{"entity": "journal", "iuid": "6ad7148e5d58475596a23a71fee905ad", "timestamp": "2026-08-11T07:46:10.499Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Proteomics.json"}, "display": {"href": "https://publications.scilifelab.se/journal/Proteomics"}}, "title": "Proteomics", "issn": "1615-9861", "issn-l": "1615-9853", "publications_count": 19, "publications": [{"entity": "publication", "iuid": "a51aace6039f4479909a5aafa46886fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a51aace6039f4479909a5aafa46886fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a51aace6039f4479909a5aafa46886fb"}}, "title": "Proteomic and Lipidomic Profiling of Immune Cell\u2010Derived Subpopulations of Extracellular Vesicles", "authors": [{"family": "Lischnig", "given": "Anna", "initials": "A", "orcid": "0000-0001-7742-6905", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c26ce2f15ee46a9b19d59ebd3af7b96.json"}}, {"family": "Karimi", "given": "Nasibeh", "initials": "N", "orcid": "0000-0003-1499-6876", "researcher": {"href": "https://publications.scilifelab.se/researcher/14632eec875c42038aa0b6983e0ec107.json"}}, {"family": "Larsson", "given": "Per", "initials": "P", "orcid": "0000-0002-0456-8192", "researcher": {"href": "https://publications.scilifelab.se/researcher/d642894225474576b4a7c055fa7cb963.json"}}, {"family": "Ekstr\u00f6m", "given": "Karin", "initials": "K", "orcid": "0000-0001-7808-4572", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1922e7379bb4a5ca81b7db180a2d694.json"}}, {"family": "Crescitelli", "given": "Rossella", "initials": "R", "orcid": "0000-0002-1714-3169", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d4b955f26ca4a679deb090e30d0ccf1.json"}}, {"family": "Olin", "given": "Anna\u2010Carin", "initials": "A"}, {"family": "L\u00e4sser", "given": "Cecilia", "initials": "C", "orcid": "0000-0003-1279-1746", "researcher": {"href": "https://publications.scilifelab.se/researcher/e14e17d2cdb24a9f93991d83811c78b9.json"}}], "type": "journal-article", "published": "2026-01-10", "journal": {"title": "Proteomics", "issn": "1615-9853", "issn-l": null, "volume": null, "issue": null, "pages": "e70096"}, "abstract": "Extracellular vesicles (EVs) are heterogeneous and play important roles in intercellular communication, contributing to physiological and pathological processes. Since few markers currently exist to differentiate subtypes of EVs, this study aimed to determine proteomic and lipidomic differences among four EV subpopulations. Large and small EVs (L-EVs and S-EVs) were isolated from human mast cells (HMC-1) and monocytes (THP-1) by differential ultracentrifugation and then further separated by density cushions into two different densities [low-density (LD) and high-density (HD)]. L-EVs were pelleted at 16,500 \u00d7 g, and S-EVs were pelleted at 118,000 \u00d7 g. LD EVs were collected at 1.079-1.146 g/mL, while HD EVs were collected at 1.146-1.185 g/mL. The morphology, size and yield of EVs were determined by TEM and western blot. The proteome and lipidome of the EV subpopulations were determined with mass spectrometry. A total of 5364 proteins were quantified, and L-EVs LD were enriched in mitochondrial proteins such as TIMM/TOMM and MICOS proteins, while L-EVs HD were enriched in cytoskeleton- and cytokinesis-associated proteins, such as KIF proteins. S-EVs LD were enriched in tetraspanins, ADAM10 and ESCRT machinery proteins, while S-EVs HD were enriched in proteins commonly viewed as contaminants, such as histones, complement factors and collagen. Proteins involved in membrane trafficking between the plasma membrane and organelles, such as adaptor protein complexes, the conserved oligomeric Golgi complex, the trafficking protein particle complex, sortin-nexins, TBC1 domain proteins and coatomer subunits, were expressed at similar levels across all EV subtypes. Furthermore, 107 lipids were quantified, and phosphatidylethanolamine (PE) was less abundant in L-EVs LD as compared to the other EV subtypes, while ceramides were enriched in L-EVs as compared to S-EVs.This study demonstrates that there is a core proteome and lipidome that is similar across all four EV subtypes, but importantly, it also shows that a portion of the proteome and lipidome differs in EV subpopulations separated based on size and density. We suggest that these could be important markers in future EV studies and that they may reflect a different biogenesis and EV function.", "doi": "10.1002/pmic.70096", "pmid": "41518059", "labels": {"Glycoproteomics and MS Proteomics": "Service", "Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [], "notes": [], "created": "2026-01-27T13:33:15.036Z", "modified": "2026-02-11T12:53:10.765Z"}, {"entity": "publication", "iuid": "b1f3896baa1448779430a94590060e0b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b1f3896baa1448779430a94590060e0b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b1f3896baa1448779430a94590060e0b"}}, "title": "Isobaric labeling-based quantitative proteomics of FACS-purified immune cells and epithelial cells from the intestine of Crohn's disease patients reveals proteome changes of potential importance in disease pathogenesis.", "authors": [{"family": "Alfredsson", "given": "Johannes", "initials": "J"}, {"family": "Fabrik", "given": "Ivo", "initials": "I"}, {"family": "Gorreja", "given": "Frida", "initials": "F"}, {"family": "Ca\u00ebr", "given": "Charles", "initials": "C"}, {"family": "Sihlbom", "given": "Carina", "initials": "C"}, {"family": "Block", "given": "Mattias", "initials": "M"}, {"family": "B\u00f6rjesson", "given": "Lars G", "initials": "LG"}, {"family": "Lindskog", "given": "Elinor Bexe", "initials": "EB"}, {"family": "Wick", "given": "Mary Jo", "initials": "MJ"}], "type": "journal article", "published": "2023-03-00", "journal": {"title": "Proteomics", "issn": "1615-9861", "volume": "23", "issue": "5", "pages": "e2200366", "issn-l": "1615-9853"}, "abstract": "Crohn's disease (CD) is a chronic condition characterized by recurrent flares of inflammation in the gastrointestinal tract. Disease etiology is poorly understood and is characterized by dysregulated