{"entity": "journal", "iuid": "624734f480604c8ca386d1eaf7e7768f", "timestamp": "2026-07-15T08:11:39.610Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Methods%20Mol.%20Biol..json"}, "display": {"href": "https://publications.scilifelab.se/journal/Methods%20Mol.%20Biol."}}, "title": "Methods Mol. Biol.", "issn": "1940-6029", "issn-l": "1064-3745", "publications_count": 42, "publications": [{"entity": "publication", "iuid": "347e692b0c264b76bcc65c0e8231ec83", "links": {"self": {"href": "https://publications.scilifelab.se/publication/347e692b0c264b76bcc65c0e8231ec83.json"}, "display": {"href": "https://publications.scilifelab.se/publication/347e692b0c264b76bcc65c0e8231ec83"}}, "title": "Exploring the O-glycomic Degradome Using Natural Mucin Libraries.", "authors": [{"family": "Tofthagen", "given": "Marthe", "initials": "M"}, {"family": "Jin", "given": "Chunsheng", "initials": "C"}, {"family": "Patel", "given": "Piyush", "initials": "P"}, {"family": "Sj\u00f6berg", "given": "Fei", "initials": "F"}, {"family": "Luis", "given": "Ana S", "initials": "AS"}, {"family": "Maciej-Hulme", "given": "Marissa L", "initials": "ML"}, {"family": "Karlsson", "given": "Niclas G", "initials": "NG"}], "type": "journal article", "published": "2025-06-11", "journal": {"title": "Methods Mol. Biol.", "issn": "1940-6029", "volume": "2942", "pages": "145-156", "issn-l": "1064-3745"}, "abstract": "The interactions between intestinal mucins and the gut microbiota significantly influence digestive processes, metabolic activities, and pathogen resistance in the gastrointestinal tract. To explore this dynamic relationship, this chapter describes a workflow for studying the degradation of mucin oligosaccharides from isolated mucins. The approach involves purifying mucins from intestinal tissues and then subjecting them to a mixture of fecal glycosidases originating from commensal bacteria. The remaining oligosaccharides attached to the mucins after glycosidase treatment are released and then characterized and quantified using liquid chromatography-mass spectrometry (LC-MS)2. This approach identifies relevant intestinal oligosaccharides that are degraded by commensal flora. By combining natural oligosaccharide characterization with measurement of their degradation, we expand the repertoire of glycan structures for studying the intestinal glycomic degradome. Few commercially available characterized glycans or glycoproteins exist that cover the unique type of glycan mixtures found in the intestines where most microbes in the gastrointestinal tract reside. The presented workflow uses relevant glyco-substrates to investigate mucus degradation patterns, which are crucial for discerning pathological conditions associated with intestinal dysbiosis.", "doi": "10.1007/978-1-0716-4627-4_12", "pmid": "40498313", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-10-23T13:27:11.477Z", "modified": "2025-11-20T18:35:23.766Z"}, {"entity": "publication", "iuid": "4002a1904ac34083802f4ed7462d16a2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4002a1904ac34083802f4ed7462d16a2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4002a1904ac34083802f4ed7462d16a2"}}, "title": "UniCarb-DB: An MS/MS Experimental Glycomic Fragmentation Database.", "authors": [{"family": "Jin", "given": "Chunsheng", "initials": "C"}, {"family": "Venkatakrishnan", "given": "Vignesh", "initials": "V"}, {"family": "Thomsson", "given": "Kristina A", "initials": "KA"}, {"family": "Aoki", "given": "Nobuyuki P", "initials": "NP"}, {"family": "Shinmachi", "given": "Daisuke", "initials": "D"}, {"family": "Aoki-Kinoshita", "given": "Kiyoko F", "initials": "KF"}, {"family": "Hayes", "given": "Catherine A", "initials": "CA"}, {"family": "Lisacek", "given": "Fr\u00e9d\u00e9rique", "initials": "F"}, {"family": "Karlsson", "given": "Niclas G", "initials": "NG"}], "type": "journal article", "published": "2024-07-12", "journal": {"title": "Methods Mol. Biol.", "issn": "1940-6029", "volume": "2836", "pages": "77-96", "issn-l": "1064-3745"}, "abstract": "Glycosylation is a unique posttranslational modification that dynamically shapes the surface of cells. Glycans attached to proteins or lipids in a cell or tissue are studied as a whole and collectively designated as a glycome. UniCarb-DB is a glycomic spectral library of tandem mass spectrometry (MS/MS) fragment data. The current version of the database consists of over 1500 entries and over 1000 unique structures. Each entry contains parent ion information with associated MS/MS spectra, metadata about the original publication, experimental conditions, and biological origin. Each structure is also associated with the GlyTouCan glycan structure repository allowing easy access to other glycomic resources. The database can be directly utilized by mass spectrometry (MS) experimentalists through the conversion of data generated by MS into structural information. Flexible online search tools along with a downloadable version of the database are easily incorporated in either commercial or open-access MS software. This chapter highlights UniCarb-DB online search tool to browse differences of isomeric structures between spectra, a peak matching search between user-generated MS/MS spectra and spectra stored in UniCarb-DB and more advanced MS tools for combined quantitative and qualitative glycomics.", "doi": "10.1007/978-1-0716-4007-4_6", "pmid": "38995537", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2024-11-27T14:03:01.535Z", "modified": "2025-11-20T18:35:25.238Z"}, {"entity": "publication", "iuid": "2b0f8e93d15043c893f2cf9373b87ac3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2b0f8e93d15043c893f2cf9373b87ac3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2b0f8e93d15043c893f2cf9373b87ac3"}}, "title": "Array-Based Multiplex and High-Throughput Serology Assays.", "authors": [{"family": "Olofsson", "given": "Jennie", "initials": "J"}, {"family": "Hellstr\u00f6m", "given": "Ceke", "initials": "C"}, {"family": "Andersson", "given": "Eni", "initials": "E"}, {"family": "Yousef", "given": "Jamil", "initials": "J"}, {"family": "Skoglund", "given": "Lovisa", "initials": "L"}, {"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R"}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A"}, {"family": "Nilsson", "given": "Peter", "initials": "P"}, {"family": "Pin", "given": "Elisa", "initials": "E"}], "type": "journal article", "published": "2023-02-14", "journal": {"title": "Methods Mol. Biol.", "issn": "1940-6029", "volume": "2628", "pages": "535-553", "issn-l": "1064-3745"}, "abstract": "The detection of antibody responses using serological tests provides means to diagnose infections, follow disease transmission, and monitor vaccination responses. The coronavirus disease 2019 (COVID-19) pandemic, caused by the SARS-CoV-2 virus, highlighted the need for rapid development of robust and reliable serological tests to follow disease spreading. Moreover, the rise of SARS-CoV-2 variants emphasized the need to monitor their transmission and prevalence in the population. For this reason, multiplex and flexible serological assays are needed to allow for rapid inclusion of antigens representing new variants as soon as they appear. In this chapter, we describe the generation and application of a multiplex serological test, based on bead array technology, to detect anti-SARS-CoV-2 antibodies in a high-throughput manner, using only a few microliters of sample. This method is currently expanding to include a multi-disease antigen panel that will