": "Roger", "initials": "R", "orcid": "0000-0002-5919-2639", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd9b10fd0fa34dd9a3de96f3c4860e32.json"}}], "type": "journal article", "published": "2025-12-05", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "24", "issue": "12", "pages": "6154-6173", "issn-l": "1535-3893"}, "abstract": "Streptococcus pneumoniae (pneumococcus) is a prominent cause of bacterial pneumonia, meningitis, and septicemia, causing high morbidity and high mortality, particularly in children and the elderly. In this study, proteomics- and genomics-based approaches were used for the identification of pneumococcal protein and peptide biomarkers of S. pneumoniae for diagnostics and prospective targets for treatment. Through a pan-genome analysis, 11 S. pneumoniae strains, demonstrating genetic variation within the species, were selected for proteomic characterization. Mass spectrometry-based proteomics, in combination with bacterial surface-shaving, were used to study the cell-surface proteome of S. pneumoniae. The data obtained from three biological replicates per strain were analyzed to identify and rank the proteins and peptides according to their presence in the strains, as well as their presence in all available S. pneumoniae proteomes (8,892) archived in public databases. Several highly ranked proteins have been described as \"species-specific\" for S. pneumoniae and as surface-associated virulence factors or demonstrate highly antigenic properties. Proteins (34) previously not recognized as S. pneumoniae-specific were proposed to be novel biomarkers, demonstrating high degrees of prevalence in all analyzed proteomes, with little or no sequence similarities to closely related species but common among the genetically diverse strains included in this study.", "doi": "10.1021/acs.jproteome.5c00716", "pmid": "41212599", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12687362"}], "notes": [], "created": "2025-11-20T18:17:19.599Z", "modified": "2026-01-26T15:08:00.860Z"}, {"entity": "publication", "iuid": "7b2118e734d34424950d390248954deb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7b2118e734d34424950d390248954deb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7b2118e734d34424950d390248954deb"}}, "title": "Insights into the Metabolic Adaptations of a Carbapenem-Resistant Klebsiella pneumoniae Strain on Exposure to Sublethal Concentrations of Ertapenem.", "authors": [{"family": "Ja\u00e9n-Luchoro", "given": "Daniel", "initials": "D", "orcid": "0000-0002-5988-6227", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a821a703a144b5aa5a783e7f8043d86.json"}}, {"family": "Salv\u00e0-Serra", "given": "Francisco", "initials": "F", "orcid": "0000-0003-0173-560X", "researcher": {"href": "https://publications.scilifelab.se/researcher/49d15be15c484e6a99f22b466bf99166.json"}}, {"family": "Pi\u00f1eiro-Iglesias", "given": "Beatriz", "initials": "B", "orcid": "0000-0003-3125-0822", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f4f8871d0ce48149f88b24b6fb42c6c.json"}}, {"family": "Marathe", "given": "Nachiket", "initials": "N", "orcid": "0000-0003-2955-3402", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b806ecb68c246beacbf04550e422714.json"}}, {"family": "Moore", "given": "Edward R B", "initials": "ERB", "orcid": "0000-0001-7693-924X", "researcher": {"href": "https://publications.scilifelab.se/researcher/10b1c68436094391bfefd7de22757aba.json"}}, {"family": "Karlsson", "given": "Roger", "initials": "R", "orcid": "0000-0002-5919-2639", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd9b10fd0fa34dd9a3de96f3c4860e32.json"}}], "type": "journal article", "published": "2025-09-15", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "26", "issue": "18", "issn-l": null}, "abstract": "Klebsiella pneumoniae strains that are resistant to carbapenems are of great concern. Exposure to low concentrations of antibiotics may influence tolerance to antibiotics. Novel antibiotics and treatment options are thus