{"entity": "journal", "iuid": "2942ef1438c84115bdce49f1bf19b6d9", "timestamp": "2026-07-13T03:06:09.207Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Proteomics%20Clin%20Appl.json"}, "display": {"href": "https://publications.scilifelab.se/journal/Proteomics%20Clin%20Appl"}}, "title": "Proteomics Clin Appl", "issn": "1862-8354", "issn-l": "1862-8346", "publications_count": 4, "publications": [{"entity": "publication", "iuid": "7362064a1f044c14a2e50a26392e171a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7362064a1f044c14a2e50a26392e171a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7362064a1f044c14a2e50a26392e171a"}}, "title": "CSF profiling of the human brain enriched proteome reveals associations of neuromodulin and neurogranin to Alzheimer's disease.", "authors": [{"family": "Remnest\u00e5l", "given": "Julia", "initials": "J"}, {"family": "Just", "given": "David", "initials": "D"}, {"family": "Mitsios", "given": "Nicholas", "initials": "N"}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Kultima", "given": "Kim", "initials": "K"}, {"family": "Ingelsson", "given": "Martin", "initials": "M"}, {"family": "Kilander", "given": "Lena", "initials": "L"}, {"family": "Lannfelt", "given": "Lars", "initials": "L"}, {"family": "Svenningsson", "given": "Per", "initials": "P"}, {"family": "Nellg\u00e5rd", "given": "Bengt", "initials": "B"}, {"family": "Zetterberg", "given": "Henrik", "initials": "H"}, {"family": "Blennow", "given": "Kaj", "initials": "K"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "H\u00e4ggmark-M\u00e5nberg", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2016-12-00", "journal": {"volume": "10", "issn": "1862-8354", "issue": "12", "pages": "1242-1253", "title": "Proteomics Clin Appl", "issn-l": "1862-8346"}, "abstract": "This study is part of a larger effort aiming to expand the knowledge of brain-enriched proteins in human cerebrospinal fluid (CSF) and to provide novel insight into the relation between such proteins and different neurodegenerative diseases.\n\nHere 280 brain-enriched proteins in CSF from patients with Alzheimer's disease (AD), Parkinson's disease (PD) and dementia with Lewy bodies (DLB) are profiled. In total, 441 human samples of ventricular CSF collected post mortem and lumbar CSF collected ante mortem are analyzed using 376 antibodies in a suspension bead array setup, utilizing a direct labelling approach.\n\nAmong several proteins displaying differentiated profiles between sample groups, we focus here on two synaptic proteins, neuromodulin (GAP43) and neurogranin (NRGN). They are both found at elevated levels in CSF from AD patients in two independent cohorts, providing disease-associated profiles in addition to verifying and strengthening previously observed patterns. Increased levels are also observed for patients for whom the AD diagnosis was not established at the time of sampling.\n\nThese findings indicate that analyzing the brain-enriched proteins in CSF is of particular interest to increase the understanding of the CSF proteome and its relation to neurodegenerative disorders. In addition, this study lends support to the notion that measurements of these synaptic proteins could potentially be of great relevance in future diagnostic tests for AD.", "doi": "10.1002/prca.201500150", "pmid": "27604409", "labels": {"Fluorescence Tissue Profiling": "Collaborative", "Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC5157753"}], "notes": [], "created": "2017-05-03T12:59:05.983Z", "modified": "2021-07-08T13:44:33.352Z"}, {"entity": "publication", "iuid": "90b020cf6aaf415fbd5f81ac9c8c3fc8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/90b020cf6aaf415fbd5f81ac9c8c3fc8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/90b020cf6aaf415fbd5f81ac9c8c3fc8"}}, "title": "Neuroproteomic profiling of human body fluids.", "authors": [{"family": "H\u00e4ggmark", "given": "Anna", "initials": "A"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "journal article", "published": "2016-04-00", "journal": {"volume": "10", "issn": "1862-8354", "issue": "4", "pages": "485-502", "title": "Proteomics Clin Appl", "issn-l": "1862-8346"}, "abstract": "Analysis of protein expression and abundance provides a possibility to extend the current knowledge on disease-associated processes and pathways. The human brain is a complex organ and dysfunction or damage can give rise to a variety of neurological diseases. Although many proteins potentially reflecting disease progress are originating from brain, the scarce availability of human tissue material has lead to utilization of body fluids such as cerebrospinal fluid and blood in disease-related research. Within the most common neurological disorders, much effort has been spent on studying the role of a few hallmark proteins in disease pathogenesis but despite extensive investigation, the signatures they provide seem insufficient to fully understand and predict disease progress. In order to expand the view the field of neuroproteomics has lately emerged alongside developing technologies, such as affinity proteomics and mass spectrometry, for multiplexed and high-throughput protein profiling. Here, we provide an overview of how such technologies have been applied to study neurological disease and we also discuss some important considerations concerning discovery of disease-associated profiles.", "doi": "10.1002/prca.201500065", "pmid": "26286680", "labels": {"Autoimmunity and Serology Profiling": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-11-02T11:42:43.819Z", "modified": "2021-07-08T12:07:34.180Z"}, {"entity": "publication", "iuid": "0a87e15a24134172b31a8ce9ed2a3b37", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0a87e15a24134172b31a8ce9ed2a3b37.