allow parallel detection of antibodies towards several infectious agents.", "doi": "10.1007/978-1-0716-2978-9_31", "pmid": "36781805", "labels": {"Autoimmunity and Serology Profiling": "Technology development"}, "xrefs": [], "notes": [], "created": "2023-02-14T20:37:35.973Z", "modified": "2023-02-14T20:37:35.977Z"}, {"entity": "publication", "iuid": "ccec93113b0046be88a42d4641dcdbdb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ccec93113b0046be88a42d4641dcdbdb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ccec93113b0046be88a42d4641dcdbdb"}}, "title": "Affinity-Purification Combined with Crosslinking Mass Spectrometry for Identification and Structural Modeling of Host\u2013Pathogen Protein\u2013Protein Complexes", "authors": [{"family": "Happonen", "given": "Lotta J", "initials": "LJ"}], "type": "book-chapter", "published": "2023-00-00", "journal": {"title": "Methods Mol. Biol.", "issn": "1064-3745", "volume": "2674", "pages": "181-200", "issn-l": null}, "abstract": "Host-pathogen protein-protein interactions are highly complex and dynamic and mediate key steps in pathogen adhesion to host, host invasion, and colonization as well as immune evasion. In bacteria, these interactions most often involve specialized virulence factors or effector proteins that specifically target central host proteins. Here, I present a mass spectrometry-based proteomics approach starting with the identification of host-pathogen interactions by affinity-purification followed by mapping the specific host-pathogen protein-protein interaction interfaces by crosslinking mass spectrometry and structural modeling of the complexes.", "doi": "10.1007/978-1-0716-3243-7_12", "pmid": "37258968", "labels": {"Structural Proteomics": "Technology development"}, "xrefs": [], "notes": [], "created": "2023-12-01T13:18:08.770Z", "modified": "2023-12-01T13:20:08.290Z"}, {"entity": "publication", "iuid": "ecd740dc5c70415cb6bb93d0d667f25f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ecd740dc5c70415cb6bb93d0d667f25f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ecd740dc5c70415cb6bb93d0d667f25f"}}, "title": "Read-Based Phasing and Analysis of Phased Variants with WhatsHap.", "authors": [{"family": "Martin", "given": "Marcel", "initials": "M"}, {"family": "Ebert", "given": "Peter", "initials": "P"}, {"family": "Marschall", "given": "Tobias", "initials": "T"}], "type": "journal article", "published": "2022-11-07", "journal": {"title": "Methods Mol. Biol.", "issn": "1940-6029", "volume": "2590", "pages": "127-138", "issn-l": "1064-3745"}, "abstract": "WhatsHap is a command-line tool for phasing and phasing-related tasks. It allows to infer haplotypes in diploid and polyploid samples based on (preferably long) reads covering at least two heterozygous variants. It offers additional tools for working with phased variant calls such as computing statistics, comparing different phasings and assigning reads in alignment files to their haplotype.", "doi": "10.1007/978-1-0716-2819-5_8", "pmid": "36335496", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2023-11-02T09:12:06.368Z", "modified": "2023-11-02T09:12:06.371Z"}, {"entity": "publication", "iuid": "c23f193faa974137a510630b605f1aa8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c23f193faa974137a510630b605f1aa8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c23f193faa974137a510630b605f1aa8"}}, "title": "Proteome Integral Solubility Alteration (PISA) for High-Throughput Ligand Target Deconvolution with Increased Statistical Significance and Reduced Sample Amount.", "authors": [{"family": "Gaetani", "given": "Massimiliano", "initials": "M"}, {"family": "Zubarev", "given": "Roman A", "initials": "RA"}], "type": "journal article", "published": "2022-10-01", "journal": {"title": "Methods Mol. Biol.", "issn": "1940-6029", "issn-l": "1064-3745", "volume": "2554", "issue": null, "pages": "91-106"}, "abstract": "Proteome Integral Solubility Alteration (PISA) is a recently developed mass spectrometry-based, deep proteomics method for unbiased, proteome-wide target deconvolution of ligands, requiring no chemical ligand modification. PISA can be applied to living cells for studying target engagement in vivo or alternatively to protein extracts to identify in vitro ligand-interacting proteins. Here we describe the PISA workflow optimized in our lab. PISA improves the target discovery throughput 10-100 folds compared to the previously used proteomics methods and provides higher statistical significance for target candidates by enabling several biological replicates. Sample multiplexing makes all-in-one analysis of multiple ligands simultaneously possible. PISA dramatically reduces analysis costs, allowing many research questions in need of target deconvolution to be addressed, and unlocks the potential of miniaturizing biological models, including primary cells.", "doi": "10.1007/978-1-0716-2624-5_7", "pmid": "36178622", "labels": {"Chemical Proteomics": "Technology development"}, "xrefs": [], "notes": [], "created": "2022-10-20T17:29:58.792Z", "modified": "2022-11-04T15:03:23.473Z"}, {"entity": "publication", "iuid": "4e6c5b359e664604a53e7bc667eb424d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4e6c5b359e664604a53e7bc667eb424d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4e6c5b359e664604a53e7bc667eb424d"}}, "title": "Untargeted Metabolomics Based on Liquid Chromatography-Mass Spectrometry for the Analysis of Plasma and Erythrocyte Samples in Childhood Obesity.", "authors": [{"family": "Gonz\u00e1lez-Dom\u00ednguez", "given": "\u00c1lvaro", "initials": "\u00c1"}, {"family": "Armeni", "given": "Marina", "initials": "M"}, {"family": "Savolainen", "given": "Otto", "initials": "O"}, {"family": "Lechuga-Sancho", "given": "Alfonso Mar\u00eda", "initials": "AM"}, {"family": "Landberg", "given": "Rikard", "initials": "R"}, {"family": "Gonz\u00e1lez-Dom\u00ednguez", "given": "Ra\u00fal", "initials": "R"}], "type": "journal article", "published": "2022-09-25", "journal": {"title": "Methods Mol. Biol.", "issn": "1940-6029", "volume": "2571", "pages": "115-122", "issn-l": "1064-3745"}, "abstract": "The circulating metabolome of human peripheral blood provides valuable information to investigate the molecular mechanisms underlying the development of diseases and to discover candidate biomarkers. In particular, erythrocytes have been proposed as potential systemic indicators of the metabolic and redox status of the organism. To accomplish wide-coverage metabolomics analysis, the combination of complementary analytical techniques is necessary to manage the physicochemical complexity of the human metabolome. Herein, we describe an untargeted metabolomics method to capture the plasmatic and erythroid metabolomes based on ultrahigh-performance liquid chromatography coupled to high-resolution mass spectrometry, combining reversed-phase liquid chromatography and hydrophilic interaction liquid chromatography. The method provides comprehensive metabolomics fingerprinting of plasma and erythrocyte samples, thereby enabling the elucidation of the distinctive metabolic disturbances behind childhood obesity and associated comorbidities, such as insulin resistance.", "doi": "10.1007/978-1-0716-2699-3_11", "pmid": "36152155", "labels": {"Chalmers Mass Spectrometry Infrastructure": "Collaborative"}, "xrefs": [], "notes": [], "created": "2023-12-05T06:21:09.234Z", "modified": "2024-01-10T14:29:50.428Z"}, {"entity": "publication", "iuid": "96e5f6a37f39433689dcc1b63ba0c12a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/96e5f6a37f39433689dcc1b63ba0c12a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/96e5f6a37f39433689dcc1b63ba0c12a"}}, "title": "Detecting