immune activation that progressively destroys intestinal tissue. Key cellular compartments in disease pathogenesis are the intestinal epithelial layer and its underlying lamina propria. While the epithelium contains predominantly epithelial cells, the lamina propria is enriched in immune cells. Deciphering proteome changes in different cell populations is important to understand CD pathogenesis. Here, using isobaric labeling-based quantitative proteomics, we perform an exploratory study to analyze in-depth proteome changes in epithelial cells, immune cells and stromal cells in CD patients compared to controls using cells purified by FACS. Our study revealed increased proteins associated with neutrophil degranulation and mitochondrial metabolism in immune cells of CD intestinal mucosa. We also found upregulation of proteins involved in glycosylation and secretory pathways in epithelial cells of CD patients, while proteins involved in mitochondrial metabolism were reduced. The distinct alterations in protein levels in immune- versus epithelial cells underscores the utility of proteome analysis of defined cell types. Moreover, our workflow allowing concomitant assessment of cell-type specific changes on an individual basis enables deeper insight into disease pathogenesis.", "doi": "10.1002/pmic.202200366", "pmid": "36479858", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2023-03-07T14:29:38.352Z", "modified": "2024-01-16T13:46:27.736Z"}, {"entity": "publication", "iuid": "d40a7e507830445abf8a74c7d18503ad", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d40a7e507830445abf8a74c7d18503ad.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d40a7e507830445abf8a74c7d18503ad"}}, "title": "Protein Paucimannosylation Is an Enriched N-Glycosylation Signature of Human Cancers.", "authors": [{"family": "Chatterjee", "given": "Sayantani", "initials": "S"}, {"family": "Lee", "given": "Ling Y", "initials": "LY"}, {"family": "Kawahara", "given": "Rebeca", "initials": "R"}, {"family": "Abrahams", "given": "Jodie L", "initials": "JL"}, {"family": "Adamczyk", "given": "Barbara", "initials": "B"}, {"family": "Anugraham", "given": "Merrina", "initials": "M"}, {"family": "Ashwood", "given": "Christopher", "initials": "C"}, {"family": "Sumer-Bayraktar", "given": "Zeynep", "initials": "Z"}, {"family": "Briggs", "given": "Matthew T", "initials": "MT"}, {"family": "Chik", "given": "Jenny H L", "initials": "JHL"}, {"family": "Everest-Dass", "given": "Arun", "initials": "A"}, {"family": "F\u00f6rster", "given": "Sarah", "initials": "S"}, {"family": "Hinneburg", "given": "Hannes", "initials": "H"}, {"family": "Leite", "given": "Katia R M", "initials": "KRM"}, {"family": "Loke", "given": "Ian", "initials": "I"}, {"family": "M\u00f6ginger", "given": "Uwe", "initials": "U"}, {"family": "Moh", "given": "Edward S X", "initials": "ESX"}, {"family": "Nakano", "given": "Miyako", "initials": "M"}, {"family": "Recuero", "given": "Saulo", "initials": "S"}, {"family": "Sethi", "given": "Manveen K", "initials": "MK"}, {"family": "Srougi", "given": "Miguel", "initials": "M"}, {"family": "Stavenhagen", "given": "Kathrin", "initials": "K"}, {"family": "Venkatakrishnan", "given": "Vignesh", "initials": "V"}, {"family": "Wongtrakul-Kish", "given": "Katherine", "initials": "K"}, {"family": "Diestel", "given": "Simone", "initials": "S"}, {"family": "Hoffmann", "given": "Peter", "initials": "P"}, {"family": "Karlsson", "given": "Niclas G", "initials": "NG"}, {"family": "Kolarich", "given": "Daniel", "initials": "D"}, {"family": "Molloy", "given": "Mark P", "initials": "MP"}, {"family": "Muders", "given": "Michael H", "initials": "MH"}, {"family": "Oehler", "given": "Martin K", "initials": "MK"}, {"family": "Packer", "given": "Nicolle H", "initials": "NH"}, {"family": "Palmisano", "given": "Giuseppe", "initials": "G"}, {"family": "Thaysen-Andersen", "given": "Morten", "initials": "M"}], "type": "journal article", "published": "2019-11-00", "journal": {"title": "Proteomics", "issn": "1615-9861", "volume": "19", "issue": "21-22", "pages": "e1900010", "issn-l": "1615-9853"}, "abstract": "While aberrant protein glycosylation is a recognized characteristic of human cancers, advances in glycoanalytics continue to discover new associations between glycoproteins and tumorigenesis. This glycomics-centric study investigates a possible link between protein paucimannosylation, an under-studied class of human N-glycosylation [Man 1-3 GlcNAc2 Fuc0-1 ], and cancer. The paucimannosidic glycans (PMGs) of 34 cancer cell lines and 133 tissue samples spanning 11 cancer types and matching non-cancerous specimens are profiled from 467 published and unpublished PGC-LC-MS/MS N-glycome datasets collected over a decade. PMGs, particularly Man2-3 GlcNAc2 Fuc1 , are prominent features of 29 cancer cell lines, but the PMG level varies dramatically across and within the cancer types (1.0-50.2%). Analyses of paired (tumor/non-tumor) and stage-stratified tissues demonstrate that PMGs are significantly enriched in tumor tissues from several cancer types including liver cancer (p = 0.0033) and colorectal cancer (p = 0.0017) and is elevated as a result of prostate cancer and chronic lymphocytic leukaemia progression (p < 0.05). Surface expression of paucimannosidic epitopes is demonstrated on human glioblastoma cells using immunofluorescence while biosynthetic involvement of N-acetyl-\u03b2-hexosaminidase is indicated by quantitative proteomics. This intriguing association between protein paucimannosylation and human cancers warrants further exploration to detail the biosynthesis, cellular location(s), protein carriers, and functions of paucimannosylation in tumorigenesis and metastasis.", "doi": "10.1002/pmic.201900010", "pmid": "31419058", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2020-01-30T16:23:52.805Z", "modified": "2024-01-16T13:46:31.263Z"}, {"entity": "publication", "iuid": "258308396bfd46d4a0e8e2cb27558cd1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/258308396bfd46d4a0e8e2cb27558cd1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/258308396bfd46d4a0e8e2cb27558cd1"}}, "title": "Systematic