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0a87e15a24134172b31a8ce9ed2a3b37"}}, "title": "Is label-free LC-MS/MS ready for biomarker discovery?", "authors": [{"family": "Sandin", "given": "Marianne", "initials": "M"}, {"family": "Chawade", "given": "Aakash", "initials": "A"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2015-04-00", "journal": {"volume": "9", "issn": "1862-8354", "issue": "3-4", "pages": "289-294", "title": "Proteomics Clin Appl", "issn-l": "1862-8346"}, "abstract": "Label-free LC-MS methods are attractive for high-throughput quantitative proteomics, as the sample processing is straightforward and can be scaled to a large number of samples. Label-free methods therefore facilitate biomarker discovery in studies involving dozens of clinical samples. However, despite the increased popularity of label-free workflows, there is a hesitance in the research community to use it in clinical proteomics studies. Therefore, we here discuss pros and cons of label-free LC-MS/MS for biomarker discovery, and delineate the main prerequisites for its successful employment. Furthermore, we cite studies where label-free LC-MS/MS was successfully used to identify novel biomarkers, and foresee an increased acceptance of label-free techniques by the proteomics community in the near future.", "doi": "10.1002/prca.201400202", "pmid": "25656266", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [], "notes": [], "created": "2017-05-02T12:58:29.693Z", "modified": "2020-01-21T13:53:20.283Z"}, {"entity": "publication", "iuid": "51f66210bc9f4fdc8ad849038b7e87cc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/51f66210bc9f4fdc8ad849038b7e87cc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/51f66210bc9f4fdc8ad849038b7e87cc"}}, "title": "High nuclear RBM3 expression is associated with an improved prognosis in colorectal cancer.", "authors": [{"family": "Hjelm", "given": "Barbara", "initials": "B"}, {"family": "Brennan", "given": "Donal J", "initials": "DJ"}, {"family": "Zendehrokh", "given": "Nooreldin", "initials": "N"}, {"family": "Eberhard", "given": "Jakob", "initials": "J"}, {"family": "Nodin", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Gaber", "given": "Alexander", "initials": "A"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Johannesson", "given": "Henrik", "initials": "H"}, {"family": "Smaragdi", "given": "Kristina", "initials": "K"}, {"family": "Frantz", "given": "Christian", "initials": "C"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Johnson", "given": "Louis B", "initials": "LB"}, {"family": "P\u00e5hlman", "given": "Sven", "initials": "S"}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2011-12-00", "journal": {"volume": "5", "issn": "1862-8354", "issue": "11-12", "pages": "624-635", "title": "Proteomics Clin Appl", "issn-l": "1862-8346"}, "abstract": "In this study, we investigated the prognostic impact of human RBM3 expression in colorectal cancer using tissue microarray-based immunohistochemical analysis.\n\nOne polyclonal antibody and four monoclonal anti-RBM3 antibodies were generated and epitope mapped using two different methods. Bacterial display revealed five distinct epitopes for the polyclonal antibody, while the four mouse monoclonal antibodies were found to bind to three of the five epitopes. A peptide suspension bead array assay confirmed the five epitopes of the polyclonal antibody, while only one of the monoclonal antibodies could be mapped using this approach. Antibody specificity was confirmed by Western blotting and immunohistochemistry, including siRNA-mediated knock-down. Two of the antibodies (polyclonal and monoclonal) were subsequently used to analyze RBM3 expression in tumor samples from two independent colorectal cancer cohorts, one consecutive cohort (n=270) and one prospectively collected cohort of patients with cancer of the sigmoid colon (n=305). RBM3-expression was detected, with high correlation between both antibodies (R=0.81, p<0.001).\n\nIn both cohorts, tumors with high nuclear RBM3 staining had significantly prolonged the overall survival. This was also confirmed in multivariate analysis, adjusted for established prognostic factors.\n\nThese data demonstrate that high tumor-specific nuclear expression of RBM3 is an independent predictor of good prognosis in colorectal cancer.", "doi": "10.1002/prca.201100020", "pmid": "21956899", "labels": {"Tissue Profiling": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:48.538Z", "modified": "2021-07-08T13:44:33.250Z"}], "created": "2017-05-09T09:12:13.785Z", "modified": "2020-11-27T13:14:07.270Z"}