DNA Methylations in the Hyperthermoacidophilic Crenarchaeon Sulfolobus acidocaldarius Using SMRT Sequencing.", "authors": [{"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Couturier", "given": "Mohea", "initials": "M"}], "type": "journal article", "published": "2022-08-04", "journal": {"title": "Methods Mol. Biol.", "issn": "1940-6029", "volume": "2516", "pages": "39-50", "issn-l": "1064-3745"}, "abstract": "DNA methylations are one of the most well-known epigenetic modifications along with histone modifications and noncoding RNAs. They are found at specific sites along the DNA in all domains of life, with 5-mC and 6-mA/4-mC being well-characterized in eukaryotes and bacteria respectively, and they have not only been described as contributing to the structure of the double helix itself but also as regulators of DNA-based processes such as replication, transcription, and recombination. Different methods have been developed to accurately identify and/or map methylated motifs to decipher the involvement of DNA methylations in regulatory networks that affect the cellular state.Although DNA methylations have been detected along archaeal genomes, their involvement as regulators of DNA-based processes remains the least known. To highlight the importance of DNA methylations in the control of key cellular mechanisms and their dynamics in archaea cells, we have used single-molecule real-time (SMRT) sequencing. This sequencing technology allows the identification and direct mapping of the methylated motifs along the genome of an organism. In this chapter, we present a step-by-step protocol for detecting DNA methylations in the hyperthermophilic crenarchaeon Sulfolobus acidocaldarius using SMRT sequencing. This protocol can easily be adapted to other prokaryotes.", "doi": "10.1007/978-1-0716-2413-5_3", "pmid": "35922620", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Technology development", "NGI Long read": "Technology development", "National Genomics Infrastructure": "Technology development"}, "xrefs": [], "notes": [], "created": "2022-11-21T09:54:59.083Z", "modified": "2022-11-21T09:54:59.087Z"}, {"entity": "publication", "iuid": "6bff612fe3ec481fac4d9121712adcf7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6bff612fe3ec481fac4d9121712adcf7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6bff612fe3ec481fac4d9121712adcf7"}}, "title": "Targeted Chromosome Conformation Capture (HiCap).", "authors": [{"family": "Zhigulev", "given": "Artemy", "initials": "A"}, {"family": "Sahl\u00e9n", "given": "Pelin", "initials": "P"}], "type": "journal article", "published": "2022-07-23", "journal": {"title": "Methods Mol. Biol.", "issn": "1940-6029", "volume": "2532", "pages": "75-94", "issn-l": "1064-3745"}, "abstract": "Targeted chromosome conformation capture (HiCap) is an experimental method for detecting spatial interactions of genomic features such as promoters and/or enhancers. The protocol first describes the design of sequence capture probes. After that, it provides details on the chromosome conformation capture adapted for next-generation sequencing (Hi-C). Finally, the methodology for coupling Hi-C with sequence capture technology is described.", "doi": "10.1007/978-1-0716-2497-5_5", "pmid": "35867246", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2024-03-18T09:46:10.209Z", "modified": "2024-03-18T09:46:10.214Z"}, {"entity": "publication", "iuid": "9549996dd13046b4bd9b59646e09b7c3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9549996dd13046b4bd9b59646e09b7c3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9549996dd13046b4bd9b59646e09b7c3"}}, "title": "Proteome Integral Solubility Alteration (PISA) for High-Throughput Ligand Target Deconvolution with Increased Statistical Significance and Reduced Sample Amount (Book chapter)", "authors": [{"family": "Gaetani_M_and_Zubarev_RA", "given": "", "initials": ""}], "type": null, "published": "2021-12-09", "journal": {"title": "Methods in Molecular Biology", "issn": "1940-6029", "issn-l": "1064-3745", "volume": "in press", "issue": null, "pages": null}, "abstract": null, "doi": null, "pmid": null, "labels": {"Chemical Proteomics": "Technology development"}, "xrefs": [], "notes": [], "created": "2021-12-09T09:49:22.089Z", "modified": "2021-12-09T09:55:07.203Z"}, {"entity": "publication", "iuid": "0450402f0d164a609c7201972ac825c7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0450402f0d164a609c7201972ac825c7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0450402f0d164a609c7201972ac825c7"}}, "title": "A Glycoproteomic Approach to Identify Novel Proteoglycans.", "authors": [{"family": "Noborn", "given": "Fredrik", "initials": "F"}, {"family": "Nikpour", "given": "Mahnaz", "initials": "M"}, {"family": "Persson", "given": "Andrea", "initials": "A"}, {"family": "Sihlbom", "given": "Carina", "initials": "C"}, {"family": "Nilsson", "given": "Jonas", "initials": "J"}, {"family": "Larson", "given": "G\u00f6ran", "initials": "G"}], "type": "journal article", "published": "2021-10-10", "journal": {"title": "Methods Mol. Biol.", "issn": "1940-6029", "issn-l": "1064-3745", "volume": "2303", "issue": null, "pages": "71-85"}, "abstract": "In this chapter, we describe a glycoproteomic approach for the identification of novel chondroitin sulfate proteoglycans (CSPGs) using a combination of biochemical enrichments, enzymatic digestions, and nanoscale liquid chromatography tandem mass spectrometry (nLC-MS/MS) analysis. The identification is achieved by trypsin digestion of CSPG-containing samples, followed by enrichment of chondroitin sulfate (CS) glycopeptides by strong anion exchange chromatography (SAX). The enriched CS glycopeptides are then digested with chondroitinase ABC to depolymerize the CS polysaccharides, generating a residual hexasaccharide structure, composed of the linkage region tetrasaccharide extended with a terminal dehydrated disaccharide, still attached to the peptide. The obtained CS glycopeptides are analyzed by nLC-MS/MS, and the generated data sets are evaluated through proteomic software with adjustment in the settings to allow for glycopeptide identification. This approach has enabled the identification of several novel core proteins in human samples and in Caenorhabditis elegans. Here we specifically describe the procedure for the enrichment and characterization of CS glycopeptides from human cerebrospinal fluid (CSF).", "doi": "10.1007/978-1-0716-1398-6_7", "pmid": "34626371", "labels": {"Glycoproteomics and MS Proteomics": "Technology development"}, "xrefs": [], "notes": [], "created": "2021-12-09T21:09:01.121Z", "modified": "2024-01-16T13:46:30.043Z"}, {"entity": "publication", "iuid": "28b16b8dfd734823b09881b88015de95", "links": {"self": {"href": "https://publications.scilifelab.se/publication/28b16b8dfd734823b09881b88015de95.json"}, "display": {"href": "https://publications.scilifelab.se/publication/28b16b8dfd734823b09881b88015de95"}}, "title": "Methods to Identify and Study the Evolution of Pseudogenes Using a Phylogenetic Approach.", "authors": [{"family": "Dainat", "given": "Jacques", "initials": "J"}, {"family": "Pontarotti", "given": "Pierre", "initials": "P"}], "type": "journal article", "published": "2021-06-25", "journal": {"title": "Methods Mol. Biol.", "issn": "1940-6029", "volume": "2324", "pages": "21-34", "issn-l": "1064-3745"}, "abstract": "The