Development of Sandwich Immunoassays for the Plasma Secretome.", "authors": [{"family": "H\u00e4ussler", "given": "Ragna S", "initials": "RS", "orcid": "0000-0003-1664-8875", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca04d9b9132747efb7db0efb6e34756a.json"}}, {"family": "Bendes", "given": "Annika", "initials": "A"}, {"family": "Iglesias", "given": "MariaJesus", "initials": "M"}, {"family": "Sanchez-Rivera", "given": "Laura", "initials": "L"}, {"family": "Dodig-Crnkovi\u0107", "given": "Tea", "initials": "T"}, {"family": "Bystr\u00f6m", "given": "Sanna", "initials": "S"}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Birgersson", "given": "Elin", "initials": "E"}, {"family": "Dale", "given": "Matilda", "initials": "M"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}, {"family": "Tegel", "given": "Hanna", "initials": "H"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Qundos", "given": "Ulrika", "initials": "U"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2019-08-00", "journal": {"title": "Proteomics", "issn": "1615-9861", "volume": "19", "issue": "15", "pages": "e1900008", "issn-l": "1615-9853"}, "abstract": "The plasma proteome offers a clinically useful window into human health. Recent advances from highly multiplexed assays now call for appropriate pipelines to validate individual candidates. Here, a workflow is developed to build dual binder sandwich immunoassays (SIA) and for proteins predicted to be secreted into plasma. Utilizing suspension bead arrays, \u22481800 unique antibody pairs are first screened against 209 proteins with recombinant proteins as well as EDTA plasma. Employing 624 unique antibodies, dilution-dependent curves in plasma and concentration-dependent curves of full-length proteins for 102 (49%) of the targets are obtained. For 22 protein assays, the longitudinal, interindividual, and technical performance is determined in a set of plasma samples collected from 18 healthy subjects every third month over 1 year. Finally, 14 of these assays are compared with with SIAs composed of other binders, proximity extension assays, and affinity-free targeted mass spectrometry. The workflow provides a multiplexed approach to screen for SIA pairs that suggests using at least three antibodies per target. This design is applicable for a wider range of targets of the plasma proteome, and the assays can be applied for discovery but also to validate emerging candidates derived from other platforms.", "doi": "10.1002/pmic.201900008", "pmid": "31278833", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2020-01-08T10:38:13.224Z", "modified": "2021-07-08T13:44:33.106Z"}, {"entity": "publication", "iuid": "527b93a1737346c4810dd8d61f246859", "links": {"self": {"href": "https://publications.scilifelab.se/publication/527b93a1737346c4810dd8d61f246859.json"}, "display": {"href": "https://publications.scilifelab.se/publication/527b93a1737346c4810dd8d61f246859"}}, "title": "Proteomic Analysis of Endothelial Cells Exposed to Ultrasmall Nanoparticles Reveals Disruption in Paracellular and Transcellular Transport.", "authors": [{"family": "Kuruvilla", "given": "Jacob", "initials": "J"}, {"family": "Bayat", "given": "Narges", "initials": "N"}, {"family": "Cristobal", "given": "Susana", "initials": "S"}], "type": "journal article", "published": "2019-03-00", "journal": {"volume": "19", "issn": "1615-9861", "issue": "5", "pages": "e1800228", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "The large interactive surfaces of nanoparticles (NPs) increase the opportunities to develop NPs for vascular targeting. Proteomic analysis of endothelial cells exposed to NPs reveals the cellular response and turns the focus into the impairment of the endothelial permeability. Here, quantitative proteomics and transcriptome sequencing are combined to evaluate the effects of exposure to sub-lethal concentrations of TiO 2 -USNPs and TiO2 -NPs on human dermal microvascular endothelial cells. Endothelial cells react to preserve the semi-permeable properties that are essential for vascular tissue fluid homeostasis, vascular development, and angiogenesis. The main impact of the exposure was alteration of functional complexes involved in cell adhesion, vesicular transport, and cytoskeletal structure. Those are the core cellular structures that are linked to the permeability and the integrity of the endothelial tissue. Moreover, the extracellular proteins uptake along wih the NPs into the endothelial cells escape the lysosomal degradation pathway. These findings improve the understanding of the interaction of NPs with endothelial cell. The effects of the studied NPs modulating cell-cell adhesion and vesicular transport can help to evaluate the distribution of NPs via intravenous administration.", "doi": "10.1002/pmic.201800228", "pmid": "30632670", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2019-12-02T16:53:03.662Z", "modified": "2020-01-21T13:56:15.520Z"}, {"entity": "publication", "iuid": "dab092f386fa4f4cb7b66dc72ebd6ce8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dab092f386fa4f4cb7b66dc72ebd6ce8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dab092f386fa4f4cb7b66dc72ebd6ce8"}}, "title": "Mass spectrometric analysis of synaptosomal membrane preparations for the determination of brain receptors, transporters and channels.", "authors": [{"family": "Sialana", "given": "Fernando J", "initials": "FJ"}, {"family": "Gulyassy", "given": "Peter", "initials": "P"}, {"family": "M\u00e1jek", "given": "Peter", "initials": "P"}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E"}, {"family": "Kis", "given": "Viktor", "initials": "V"}, {"family": "M\u00fcller", "given": "Andr\u00e9 C", "initials": "AC"}, {"family": "Rudashevskaya", "given": "Elena L", "initials": "EL"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Bennett", "given": "Keiryn L", "initials": "KL"}, {"family": "Lubec", "given": "Gert", "initials": "G"}], "type": "journal article", "published": "2016-11-00", "journal": {"title": "Proteomics", "issn": "1615-9861", "volume": "16", "issue": "22", "pages": "2911-2920", "issn-l": "1615-9853"}, "abstract": "The