needed, and this need is exacerbated by the rapid and global spread of antibiotic resistance. In this study, we determined the global proteome changes in a K. pneumoniae strain (CCUG 70747) carrying carbapenem resistance genes when exposed to low concentrations of ertapenem. Quantitative proteomics was achieved by the tandem mass tag labeling of peptides generated by trypsin proteolysis and mass spectrometry analysis. Bioinformatics analyses were used to observe changes in protein abundance, as well as the gene ontology (GO) terms and pathways associated with the differentially expressed proteins. The number of proteins detected with significant differential abundance were 87 at the highest concentration applied and 61 in the lowest concentration, all compared with the strain cultured without any antibiotics present. Several of these proteins, as well as the GO terms and pathways associated with the proteins, were linked to mechanisms of antibiotic resistance. However, this strain encodes a carbapenemase and other beta-lactamases, and thus, as expected, presented a reasonably modest adaptation in the global proteome upon exposure to the low concentrations of ertapenem applied. Nevertheless, our study identifies pathways that may lead to adaptation under sublethal concentrations of antibiotics leading to strains with higher tolerance.", "doi": "10.3390/ijms26188988", "pmid": "41009554", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12470040"}, {"db": "pii", "key": "ijms26188988"}], "notes": [], "created": "2025-10-23T12:42:51.224Z", "modified": "2025-10-23T12:42:51.506Z"}, {"entity": "publication", "iuid": "322034029b43432995b1728787b2cbba", "links": {"self": {"href": "https://publications.scilifelab.se/publication/322034029b43432995b1728787b2cbba.json"}, "display": {"href": "https://publications.scilifelab.se/publication/322034029b43432995b1728787b2cbba"}}, "title": "Mass Spectrometry-Based Analysis of Surface Proteins in Staphylococcus aureus Clinical Strains: Identification of Promising k-mer Targets for Diagnostics.", "authors": [{"family": "Svetlicic", "given": "Ema", "initials": "E", "orcid": "0009-0001-5062-5805", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f3d7fa745d34006ba08ceed4ff2c452.json"}}, {"family": "Alarcon", "given": "Leonarda A", "initials": "LA"}, {"family": "Karlsson", "given": "Roger", "initials": "R", "orcid": "0000-0002-5919-2639", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd9b10fd0fa34dd9a3de96f3c4860e32.json"}}, {"family": "Jers", "given": "Carsten", "initials": "C"}, {"family": "Mijakovic", "given": "Ivan", "initials": "I", "orcid": "0000-0002-8860-6853", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0e5dfcc215b494a860ca6d9254b0b56.json"}}], "type": "journal article", "published": "2025-09-05", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "24", "issue": "9", "pages": "4575-4585", "issn-l": "1535-3893"}, "abstract": "Surface proteins of Gram-positive bacteria are critical for adherence to host tissues, evasion of the immune system, and interaction with the environment. They can be utilized as biomarkers in diagnostics, for vaccine development, and as therapeutic targets due to their accessibility and role in pathogenicity. If utilized as diagnostic targets, surface biomarkers should be highly conserved across different strains of the pathogen, unique to the species to avoid cross-reactivity, abundantly expressed on the bacterial surface, and accessible to antibodies or detection reagents. Mass spectrometry-based proteomics methods have advanced the studies of surface proteins, often in combination with selective enrichment strategies such as tryptic \"shaving\". In this study, 11 clinical strains of Staphylococcus aureus underwent tryptic shaving to identify common surface proteins. Further bioinformatics analysis confirmed that these proteins are encoded in the core genome of S. aureus strains and contain species-specific peptides. In silico analysis identified 26 k-mer peptides