discovery that pseudogenes are involved in important biological processes has excited enthusiasm and increased the research interest on them. An accurate detection and analysis of pseudogenes can be achieved using comparative methods, but only the use of phylogenetic tools can provide accurate information about their birth, their evolution and their death, hence about the impact that they have on genes and genomes. Here, phylogenetic methods that allow for studying pseudogene history are described.", "doi": "10.1007/978-1-0716-1503-4_2", "pmid": "34165706", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2021-12-10T09:55:35.691Z", "modified": "2021-12-10T09:55:35.696Z"}, {"entity": "publication", "iuid": "825c65c0adab4e2d8963acbc27d577fd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/825c65c0adab4e2d8963acbc27d577fd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/825c65c0adab4e2d8963acbc27d577fd"}}, "title": "Bead-Based Assays for Validating Proteomic Profiles in Body Fluids.", "authors": [{"family": "Bendes", "given": "Annika", "initials": "A"}, {"family": "Dale", "given": "Matilda", "initials": "M"}, {"family": "Mattsson", "given": "Cecilia", "initials": "C"}, {"family": "Dodig-Crnkovi\u0107", "given": "Tea", "initials": "T"}, {"family": "Iglesias", "given": "Maria Jesus", "initials": "MJ"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM"}, {"family": "Fredolini", "given": "Claudia", "initials": "C"}], "type": "journal article", "published": "2021-06-12", "journal": {"title": "Methods Mol. Biol.", "issn": "1940-6029", "issn-l": "1064-3745", "volume": "2344", "issue": null, "pages": "65-78"}, "abstract": "Protein biomarkers in biological fluids represent an important resource for improving the clinical management of diseases. Current proteomics technologies are capable of performing high-throughput and multiplex profiling in different types of fluids, often leading to the shortlisting of tens of candidate biomarkers per study. However, before reaching any clinical setting, these discoveries require thorough validation and an assay that would be suitable for routine analyses. In the path from biomarker discovery to validation, the performance of the assay implemented for the intended protein quantification is extremely critical toward achieving reliable and reproducible results. Development of robust sandwich immunoassays for individual candidates is challenging and labor and resource intensive, and multiplies when evaluating a panel of interesting candidates at the same time. Here we describe a versatile pipeline that facilitates the systematic and parallel development of multiple sandwich immunoassays using a bead-based technology.", "doi": "10.1007/978-1-0716-1562-1_5", "pmid": "34115352", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2021-10-05T16:26:35.615Z", "modified": "2021-11-30T15:13:57.857Z"}, {"entity": "publication", "iuid": "8d1eb5eb8a724e6eb65c2e12e279b329", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8d1eb5eb8a724e6eb65c2e12e279b329.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8d1eb5eb8a724e6eb65c2e12e279b329"}}, "title": "Recording In-Cell NMR-Spectra in Living Mammalian Cells.", "authors": [{"family": "Mate\u010dko-Burmann", "given": "Irena", "initials": "I"}, {"family": "Burmann", "given": "Bj\u00f6rn M", "initials": "BM"}], "type": "journal article", "published": "2020-07-23", "journal": {"title": "Methods Mol. Biol.", "issn": "1940-6029", "volume": "2141", "issue": null, "pages": "857-871", "issn-l": "1064-3745"}, "abstract": "At the foundation of many cellular processes as well as a large number of diseases is the (mis)folding of important intrinsically disordered proteins (IDPs). Despite tremendous scientific efforts, the factors driving their structural changes within the cellular context remain poorly understood. In-cell NMR spectroscopy enables investigation of IDPs directly in the living eukaryotic cell enabling investigation of its intermolecular interactions and ensuing modifications at an unprecedented atomic resolution. In the following protocol, we describe how to prepare in-cell NMR samples of IDPs within eukaryotic cells and how to measure these in-cell NMR samples of an IDP in its natural environment, the living mammalian cell. Furthermore, we outline a procedure to assess the intracellular recombinant protein concentration of the studied IDP based on in-cell NMR methods. We use \u03b1-synuclein as a model protein, but the presented approach is highly modular and therefore should be easily adapted and altered to the desired needs for the studies of different IDPs.", "doi": "10.1007/978-1-0716-0524-0_44", "pmid": "32696393", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2020-12-11T09:08:06.143Z", "modified": "2025-10-17T13:03:56.691Z"}, {"entity": "publication", "iuid": "e86e6226ab92413298667c47d9f2e5f1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e86e6226ab92413298667c47d9f2e5f1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e86e6226ab92413298667c47d9f2e5f1"}}, "title": "Cell-Free Protein Synthesis of Small Intrinsically Disordered Proteins for NMR Spectroscopy.", "authors": [{"family": "Isaksson", "given": "Linn\u00e9a", "initials": "L"}, {"family": "Pedersen", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2020-07-23", "journal": {"title": "Methods Mol. Biol.", "issn": "1940-6029", "volume": "2141", "issue": null, "pages": "233-245", "issn-l": "1064-3745"}, "abstract": "Cell-free protein synthesis (CFPS) is an established method to produce recombinant proteins and has been used in a wide variety of applications. The use of CFPS has almost from the onset been favorably linked to the production of isotopically labelled proteins for NMR spectroscopy as the resulting labelling of the produced protein is defined by the chosen amino acids during reaction setup. Here we describe how to set up production and isotopic labelling of small intrinsically disordered proteins (IDPs) for NMR spectroscopy applications using an E. coli-based CFPS system in batch mode.", "doi": "10.1007/978-1-0716-0524-0_11", "pmid": "32696360", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2020-12-11T09:16:35.546Z", "modified": "2025-10-17T13:03:56.727Z"}, {"entity": "publication", "iuid": "2e9d703d4303487d9fd51f2e81e7f751", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2e9d703d4303487d9fd51f2e81e7f751.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2e9d703d4303487d9fd51f2e81e7f751"}}, "title": "In Situ Sequencing: A High-Throughput, Multi-Targeted Gene Expression Profiling Technique for Cell Typing in Tissue Sections", "authors": [{"family": "Hilscher", "given": "Markus M", "initials": "MM", "orcid": "0000-0001-7782-0830", "researcher": {"href": "https://publications.scilifelab.se/researcher/1de5317c53f34bc89dabfddb0be44983.json"}}, {"family": "Gyllborg", "given": "Daniel", "initials": "D"}, {"family": "Yokota", "given": "Chika", "initials": "C"}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}], "type": "book-chapter", "published": "2020-00-00", "journal": {"title": "Methods Mol. Biol.", "issn": "1064-3745", "issn-l": null, "volume": "2148", "issue": null, "pages": "313-329"}, "abstract": "Recent advances of image-based in situ mRNA quantification methods allow to visualize where in a tissue section a set of genes is expressed. It enables to map large numbers of genes in parallel and by capturing cellular boundaries allows to assign genes to cells. Here, we present a high-throughput, multi-targeted gene expression profiling technique called in situ sequencing that is capable of localizing hundreds of genes simultaneously and supports cell type classifications that follow transcriptome-based taxonomy. In situ sequencing is a targeted, amplified, and barcoded approach using padlock probes (PLPs) and rolling circle amplification (RCA). The current protocol relies on mRNA fixation, mRNA reverse transcription, residual mRNA degradation, and PLP hybridization. PLPs are amplified by RCA and labeled with fluorophore-conjugated probes, allowing their detection under conventional fluorescence microscopes.", "doi": "10.1007/978-1-0716-0623-0_20", "pmid": "32394391", "labels": {"Bioinformatics Support for Computational Resources": "Service", "In Situ Sequencing": "Collaborative"}, "xrefs": [], "notes": [], "created": "2020-12-11T18:54:19.422Z", "modified": "2025-10-17T13:02:18.194Z"}, {"entity": "publication", "iuid": "d7fdfd620a754dffb5455e4782d7c3ec", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d7fdfd620a754dffb5455e4782d7c3ec.