molecular composition of synaptic signal transduction machineries shapes synaptic neurotransmission. The repertoire of receptors, transporters and channels (RTCs) comprises major signaling events in the brain. RTCs are conventionally studied by candidate immunohistochemistry and biochemistry, which are low throughput with resolution greatly affected by available immunoreagents and membrane interference. Therefore, a comprehensive resource of synaptic brain RTCs is still lacking. In particular, studies on the detergent-soluble synaptosomal fraction, known to contain transporters and channels, are limited. We, therefore, performed sub-synaptosomal fractionation of rat cerebral cortex, followed by trypsin/chymotrypsin sequential digestion of a detergent-soluble synaptosomal fraction and a postsynaptic density preparation, stable-isotope tryptic peptide labeling and liquid chromatography mass spectrometry. Based on the current study, a total of 4784 synaptic proteins were submitted to the ProteomExchange database (PXD001948), including 274 receptors, 394 transporters/channels and 1377 transmembrane proteins. Function-based classification assigned 1781 proteins as probable drug targets with 834 directly linked to brain disorders. The analytical approach identified 499 RTCs that are not listed in the largest, curated database for synaptosomal proteins (SynProt). This is a threefold RTC increase over all other data collected to date. Taken together, we present a protein discovery resource that can serve as a benchmark for future molecular interrogation of synaptic connectivity.", "doi": "10.1002/pmic.201600234", "pmid": "27759936", "labels": {"Tissue Profiling": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-11-05T13:10:32.334Z", "modified": "2017-11-05T13:10:32.351Z"}, {"entity": "publication", "iuid": "85b580ab4d7e4730975f19bb07edecfd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/85b580ab4d7e4730975f19bb07edecfd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/85b580ab4d7e4730975f19bb07edecfd"}}, "title": "Tissue microarray profiling in human heart failure.", "authors": [{"family": "Lal", "given": "Sean", "initials": "S"}, {"family": "Nguyen", "given": "Lisa", "initials": "L"}, {"family": "Tezone", "given": "Rhenan", "initials": "R"}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}, {"family": "Odeberg", "given": "Jacob", "initials": "J"}, {"family": "Li", "given": "Amy", "initials": "A"}, {"family": "Dos Remedios", "given": "Cristobal", "initials": "C"}], "type": "journal article", "published": "2016-09-00", "journal": {"volume": "16", "issn": "1615-9861", "issue": "17", "pages": "2319-2326", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "Tissue MicroArrays (TMAs) are a versatile tool for high-throughput protein screening, allowing qualitative analysis of a large number of samples on a single slide. We have developed a customizable TMA system that uniquely utilizes cryopreserved human cardiac samples from both heart failure and donor patients to produce formalin-fixed paraffin-embedded sections. Confirmatory upstream or downstream molecular studies can then be performed on the same (biobanked) cryopreserved tissue. In a pilot study, we applied our TMAs to screen for the expression of four-and-a-half LIM-domain 2 (FHL2), a member of the four-and-a-half LIM family. This protein has been implicated in the pathogenesis of heart failure in a variety of animal models. While FHL2 is abundant in the heart, not much is known about its expression in human heart failure. For this purpose, we generated an affinity-purified rabbit polyclonal anti-human FHL2 antibody. Our TMAs allowed high-throughput profiling of FHL2 protein using qualitative and semiquantitative immunohistochemistry that proved complementary to Western blot analysis. We demonstrated a significant relative reduction in FHL2 protein expression across different forms of human heart failure.", "doi": "10.1002/pmic.201600135", "pmid": "27364902", "labels": {"Tissue Profiling": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-03T12:59:16.084Z", "modified": "2017-11-05T12:52:25.085Z"}, {"entity": "publication", "iuid": "51d03343148f40518927bc37a26e37cd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/51d03343148f40518927bc37a26e37cd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/51d03343148f40518927bc37a26e37cd"}}, "title": "Multiplexed protein profiling by sequential affinity capture.", "authors": [{"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "Birgersson", "given": "Elin", "initials": "E"}, {"family": "Mezger", "given": "Anja", "initials": "A", "orcid": "0000-0002-7337-9547", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebf61fe41e6f43e4aec2be101de688d4.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2016-04-00", "journal": {"volume": "16", "issn": "1615-9861", "issue": "8", "pages": "1251-1256", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "Antibody microarrays enable parallelized and miniaturized analysis of clinical samples, and have proven to provide novel insights for the analysis of different proteomes. However, there are concerns that the performance of such direct labeling and single antibody assays are prone to off-target binding due to the sample context. To improve selectivity and sensitivity while maintaining the possibility to conduct multiplexed protein profiling, we developed a multiplexed and semi-automated sequential capture assay. This novel bead-based procedure encompasses a first antigen capture, labeling of captured protein targets on magnetic particles, combinatorial target elution and a read-out by a secondary capture bead array. We demonstrate in a proof-of-concept setting that target detection via two sequential affinity interactions reduced off-target contribution, while lowered background and noise levels, improved correlation to clinical values compared to single binder assays. We also compared sensitivity levels with single binder and classical sandwich assays, explored the possibility for DNA-based signal amplification, and demonstrate the applicability of the dual capture bead-based antibody microarray for biomarker analysis. Hence, the described concept enhances the possibilities for antibody array assays to be utilized for protein profiling in body fluids and beyond.", "doi": "10.1002/pmic.201500398", "pmid": "26935855", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC5071697"}], "notes": [], "created": "2017-05-03T12:59:05.678Z", "modified": "2021-07-08T13:44:33.244Z"}, {"entity": "publication", "iuid": "2f8df27edfb14ac7b9eeddf216394a87", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2f8df27edfb14ac7b9eeddf216394a87.