in 15 surface proteins with structural accessibility to detection agents, making them the ideal targets for molecular diagnostics or as linear epitope targets for vaccine development or therapeutics. Among the identified candidates were known virulence-associated proteins such as PbpA, Sbi, and Asp23\u2500previously studied in the context of vaccines\u2500as well as uncharacterized proteins encoded by the gene loci SAUSA300_1904 and SAUSA300_1685, whose unique and surface-exposed features suggest unexplored diagnostic potential.", "doi": "10.1021/acs.jproteome.5c00321", "pmid": "40772958", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12418492"}], "notes": [], "created": "2025-10-23T16:02:13.534Z", "modified": "2025-10-23T16:02:15.152Z"}, {"entity": "publication", "iuid": "c894a8b4aad0439fba39b3372706eac5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c894a8b4aad0439fba39b3372706eac5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c894a8b4aad0439fba39b3372706eac5"}}, "title": "Identification of TRIM21 and TRIM14 as Antiviral Factors Against Langat and Zika Viruses.", "authors": [{"family": "Tran", "given": "Pham-Tue-Hung", "initials": "PT", "orcid": "0000-0002-8366-9310", "researcher": {"href": "https://publications.scilifelab.se/researcher/03f2bf1bdd4049408825fe9a91815e3a.json"}}, {"family": "Kabir", "given": "Mir Himayet", "initials": "MH"}, {"family": "Asghar", "given": "Naveed", "initials": "N", "orcid": "0000-0003-4442-8503", "researcher": {"href": "https://publications.scilifelab.se/researcher/d162f92509c44b509e72b95bfcb89456.json"}}, {"family": "Hathaway", "given": "Matthew R", "initials": "MR"}, {"family": "Hayderi", "given": "Assim", "initials": "A"}, {"family": "Karlsson", "given": "Roger", "initials": "R", "orcid": "0000-0002-5919-2639", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd9b10fd0fa34dd9a3de96f3c4860e32.json"}}, {"family": "Karlsson", "given": "Anders", "initials": "A", "orcid": "0000-0002-2927-481X", "researcher": {"href": "https://publications.scilifelab.se/researcher/47af21fe1dd34c45909bc7268b6da563.json"}}, {"family": "Taylor", "given": "Travis", "initials": "T", "orcid": "0000-0002-3819-8548", "researcher": {"href": "https://publications.scilifelab.se/researcher/75eb75025424490cb6dd702ec569e966.json"}}, {"family": "Melik", "given": "Wessam", "initials": "W", "orcid": "0000-0001-9876-6239", "researcher": {"href": "https://publications.scilifelab.se/researcher/791933a0971046d0b5dbfb7c66e8853b.json"}}, {"family": "Johansson", "given": "Magnus", "initials": "M", "orcid": "0000-0003-3962-2141", "researcher": {"href": "https://publications.scilifelab.se/researcher/e62f28d803604d9b959eee6f29855b60.json"}}], "type": "journal article", "published": "2025-04-29", "journal": {"title": "Viruses", "issn": "1999-4915", "volume": "17", "issue": "5", "issn-l": "1999-4915"}, "abstract": "Flaviviruses are usually transmitted to humans via mosquito or tick bites, whose infections may lead to severe diseases and fatality. During intracellular infection, they remodel the endoplasmic reticulum (ER) membrane to generate compartments scaffolding the replication complex (RC) where replication of the viral genome takes place. In this study, we purified the ER membrane fraction of virus infected cells to identify the proteins that were enriched during flavivirus infection. We found that tripartite motif-containing proteins (TRIMs) including TRIM38, TRIM21, and TRIM14 were significantly enriched during infection with mosquito-borne (West Nile virus strain Kunjin and Zika virus (ZIKV)) and tick-borne (Langat virus (LGTV)) flaviviruses. Further characterizations showed that TRIM21 and TRIM14 act as restriction factors against ZIKV and LGTV, while TRIM38 hinders ZIKV infection. These TRIMs worked as interferon-stimulated genes to mediate IFN-I response against LGTV and ZIKV infections. Restriction of ZIKV by TRIM14 and TRIM38 coincides with their colocalization with ZIKV NS3. TRIM14-mediated LGTV restriction coincides