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d7fdfd620a754dffb5455e4782d7c3ec"}}, "title": "Array-Based Profiling of Proteins and Autoantibody Repertoires in CSF.", "authors": [{"family": "Pin", "given": "Elisa", "initials": "E"}, {"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R", "orcid": "0000-0003-1363-5796", "researcher": {"href": "https://publications.scilifelab.se/researcher/d08326da26da422ab445a26563843e79.json"}}, {"family": "Andersson", "given": "Eni", "initials": "E"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C"}, {"family": "Olofsson", "given": "Jennie", "initials": "J"}, {"family": "Jernbom Falk", "given": "August", "initials": "A"}, {"family": "Bergstr\u00f6m", "given": "Sofia", "initials": "S"}, {"family": "Remnest\u00e5l", "given": "Julia", "initials": "J"}, {"family": "Just", "given": "David", "initials": "D"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2019-08-23", "journal": {"volume": "2044", "issn": "1940-6029", "issue": null, "pages": "303-318", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "Protein profiling enabled through affinity proteomics represents a powerful strategy for analysis of complex samples such as human body fluids. Cerebrospinal fluid (CSF) is the proximal fluid of the central nervous system and is commonly analyzed in the context of neurological diseases. Through the presence of brain-derived proteins, this fluid can offer insight into the physiological state of the brain. Here, we describe multiplex and flexible protein and autoantibody profiling approaches using suspension bead arrays. Through minimal sample processing, these methods enable high-throughput analysis of hundreds of samples and proteins in one single assay and thereby provide powerful approaches for discovery of disease-associated proteins and autoantigens.", "doi": "10.1007/978-1-4939-9706-0_19", "pmid": "31432421", "labels": {"Autoimmunity and Serology Profiling": "Technology development"}, "xrefs": [], "notes": [], "created": "2019-11-06T15:11:34.083Z", "modified": "2021-07-07T15:55:21.138Z"}, {"entity": "publication", "iuid": "886ddb9b876e400c83100983072a4aa9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/886ddb9b876e400c83100983072a4aa9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/886ddb9b876e400c83100983072a4aa9"}}, "title": "Automated Cell Processing for Mass Cytometry Experiments.", "authors": [{"family": "Mikes", "given": "Jaromir", "initials": "J"}, {"family": "Olin", "given": "Axel", "initials": "A"}, {"family": "Lakshmikanth", "given": "Tadepally", "initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e81aa6b0cf4ff0a18b14098bf0fcc1.json"}}, {"family": "Chen", "given": "Yang", "initials": "Y"}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}], "type": "journal article", "published": "2019-05-12", "journal": {"volume": "1989", "issn": "1940-6029", "issue": null, "pages": "111-123", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "Mass cytometry is a powerful technology for high-dimensional single-cell measurements in millions of individual cells. Antibodies and other detection probes are coupled to elemental tags, each with a unique mass and detectable at single-cell resolution using an ICP-MS type of instrument. Given the sensitivity of the detection system, any free metal ions must be carefully removed through multiple rounds of washing in order to prevent background signal. This results in significant loss of cells. Together with cells lost during acquisition, the final data can represent as little as 10% of the starting material, seriously limiting the amount of information that can be extracted from small samples. Furthermore, complex staining protocols introduce experimental variations that limit comparisons across experiments. Here we present a cell processing and staining procedure for mass cytometry fully automated using a liquid handling robotic system and we present measures taken to optimize all steps of the protocol. These advances are applicable to both manual and automated protocols and provide a six-fold higher cell yield as compared to a standard protocol. With this increased yield and improved reproducibility this protocol now allows us to perform mass cytometry analysis using as little as 100 \u03bcL of whole blood as starting material.", "doi": "10.1007/978-1-4939-9454-0_8", "pmid": "31077102", "labels": {"Cellular Immunomonitoring": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2019-05-12T09:09:44.422Z", "modified": "2024-01-16T13:48:44.347Z"}, {"entity": "publication", "iuid": "c3f39ac7c4124db2bd9533b44d735907", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c3f39ac7c4124db2bd9533b44d735907.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c3f39ac7c4124db2bd9533b44d735907"}}, "title": "Systems-Level Immune Monitoring by Mass Cytometry.", "authors": [{"family": "Lakshmikanth", "given": "Tadepally", "initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e81aa6b0cf4ff0a18b14098bf0fcc1.json"}}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}], "type": "journal article", "published": "2019-01-23", "journal": {"volume": "1913", "issn": "1940-6029", "issue": null, "pages": "33-48", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "As therapies involving the modulation, stimulation, and deliberate excitation of the immune system are becoming routine, better methods for monitoring immune responses in human patients are needed. Mass cytometry allows for detailed profiling of all immune cell populations and their functional responses using a simple blood sample. When combined with appropriate computational analyses, the resolution for distinguishing desired responses from unproductive or even adverse reactions to immunotherapeutic interventions increases. Here we describe a core experimental and computational framework for global, systems-level immune monitoring by mass cytometry.", "doi": "10.1007/978-1-4939-8979-9_3", "pmid": "30666597", "labels": {"Cellular Immunomonitoring": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2019-01-24T12:35:10.106Z", "modified": "2024-01-16T13:48:44.813Z"}, {"entity": "publication", "iuid": "3874af5c7acd44ee826efc0f8b3c8333", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3874af5c7acd44ee826efc0f8b3c8333.