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2f8df27edfb14ac7b9eeddf216394a87"}}, "title": "Representation of selected-reaction monitoring data in the mzQuantML data standard.", "authors": [{"family": "Qi", "given": "Da", "initials": "D"}, {"family": "Lawless", "given": "Craig", "initials": "C"}, {"family": "Teleman", "given": "Johan", "initials": "J"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}, {"family": "Holman", "given": "Stephen W", "initials": "SW"}, {"family": "Hubbard", "given": "Simon", "initials": "S"}, {"family": "Jones", "given": "Andrew R", "initials": "AR"}], "type": "journal article", "published": "2015-08-00", "journal": {"volume": "15", "issn": "1615-9861", "issue": "15", "pages": "2592-2596", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "The mzQuantML data standard was designed to capture the output of quantitative software in proteomics, to support submissions to public repositories, development of visualization software and pipeline/modular approaches. The standard is designed around a common core that can be extended to support particular types of technique through the release of semantic rules that are checked by validation software. The first release of mzQuantML supported four quantitative proteomics techniques via four sets of semantic rules: (i) intensity-based (MS(1) ) label free, (ii) MS(1) label-based (such as SILAC or N(15) ), (iii) MS(2) tag-based (iTRAQ or tandem mass tags), and (iv) spectral counting. We present an update to mzQuantML for supporting SRM techniques. The update includes representing the quantitative measurements, and associated meta-data, for SRM transitions, the mechanism for inferring peptide-level or protein-level quantitative values, and support for both label-based or label-free SRM protocols, through the creation of semantic rules and controlled vocabulary terms. We have updated the specification document for mzQuantML (version 1.0.1) and the mzQuantML validator to ensure that consistent files are produced by different exporters. We also report the capabilities for production of mzQuantML files from popular SRM software packages, such as Skyline and Anubis.", "doi": "10.1002/pmic.201400281", "pmid": "25884107", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pmc", "key": "PMC4692094"}], "notes": [], "created": "2017-05-02T12:58:20.628Z", "modified": "2020-01-21T13:53:20.419Z"}, {"entity": "publication", "iuid": "9f2f8be71cb04b10bd23d217e3118645", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9f2f8be71cb04b10bd23d217e3118645.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9f2f8be71cb04b10bd23d217e3118645"}}, "title": "Proteomics for the detection of indirect markers of steroids treatment in bovine muscle.", "authors": [{"family": "Stella", "given": "Roberto", "initials": "R"}, {"family": "Biancotto", "given": "Giancarlo", "initials": "G"}, {"family": "Arrigoni", "given": "Giorgio", "initials": "G"}, {"family": "Barrucci", "given": "Federica", "initials": "F"}, {"family": "Angeletti", "given": "Roberto", "initials": "R"}, {"family": "James", "given": "Peter", "initials": "P"}], "type": "journal article", "published": "2015-07-00", "journal": {"volume": "15", "issn": "1615-9861", "issue": "13", "pages": "2332-2341", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "Despite the ban by the European Union, anabolic steroids might still be illicitly employed in bovine meat production. The surveillance of misuse of such potentially harmful molecules is necessary to guarantee consumers' health. Analytical methods for drug residue control are based on LC-MS/MS, but their efficacy can be hindered due to undetectable residual concentrations as a result of low-dosage treatments. Screening methods based on the recognition of indirect biological effects of growth promoters' administration, such as the alteration of protein expression, can improve the efficacy of surveillance. The present study was aimed at identifying modifications in the muscle protein expression pattern between bulls treated with an ear implant (Revalor-XS\u00ae) containing trenbolone acetate (200 mg) and estradiol (40 mg), and untreated animals. The analysis of skeletal muscle was carried out using a tandem mass tags shotgun proteomics approach. We defined 28 candidate protein markers with a significantly altered expression induced by steroids administration. A subset of 18 candidate markers was validated by SRM and allowed to build a predictive model based on partial least square discriminant analysis. Our findings confirm the effectiveness of the proteomics approach as potential tool to overcome analytical limitations of drug residue monitoring.", "doi": "10.1002/pmic.201400468", "pmid": "25757884", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [], "notes": [], "created": "2017-05-02T12:58:40.910Z", "modified": "2020-01-21T13:53:20.704Z"}, {"entity": "publication", "iuid": "9b8a235e5dbf47648b747e04e2210661", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9b8a235e5dbf47648b747e04e2210661.