with its colocalization with LGTV NS3 and NS5 proteins. However, TRIM21 did not colocalize with ZIKV and LGTV NS3 or NS5 protein suggesting its antiviral activity is not dependent on direct targeting the viral enzyme. Finally, we demonstrated that overexpression of TRIM21 and TRIM14 restricted LGTV replication.", "doi": "10.3390/v17050644", "pmid": "40431659", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12116035"}, {"db": "pii", "key": "v17050644"}], "notes": [], "created": "2025-10-23T16:15:17.125Z", "modified": "2025-10-23T16:15:17.777Z"}, {"entity": "publication", "iuid": "55595ac6dbaf426ebbbaa4d12d7c4901", "links": {"self": {"href": "https://publications.scilifelab.se/publication/55595ac6dbaf426ebbbaa4d12d7c4901.json"}, "display": {"href": "https://publications.scilifelab.se/publication/55595ac6dbaf426ebbbaa4d12d7c4901"}}, "title": "Surface-Shaving of Staphylococcus aureus Strains and Quantitative Proteomic Analysis Reveal Differences in Protein Abundance of the Surfaceome.", "authors": [{"family": "Karlsson", "given": "Anders", "initials": "A"}, {"family": "Alarc\u00f3n", "given": "Leonarda Ach\u00e1", "initials": "LA", "orcid": "0000-0002-9453-7479", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fa254340a5b4ec39809654b54fd3481.json"}}, {"family": "Pi\u00f1eiro-Iglesias", "given": "Beatriz", "initials": "B"}, {"family": "Jacobsson", "given": "Gunnar", "initials": "G"}, {"family": "Skovbjerg", "given": "Susann", "initials": "S"}, {"family": "Moore", "given": "Edward R B", "initials": "ERB", "orcid": "0000-0001-7693-924X", "researcher": {"href": "https://publications.scilifelab.se/researcher/10b1c68436094391bfefd7de22757aba.json"}}, {"family": "Kopparapu", "given": "Pradeep Kumar", "initials": "PK", "orcid": "0000-0003-3941-748X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d0d9c2301c8413899a867ace6877cb2.json"}}, {"family": "Jin", "given": "Tao", "initials": "T", "orcid": "0000-0001-9039-0628", "researcher": {"href": "https://publications.scilifelab.se/researcher/03ca682de4fe4a7eb667dc63cae88335.json"}}, {"family": "Karlsson", "given": "Roger", "initials": "R", "orcid": "0000-0002-5919-2639", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd9b10fd0fa34dd9a3de96f3c4860e32.json"}}], "type": "journal article", "published": "2024-08-21", "journal": {"title": "Microorganisms", "issn": "2076-2607", "volume": "12", "issue": "8", "issn-l": "2076-2607"}, "abstract": "Staphylococcus aureus is a pathogen known to cause a wide range of infections. To find new targets for identification and to understand host-pathogen interactions, many studies have focused on surface proteins. We performed bacterial-cell surface-shaving, followed by tandem mass tag for quantitative mass spectrometry proteomics, to examine the surfaceome of S. aureus. Two steps were performed, the first step including surface protein-deficient mutants of S. aureus Newman strain lacking important virulence genes (clfA and spa, important for adhesion and immune evasion and srtAsrtB, linking surface-associated virulence factors to the surface) and the second step including isolates of different clinical origin. All strains were compared to the Newman strain. In Step 1, altogether, 7880 peptides were identified, corresponding to 1290 proteins. In Step 2, 4949 peptides were identified, corresponding to 919 proteins and for each strain, approximately 20 proteins showed differential expression compared to the Newman strain. The identified surface proteins were related to host-cell-adherence and immune-system-evasion, biofilm formation, and survival under harsh conditions. The results indicate that surface-shaving of intact S. aureus bacterial strains in combination with quantitative proteomics is a useful tool to distinguish differences in protein abundance of the surfaceome, including the expression of virulence factors.", "doi": "10.3390/microorganisms12081725", "pmid": "39203567", "labels": {"Glycoproteomics and MS Proteomics": "Service", "Clinical Genomics Gothenburg": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11357550"}, {"db": "pii", "key": "microorganisms12081725"}], "notes": [], "created": "2024-09-15T11:45:41.565Z", "modified": "2024-11-27T16:31:45.417Z"}, {"entity": "publication", "iuid": "cf882206f42147129b2b2c9d993a9c65", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cf882206f42147129b2b2c9d993a9c65.