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3874af5c7acd44ee826efc0f8b3c8333"}}, "title": "Computational and Statistical Analysis of Array-Based DNA Methylation Data.", "authors": [{"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "B\u00e4cklin", "given": "Christofer", "initials": "C"}, {"family": "Raine", "given": "Amanda", "initials": "A"}], "type": "journal article", "published": "2018-11-01", "journal": {"volume": "1878", "issn": "1940-6029", "issue": null, "pages": "173-191", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "The characterization of aberrant DNA methylation is emerging as a key part of the study of cancer development and phenotype. The technical advancements and decreasing costs of methods for high-throughput profiling of DNA methylation have brought about a high interest in the use of such methods in disease association studies. Here we discuss the principles for DNA methylation analysis using data from the Infinium DNA methylation BeadChip assays and describe the computational steps and statistical considerations going from processing of the raw array data to analysis of differential methylation. Moreover, we provide detailed guidelines on how to perform tumor subtype classification based on DNA methylation signatures.", "doi": "10.1007/978-1-4939-8868-6_10", "pmid": "30378076", "labels": {"National Genomics Infrastructure": "Technology development", "NGI Uppsala (SNP&SEQ Technology Platform)": "Technology development"}, "xrefs": [], "notes": [], "created": "2019-09-26T07:44:35.122Z", "modified": "2021-07-07T14:48:21.804Z"}, {"entity": "publication", "iuid": "0919104287de4c74b1a57916ead0298b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0919104287de4c74b1a57916ead0298b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0919104287de4c74b1a57916ead0298b"}}, "title": "Multiplexed Antigen Bead Arrays for the Assessment of Antibody Selectivity and Epitope Mapping.", "authors": [{"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"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": "2018-05-02", "journal": {"volume": "1785", "issn": "1940-6029", "issue": null, "pages": "239-248", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "With the increasing number of binding reagents for affinity-based investigations of the human proteome, high-throughput tools for the characterization of the used reagents become essential. For the analysis of binding selectivity, bead-based antigen arrays offer a miniaturized and parallelized assay platform to meet such needs, as they enable two-dimensional multiplexing to analyze up to 384 samples against up to 500 analytes in a single round of analysis. In this chapter, we describe our protocols for the generation of multiplex bead arrays built on immobilized protein fragments, as well as biotinylated peptides. Combined together, these two versions of antigen arrays offer a versatile approach for multiplexed characterization of antibody binding selectivity, off-target interactions, as well as mapping for the amino acids of epitopes involved in antibody binding.", "doi": "10.1007/978-1-4939-7841-0_16", "pmid": "29714023", "labels": {"Autoimmunity and Serology Profiling": "Technology development", "Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2018-09-11T08:04:59.257Z", "modified": "2021-07-08T12:07:33.951Z"}, {"entity": "publication", "iuid": "fbf86430359d4c0da55f59a2a1c70d6a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fbf86430359d4c0da55f59a2a1c70d6a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fbf86430359d4c0da55f59a2a1c70d6a"}}, "title": "High-Density Antigen Microarrays for the Assessment of Antibody Selectivity and Off-Target Binding.", "authors": [{"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R", "orcid": "0000-0003-1363-5796", "researcher": {"href": "https://publications.scilifelab.se/researcher/d08326da26da422ab445a26563843e79.json"}}, {"family": "Andersson", "given": "Eni", "initials": "E"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C"}, {"family": "Mattsson", "given": "Cecilia", "initials": "C"}, {"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"}}, {"family": "Ayoglu", "given": "Burcu", "initials": "B"}], "type": "journal article", "published": "2018-05-02", "journal": {"volume": "1785", "issn": "1940-6029", "issue": null, "pages": "231-238", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "With the increasing availability of collections of antibodies, their evaluation in terms of binding selectivity becomes an important but challenging task. Planar antigen microarrays are very suitable tools to address this task and provide a powerful proteomics platform for the characterization of the binding selectivity of antibodies toward thousands of antigens in parallel. In this chapter, we describe our in-house developed procedures for the generation of high-density planar antigen microarrays with over 21,000 features. We also provide the details of the assay protocol, which we routinely use for the assessment of binding selectivity of the polyclonal antibodies generated within the Human Protein Atlas.", "doi": "10.1007/978-1-4939-7841-0_15", "pmid": "29714022", "labels": {"Autoimmunity and Serology Profiling": "Technology development", "Affinity Proteomics Stockholm": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2018-09-11T08:04:14.919Z", "modified": "2024-01-16T13:48:46.345Z"}, {"entity": "publication", "iuid": "16fa1723ba2f4b0a982155376fa3bac4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/16fa1723ba2f4b0a982155376fa3bac4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/16fa1723ba2f4b0a982155376fa3bac4"}}, "title": "An Application-Directed, Versatile DNA FISH Platform for Research and Diagnostics.", "authors": [{"family": "Gelali", "given": "Eleni", "initials": "E"}, {"family": "Custodio", "given": "Joaquin", "initials": "J"}, {"family": "Girelli", "given": "Gabriele", "initials": "G"}, {"family": "Wernersson", "given": "Erik", "initials": "E"}, {"family": "Crosetto", "given": "Nicola", "initials": "N"}, {"family": "Bienko", "given": "Magda", "initials": "M"}], "type": "journal article", "published": "2018-04-02", "journal": {"volume": "1766", "issn": "1940-6029", "issue": null, "pages": "303-333", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "DNA fluorescence in situ hybridization (DNA FISH) has emerged as a powerful microscopy technique that allows a unique view into the composition and arrangement of the genetic material in its natural context-be it the cell nucleus in interphase, or chromosomes in metaphase spreads. The core principle of DNA FISH is the ability of fluorescently labeled DNA probes (either double- or single-stranded DNA fragments) to bind to their complementary sequences in situ in cells or tissues, revealing the location of their target as fluorescence signals detectable with a fluorescence microscope. Numerous variants and improvements of the original DNA FISH method as well as a vast repertoire of applications have been described since its inception more than 4 decades ago. In recent years, the development of many new fluorescent dyes together with drastic advancements in methods for probe generation (Boyle et al., Chromosome Res 19:901-909, 2011; Beliveau et al., Proc Natl Acad Sci U S A 109:21301-21306, 2012; Bienko et al., Nat Methods 10:122-124, 2012), as well as improvements in the resolution of microscopy technologies, have boosted the number of DNA FISH applications, particularly in the field of genome architecture (Markaki et al., Bioessays 34:412-426, 2012; Beliveau et al., Nat Commun 6:7147, 2015). However, despite these remarkable steps forward, choosing which type of DNA FISH sample preparation protocol, probe design, hybridization