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9b8a235e5dbf47648b747e04e2210661"}}, "title": "Defining the human gallbladder proteome by transcriptomics and affinity proteomics.", "authors": [{"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Danielsson", "given": "Angelika", "initials": "A"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2014-11-00", "journal": {"volume": "14", "issn": "1615-9861", "issue": "21-22", "pages": "2498-2507", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "Global protein analysis of human gallbladder tissue is vital for identification of molecular regulators and effectors of its physiological activity. Here, we employed a genome-wide deep RNA sequencing analysis in 28 human tissues to identify the genes overrepresented in the gallbladder and complemented it with antibody-based immunohistochemistry in 48 human tissues. We characterized human gallbladder proteins and identified 140 gallbladder-specific proteins with an elevated expression in the gallbladder as compared to the other analyzed tissues. Five genes were categorized as enriched, with at least fivefold higher levels in gallbladder, 60 genes were categorized as group enriched with elevated transcript levels in gallbladder shared with at least one other tissue and 75 genes were categorized as enhanced with higher expression than the average expression in other tissues. We explored the localization of the genes within the gallbladder through cell-type specific antibody-based protein profiling and the subcellular localization of the genes through immunofluorescent-based profiling. Finally, we revealed the biological processes and metabolic functions carried out by these genes through the use of GO, KEGG Pathway, and HMR2.0 that is compilation of the human metabolic reactions. We demonstrated the results of the combined analysis of the transcriptomics and affinity proteomics.", "doi": "10.1002/pmic.201400201", "pmid": "25175928", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:56:10.318Z", "modified": "2021-07-08T13:44:33.470Z"}, {"entity": "publication", "iuid": "dc442da430d445dc9fb4f880fea083a9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dc442da430d445dc9fb4f880fea083a9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dc442da430d445dc9fb4f880fea083a9"}}, "title": "Parallel barcoding of antibodies for DNA-assisted proteomics.", "authors": [{"family": "Dezfouli", "given": "Mahya", "initials": "M"}, {"family": "Vickovic", "given": "Sanja", "initials": "S"}, {"family": "Iglesias", "given": "Maria Jesus", "initials": "MJ"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Ahmadian", "given": "Afshin", "initials": "A"}], "type": "journal article", "published": "2014-11-00", "journal": {"volume": "14", "issn": "1615-9861", "issue": "21-22", "pages": "2432-2436", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "DNA-assisted proteomics technologies enable ultra-sensitive measurements in multiplex format using DNA-barcoded affinity reagents. Although numerous antibodies are available, nowadays targeting nearly the complete human proteome, the majority is not accessible at the quantity, concentration, or purity recommended for most bio-conjugation protocols. Here, we introduce a magnetic bead-assisted DNA-barcoding approach, applicable for several antibodies in parallel, as well as reducing required reagents quantities up to a thousand-fold. The success of DNA-barcoding and retained functionality of antibodies were demonstrated in sandwich immunoassays and standard quantitative Immuno-PCR assays. Specific DNA-barcoding of antibodies for multiplex applications was presented on suspension bead arrays with read-out on a massively parallel sequencing platform in a procedure denoted Immuno-Sequencing. Conclusively, human plasma samples were analyzed to indicate the functionality of barcoded antibodies in intended proteomics applications.", "doi": "10.1002/pmic.201400215", "pmid": "25263329", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-05-04T14:58:59.241Z", "modified": "2021-07-08T12:07:34.293Z"}, {"entity": "publication", "iuid": "4a97b8bf12f54a8690d0d5080224dd19", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4a97b8bf12f54a8690d0d5080224dd19.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4a97b8bf12f54a8690d0d5080224dd19"}}, "title": "Magnetic bead assisted labeling of antibodies at nanogram scale.", "authors": [{"family": "Dezfouli", "given": "Mahya", "initials": "M"}, {"family": "Vickovic", "given": "Sanja", "initials": "S"}, {"family": "Iglesias", "given": "Maria Jesus", "initials": "MJ"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Ahmadian", "given": "Afshin", "initials": "A"}], "type": "journal article", "published": "2014-01-00", "journal": {"volume": "14", "issn": "1615-9861", "issue": "1", "pages": "14-18", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "There are currently several initiatives that aim to produce binding reagents for proteome-wide analysis. To enable protein detection, visualization, and target quantification, covalent coupling of reporter molecules to antibodies is essential. However, current labeling protocols recommend considerable amount of antibodies, require antibody purity and are not designed for automation. Given that small amounts of antibodies are often sufficient for downstream analysis, we developed a labeling protocol that combines purification and modification of antibodies at submicrogram quantities. With the support of magnetic microspheres, automated labeling of antibodies in parallel using biotin or fluorescent dyes was achieved.", "doi": "10.1002/pmic.201300283", "pmid": "24307663", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:41.037Z", "modified": "2021-07-08T12:07:34.096Z"}, {"entity": "publication", "iuid": "87e3d2bb0d5442fe9c4911cc26f86f2f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/87e3d2bb0d5442fe9c4911cc26f86f2f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/87e3d2bb0d5442fe9c4911cc26f86f2f"}}, "title": "Selectivity analysis of single binder assays used in plasma protein profiling.", "authors": [{"family": "Neiman", "given": "Maja", "initials": "M"}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Johansson", "given": "Henrik", "initials": "H"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Nygren", "given": "Per-\u00c5ke", "initials": "P"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2013-12-00", "journal": {"volume": "13", "issn": "1615-9861", "issue": "23-24", "pages": "3406-3410", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "The increasing availability of antibodies toward human proteins enables broad explorations of the proteomic landscape in cells, tissues, and body fluids. This includes assays with antibody suspension bead arrays that generate protein profiles of plasma samples by flow cytometer analysis. However, antibody selectivity is context dependent so it is necessary to corroborate on-target detection over off-target binding. To address this, we describe a concept to directly verify interactions from antibody-coupled beads by analysis of their eluates by Western blots and MS. We demonstrate selective antibody binding in complex samples with antibodies toward a set of chosen proteins with different abundance in plasma and serum, and illustrate the need to adjust sample and bead concentrations accordingly. The presented approach will serve as an important tool for resolving differential protein profiles from antibody arrays within plasma biomarker discoveries.", "doi": "10.1002/pmic.201300030", "pmid": "24151238", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC4265267"}], "notes": [], "created": "2017-05-04T14:55:38.987Z", "modified": "2021-07-08T13:44:33.385Z"}, {"entity": "publication", "iuid": "135f821176884e3480bb7c2a8062b568", "links": {"self": {"href": "https://publications.scilifelab.se/publication/135f821176884e3480bb7c2a8062b568.json"}, "display": {"href": "https://publications.scilifelab.se/publication/135f821176884e3480bb7c2a8062b568"}}, "title": "Antibody-based profiling of cerebrospinal fluid within multiple sclerosis.", "authors": [{"family": "H\u00e4ggmark", "given": "Anna", "initials": "A"}, {"family": "Bystr\u00f6m", "given": "Sanna", "initials": "S"}, {"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "Qundos", "given": "Ulrika", "initials": "U"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Khademi", "given": "Mohsen", "initials": "M"}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"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": "2013-08-00", "journal": {"volume": "13", "issn": "1615-9861", "issue": "15", "pages": "2256-2267", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "Antibody suspension bead arrays have proven to enable multiplexed and high-throughput protein profiling in unfractionated plasma and serum samples through a direct labeling approach. We here describe the development and application of an assay for protein profiling of cerebrospinal fluid (CSF). While setting up the assay, systematic intensity differences between sample groups were observed that reflected inherent sample specific total protein amounts. Supplementing the labeling reaction with BSA and IgG diminished these differences without impairing the apparent sensitivity of the assay. We also assessed the effects of heat treatment on the analysis of CSF proteins and applied the assay to profile 43 selected proteins by 101 antibodies in 339 CSF samples from a multiple sclerosis (MS) cohort. Two proteins, GAP43 and SERPINA3 were found to have a discriminating potential with altered intensity levels between sample groups. GAP43 was detected at significantly lower levels in secondary progressive MS compared to early stages of MS and the control group of other neurological diseases. SERPINA3 instead was detected at higher levels in all MS patients compared to controls. The developed assay procedure now offers new possibilities for broad-scale protein profiling of CSF within neurological disorders.", "doi": "10.1002/pmic.201200580", "pmid": "23696371", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:38.686Z", "modified": "2021-07-08T13:44:33.026Z"}, {"entity": "publication", "iuid": "582a8c67757947af8da206b409f290b2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/582a8c67757947af8da206b409f290b2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/582a8c67757947af8da206b409f290b2"}}, "title": "Membrane protein shaving with thermolysin can be used to evaluate topology predictors.", "authors": [{"family": "Bendz", "given": "Maria", "initials": "M"}, {"family": "Skwark", "given": "Marcin", "initials": "M"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Granholm", "given": "Viktor", "initials": "V"}, {"family": "Cristobal", "given": "Susana", "initials": "S"}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L"}, {"family": "Elofsson", "given": "Arne", "initials": "A"}], "type": "journal article", "published": "2013-05-00", "journal": {"volume": "13", "issn": "1615-9861", "issue": "9", "pages": "1467-1480", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "Topology analysis of membrane proteins can be obtained by enzymatic shaving in combination with MS identification of peptides. Ideally, such analysis could provide quite detailed information about the membrane spanning regions. Here, we examine the ability of some shaving enzymes to provide large-scale analysis of membrane proteome topologies. To compare different shaving enzymes, we first analyzed the detected peptides from two over-expressed proteins. Second, we analyzed the peptides from non-over-expressed Escherichia coli membrane proteins with known structure to evaluate the shaving methods. Finally, the identified peptides were used to test the accuracy of a number of topology predictors. At the end we suggest that the usage of thermolysin, an enzyme working at the natural pH of the cell for membrane shaving, is superior because: (i) we detect a similar number of peptides and proteins using thermolysin and trypsin; (ii) thermolysin shaving can be run at a natural pH and (iii) the incubation time is quite short. (iv) Fewer detected peptides from thermolysin shaving originate from the transmembrane regions. Using thermolysin shaving we can also provide a clear separation between the best and the less accurate topology predictors, indicating that using data from shaving can provide valuable information when developing new topology predictors.", "doi": "10.1002/pmic.201200517", "pmid": "23512833", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [], "notes": [], "created": "2017-05-04T14:56:28.081Z", "modified": "2020-01-21T13:53:20.509Z"}, {"entity": "publication", "iuid": "a4e87d7afcb74dcab930371d037b5828", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a4e87d7afcb74dcab930371d037b5828.