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cf882206f42147129b2b2c9d993a9c65"}}, "title": "Metataxonomic and metaproteomic profiling of the oral microbiome in oral lichen planus - a pilot study.", "authors": [{"family": "Bankvall", "given": "Maria", "initials": "M", "orcid": "0000-0003-3949-6739", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa1610a7b02e4460a6da70cd0ee8ae80.json"}}, {"family": "Carda-Di\u00e9guez", "given": "Miguel", "initials": "M", "orcid": "0000-0002-9566-0321", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcec88c7170c401f8b865b65622701ed.json"}}, {"family": "Mira", "given": "Alex", "initials": "A", "orcid": "0000-0002-9127-3877", "researcher": {"href": "https://publications.scilifelab.se/researcher/72a0e32c6e364913b6733c8475a71c7e.json"}}, {"family": "Karlsson", "given": "Anders", "initials": "A", "orcid": "0000-0002-2927-481X", "researcher": {"href": "https://publications.scilifelab.se/researcher/47af21fe1dd34c45909bc7268b6da563.json"}}, {"family": "Hass\u00e9us", "given": "Bengt", "initials": "B", "orcid": "0000-0003-3088-1550", "researcher": {"href": "https://publications.scilifelab.se/researcher/613b4f6b968b403d9d05696d40b864c7.json"}}, {"family": "Karlsson", "given": "Roger", "initials": "R", "orcid": "0000-0002-5919-2639", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd9b10fd0fa34dd9a3de96f3c4860e32.json"}}, {"family": "Robledo-Sierra", "given": "Jairo", "initials": "J", "orcid": "0000-0001-6120-8655", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b0dbeed1bd842a9b37dfb91782a4ad2.json"}}], "type": "journal article", "published": "2022-12-28", "journal": {"title": "Journal of Oral Microbiology", "issn": "2000-2297", "volume": "15", "issue": "1", "pages": "2161726", "issn-l": "2000-2297"}, "abstract": "A growing body of evidence demonstrates a different bacterial composition in the oral cavity of patients with oral lichen planus (OLP).\n\nBuccal swab samples were collected from affected and non-affected sites of six patients with reticular OLP and the healthy oral mucosa of six control subjects. 16S rRNA gene MiSeq sequencing and mass spectrometry-based proteomics were utilised to identify the metataxonomic and metaproteomic profiles of the oral microbiome in both groups.\n\nFrom the metataxonomic analysis, the most abundant species in the three subgroups were Streptococcus oralis and Pseudomonas aeruginosa, accounting for up to 70% of the total population. Principal Coordinates Analysis showed differential clustering of samples from the healthy and OLP groups. ANCOM-BC compositional analysis revealed multiple species (including P. aeruginosa and several species of Veillonella, Prevotella, Streptococcus and Neisseria) significantly over-represented in the control group and several (including Granulicatella elegans, Gemella haemolysans and G. parahaemolysans) in patients with OLP. The metaproteomic data were generally congruent and revealed that several Gemella haemolysans-belonging peptidases and other proteins with inflammatory and virulence potential were present in OLP lesions.\n\nOur data suggest that several bacterial species are associated with OLP. Future studies with larger cohorts should be conducted to determine their role in the aetiology of OLP and evaluate their potential as disease biomarkers.", "doi": "10.1080/20002297.2022.2161726", "pmid": "36605405", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9809343"}, {"db": "pii", "key": "2161726"}], "notes": [], "created": "2023-12-04T10:22:22.752Z", "modified": "2024-01-16T13:46:27.938Z"}, {"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"}]}