procedure, and detection method is best suited for a given application remains still challenging for many research labs, preventing a more widespread use of this powerful technology. Here, we present a comprehensive platform to help researchers choose which DNA FISH protocol is most suitable for their particular application. In addition, we describe computational pipelines that can be implemented for efficient DNA FISH probe design and for signal quantification. Our goal is to make DNA FISH a versatile and streamlined technique that can be easily implemented by both research and diagnostic labs.", "doi": "10.1007/978-1-4939-7768-0_17", "pmid": "29605860", "labels": {"Advanced FISH Technologies": "Technology development"}, "xrefs": [], "notes": [], "created": "2020-01-21T12:34:52.182Z", "modified": "2020-02-12T15:15:56.676Z"}, {"entity": "publication", "iuid": "8f3330c5763c4ec09b7e0026e170124c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8f3330c5763c4ec09b7e0026e170124c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8f3330c5763c4ec09b7e0026e170124c"}}, "title": "Brain Tissue Sample Stabilization and Extraction Strategies for Neuropeptidomics.", "authors": [{"family": "Fridjonsdottir", "given": "Elva", "initials": "E"}, {"family": "Nilsson", "given": "Anna", "initials": "A"}, {"family": "Wadensten", "given": "Henrik", "initials": "H"}, {"family": "Andr\u00e9n", "given": "Per E", "initials": "PE"}], "type": "journal article", "published": "2018-02-25", "journal": {"volume": "1719", "issn": "1940-6029", "issue": null, "pages": "41-49", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "Neuropeptides are bioactive peptides that are synthesized and secreted by neurons in signaling pathways in the brain. Peptides and proteins are extremely vulnerable to proteolytic cleavage when their biological surrounding changes. This makes neuropeptidomics challenging due to the rapid alterations that occur to the peptidome after harvesting of brain tissue samples. For a successful neuropeptidomic study the biological tissue sample analyzed should resemble the premortem state as much as possible. Heat stabilization has been proven to inhibit postmortem degradation by denaturing proteolytic enzymes, hence increasing identification rates of neuropeptides. Here, we describe a stabilization protocol of a frozen tissue specimen that increases the number of intact mature neuropeptides identified and minimizes interference of degradation products from abundant proteins. Additionally, we present an extraction protocol that aims to extract a wide range of hydrophilic and hydrophobic neuropeptides by using both an aqueous and an organic extraction medium.", "doi": "10.1007/978-1-4939-7537-2_2", "pmid": "29476502", "labels": {"Spatial Mass Spectrometry": "Technology development"}, "xrefs": [], "notes": [], "created": "2020-01-24T08:59:41.138Z", "modified": "2021-12-03T11:58:13.707Z"}, {"entity": "publication", "iuid": "1fbfeb18c3aa4a91b322f65e6504dbe5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1fbfeb18c3aa4a91b322f65e6504dbe5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1fbfeb18c3aa4a91b322f65e6504dbe5"}}, "title": "High-Density Serum/Plasma Reverse Phase Protein Arrays.", "authors": [{"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C"}, {"family": "Dodig-Crnkovi\u0107", "given": "Tea", "initials": "T"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"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"}}, {"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R", "orcid": "0000-0003-1363-5796", "researcher": {"href": "https://publications.scilifelab.se/researcher/d08326da26da422ab445a26563843e79.json"}}], "type": "journal article", "published": "2017-07-05", "journal": {"volume": "1619", "issn": "1940-6029", "issue": null, "pages": "229-238", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "In-depth exploration and characterization of human serum and plasma proteomes is an attractive strategy for the identification of potential prognostic or diagnostic biomarkers. The possibility of analyzing larger numbers of samples in a high-throughput fashion has markedly increased with affinity-based microarrays, thus providing higher statistical power to these biomarker studies. Here, we describe a protocol for high-density serum and plasma reverse phase protein arrays (RPPAs). We demonstrate how a biobank of 12,392 samples was immobilized and analyzed on a single microarray slide, allowing high-quality profiling of abundant target proteins across all samples in one assay.", "doi": "10.1007/978-1-4939-7057-5_18", "pmid": "28674890", "labels": {"Autoimmunity and Serology Profiling": "Technology development", "Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-11-02T11:36:59.288Z", "modified": "2021-07-08T12:07:33.995Z"}, {"entity": "publication", "iuid": "491a561955fc44909ca8782a3b02cbdd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/491a561955fc44909ca8782a3b02cbdd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/491a561955fc44909ca8782a3b02cbdd"}}, "title": "Bead-Based and Multiplexed Immunoassays for Protein Profiling via Sequential Affinity Capture.", "authors": [{"family": "Birgersson", "given": "Elin", "initials": "E"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Ayoglu", "given": "Burcu", "initials": "B"}], "type": "journal article", "published": "2017-07-05", "journal": {"volume": "1619", "issn": "1940-6029", "issue": null, "pages": "45-54", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "Antibody microarrays offer high-throughput immunoassays for multiplexed analyses of clinical samples. For such approaches, samples are either labeled in solution to enable a direct readout on the single binder assay format or detected by matched pairs of capture and detection antibodies in dual binder assay format, also known as sandwich assays. Aiming to benefit from the flexibility and capacity offered by single binder assay readout and the specificity and sensitivity of dual binder assays, we developed a multiplexed dual binder procedure that is based on a sequential, rather than combined, antigen binding. The method, entitled dual capture assay (DCA), is composed of an initial antigen capture by antibodies on beads, followed by labeling of captured protein targets on beads, combinatorial elution steps at high and low pH, and a readout using a secondary bead array. Compared to classical single binder assays, the described method demonstrated several advantages such as reduced contribution of off-target binding, lower noise levels, and improved correlation when comparing with clinical reference values. This procedure describes a novel and versatile immunoassay strategy for proteome profiling in body fluids.", "doi": "10.1007/978-1-4939-7057-5_4", "pmid": "28674876", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-10-30T10:17:20.403Z", "modified": "2021-07-08T12:07:34.090Z"}, {"entity": "publication", "iuid": "38aaed196e084a14b7adad22ab9523a9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/38aaed196e084a14b7adad22ab9523a9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/38aaed196e084a14b7adad22ab9523a9"}}, "title": "Neuroproteomic Profiling of Cerebrospinal Fluid (CSF) by Multiplexed Affinity Arrays.", "authors": [{"family": "H\u00e4ggmark-M\u00e5nberg", "given": "Anna", "initials": "A"}, {"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": "2017-05-17", "journal": {"volume": "1598", "issn": "1940-6029", "issue": null, "pages": "247-254", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "Protein