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a4e87d7afcb74dcab930371d037b5828"}}, "title": "Antibodies for profiling the human proteome-The Human Protein Atlas as a resource for cancer research.", "authors": [{"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Edqvist", "given": "Per-Henrik D", "initials": "PH"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2012-07-00", "journal": {"volume": "12", "issn": "1615-9861", "issue": "13", "pages": "2067-2077", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "In this review, we present an update on the progress of the Human Protein Atlas, with an emphasis on strategies for validating immunohistochemistry-based protein expression patterns and on the possibilities to extend the map of protein expression patterns for cancer research projects. The objectives underlying the Human Protein Atlas include (i) the generation of validated antibodies toward a major isoform of all proteins encoded by the human genome, (ii) creating an information database of protein expression patterns in normal human tissues, in cells, and in cancer, and (iii) utilizing generated antibodies and protein expression data as tools to identify clinically useful biomarkers. The success of such an effort is dependent on the validity of antibodies as specific binders of intended targets in applications used to map protein expression patterns. The development of strategies to support specific target binding is crucial and remains a challenge as a large fraction of proteins encoded by the human genome is poorly characterized, including the approximately one-third of all proteins lacking evidence of existence. Conceivable methods for validation include the use of paired antibodies, i.e. two independent antibodies targeting different and nonoverlapping epitopes on the same protein as well as comparative analysis of mRNA expression patterns with corresponding proteins.", "doi": "10.1002/pmic.201100504", "pmid": "22623277", "labels": {"Tissue Profiling": null, "Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:54.101Z", "modified": "2021-07-08T12:07:34.209Z"}, {"entity": "publication", "iuid": "64c09e829c5b4b38acb0651cdc56bed7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/64c09e829c5b4b38acb0651cdc56bed7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/64c09e829c5b4b38acb0651cdc56bed7"}}, "title": "Creation of an antibody-based subcellular protein atlas.", "authors": [{"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2010-11-00", "journal": {"volume": "10", "issn": "1615-9861", "issue": "22", "pages": "3984-3996", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "An important part for understanding the complex machinery of living cells is to know the spatial distribution of proteins all the way from organ to organelle levels. An equally important part of proteomics is to map the subcellular distribution of all human proteins. Here, we discuss methodologies for systematic subcellular profiling with emphasis on the antibody-based approach performed as a part of the Human Protein Atlas project. The considerations made when creating the subcellular protein atlas and critical parameters of this approach are discussed.", "doi": "10.1002/pmic.201000125", "pmid": "20648481", "labels": {"Spatial Proteomics": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:08.056Z", "modified": "2021-07-08T13:44:33.324Z"}, {"entity": "publication", "iuid": "948787308e4448c8b8ce4ef0438881e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/948787308e4448c8b8ce4ef0438881e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/948787308e4448c8b8ce4ef0438881e2"}}, "title": "Comparative protein profiling of serum and plasma using an antibody suspension bead array approach.", "authors": [{"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Igel", "given": "Ulrika", "initials": "U"}, {"family": "Kato", "given": "Bernet S", "initials": "BS"}, {"family": "Nicholson", "given": "George", "initials": "G"}, {"family": "Karpe", "given": "Fredrik", "initials": "F"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "comparative study", "published": "2010-02-00", "journal": {"volume": "10", "issn": "1615-9861", "issue": "3", "pages": "532-540", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "In the pursuit towards a systematic analysis of human diseases, array-based approaches within antibody proteomics offer high-throughput strategies to discover protein biomarkers in serum and plasma. To investigate the influence of sample preparation on such discovery attempts, we report on a systematic effort to compare serum and plasma protein profiles determined with an antibody suspension bead array. The intensity levels were used to define protein profiles and no significant differences between serum and plasma were observed for 79% of the 174 antibodies (targeting 156 proteins). By excluding 36 antibodies giving rise to differential intensity levels, cluster analysis revealed donor-specific rather than preparation-dependent grouping. With a cohort from a clinically relevant medical condition, the metabolic syndrome, the influence of the sample type on a multiplexed biomarker discovery approach was further investigated. Independent comparisons of protein profiles in serum and plasma revealed an antibody targeting ADAMTSL-4, a protein that would qualify to be studied further in association with the condition. In general, the preparation type had an impact on the results of the applied antibody suspension bead array, and while the technical variability was equal, plasma offered a greater biological variability and allowed to give rise to more discoveries than serum.", "doi": "10.1002/pmic.200900657", "pmid": "19953555", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:29.681Z", "modified": "2021-07-08T13:44:33.443Z"}], "created": "2017-05-09T09:12:01.329Z", "modified": "2020-11-27T13:14:06.144Z"}