profiling through affinity proteomic approaches represents a powerful strategy for the analysis of human body fluids. Cerebrospinal fluid (CSF), being the fluid proximal to the central nervous system, is commonly analyzed in the context of neurological diseases, and can offer novel insights into the physiological state of the brain. Ultimately, and by analyzing the presence of brain-derived proteins in larger sets of samples that represent different phenotypes, profiling of CSF may serve as an important source to discover and verify disease-associated markers. Here, we describe a multiplexed and flexible protein profiling approach using antibody-based assays on suspension bead arrays. Through streamlined sample processing, protein biotinylation, and single-binder assay readout, this method enables high-throughput neuroproteomic analysis of up to 384 proteins in 384 samples.", "doi": "10.1007/978-1-4939-6952-4_11", "pmid": "28508365", "labels": {"Autoimmunity and Serology Profiling": "Technology development", "Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-10-30T10:18:02.763Z", "modified": "2021-07-08T12:07:34.045Z"}, {"entity": "publication", "iuid": "21ac326da0ee45f5bd33bf1335b9fa92", "links": {"self": {"href": "https://publications.scilifelab.se/publication/21ac326da0ee45f5bd33bf1335b9fa92.json"}, "display": {"href": "https://publications.scilifelab.se/publication/21ac326da0ee45f5bd33bf1335b9fa92"}}, "title": "Antibody Validation by Immunoprecipitation Followed by Mass Spectrometry Analysis.", "authors": [{"family": "Persson", "given": "Helena", "initials": "H"}, {"family": "Preger", "given": "Charlotta", "initials": "C"}, {"family": "Marcon", "given": "Edyta", "initials": "E"}, {"family": "Lengqvist", "given": "Johan", "initials": "J"}, {"family": "Gr\u00e4slund", "given": "Susanne", "initials": "S"}], "type": "journal article", "published": "2017-03-04", "journal": {"volume": "1575", "issn": "1940-6029", "issue": null, "pages": "175-187", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "We describe a mass spectrometry-based approach for validation of antibody specificity. This method allows validation of antibodies or antibody fragments, against their endogenous targets. It can assess if the antibody is able to bind to its native antigen in cell lysates among thousands of other proteins, DNA, RNA, and other cellular components. In addition, it identifies other proteins the antibody is able to immunoprecipitate allowing for the assessment of antibody specificity and selectivity. This method is easily scalable, adaptable to different cell lines and conditions and has been shown to be reproducible between multiple laboratories.", "doi": "10.1007/978-1-4939-6857-2_10", "pmid": "28255880", "labels": {"Drug Discovery and Development": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-25T06:05:37.967Z", "modified": "2025-10-17T13:05:08.997Z"}, {"entity": "publication", "iuid": "5764c5cc4749459d8f6eaed07872d24d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5764c5cc4749459d8f6eaed07872d24d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5764c5cc4749459d8f6eaed07872d24d"}}, "title": "Databases and Associated Tools for Glycomics and Glycoproteomics.", "authors": [{"family": "Lisacek", "given": "Frederique", "initials": "F"}, {"family": "Mariethoz", "given": "Julien", "initials": "J"}, {"family": "Alocci", "given": "Davide", "initials": "D"}, {"family": "Rudd", "given": "Pauline M", "initials": "PM"}, {"family": "Abrahams", "given": "Jodie L", "initials": "JL"}, {"family": "Campbell", "given": "Matthew P", "initials": "MP"}, {"family": "Packer", "given": "Nicolle H", "initials": "NH"}, {"family": "St\u00e5hle", "given": "Jonas", "initials": "J"}, {"family": "Widmalm", "given": "G\u00f6ran", "initials": "G"}, {"family": "Mullen", "given": "Elaine", "initials": "E"}, {"family": "Adamczyk", "given": "Barbara", "initials": "B"}, {"family": "Rojas-Macias", "given": "Miguel A", "initials": "MA"}, {"family": "Jin", "given": "Chunsheng", "initials": "C"}, {"family": "Karlsson", "given": "Niclas G", "initials": "NG"}], "type": "journal article", "published": "2016-10-16", "journal": {"volume": "1503", "issn": "1940-6029", "issue": null, "pages": "235-264", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "The access to biodatabases for glycomics and glycoproteomics has proven to be essential for current glycobiological research. This chapter presents available databases that are devoted to different aspects of glycobioinformatics. This includes oligosaccharide sequence databases, experimental databases, 3D structure databases (of both glycans and glycorelated proteins) and association of glycans with tissue, disease, and proteins. Specific search protocols are also provided using tools associated with experimental databases for converting primary glycoanalytical data to glycan structural information. In particular, researchers using glycoanalysis methods by U/HPLC (GlycoBase), MS (GlycoWorkbench, UniCarb-DB, GlycoDigest), and NMR (CASPER) will benefit from this chapter. In addition we also include information on how to utilize glycan structural information to query databases that associate glycans with proteins (UniCarbKB) and with interactions with pathogens (SugarBind).", "doi": "10.1007/978-1-4939-6493-2_18", "pmid": "27743371", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2020-01-30T16:19:31.996Z", "modified": "2024-01-16T13:46:32.944Z"}, {"entity": "publication", "iuid": "9b74e97475674662aec42e2c29afbbcc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9b74e97475674662aec42e2c29afbbcc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9b74e97475674662aec42e2c29afbbcc"}}, "title": "High-Throughput Analysis of the Plasma N-Glycome by UHPLC.", "authors": [{"family": "Adamczyk", "given": "Barbara", "initials": "B"}, {"family": "St\u00f6ckmann", "given": "Henning", "initials": "H"}, {"family": "O'Flaherty", "given": "R\u00f3is\u00edn", "initials": "R"}, {"family": "Karlsson", "given": "Niclas G", "initials": "NG"}, {"family": "Rudd", "given": "Pauline M", "initials": "PM"}], "type": "journal article", "published": "2016-10-16", "journal": {"title": "Methods Mol. Biol.", "issn": "1940-6029", "volume": "1503", "issue": null, "pages": "97-108", "issn-l": "1064-3745"}, "abstract": "The understanding of glycosylation alterations in health and disease has evolved significantly and glycans are considered to be relevant biomarker candidates. High-throughput analytical technologies capable of generating high-quality, large-scale glycoprofiling data are in high demand. Here, we describe an automated sample preparation workflow and analysis of N-linked glycans from plasma samples using hydrophilic interaction liquid chromatography with fluorescence detection on an ultrahigh-performance liquid chromatography (UHPLC) instrument. Samples are prepared in 96-well plates and the workflow features rapid glycoprotein denaturation, enzymatic glycan release, glycan purification on solid-supported hydrazide, fluorescent labeling, and post-labeling cleanup with solid-phase extraction. The development of a novel approach for plasma N-glycan analysis and its implementation on a robotic platform significantly reduces the time required for sample preparation and minimizes technical variation. It is anticipated that the developed method will contribute to expanding high-throughput capabilities to analyze protein glycosylation.", "doi": "10.1007/978-1-4939-6493-2_8", "pmid": "27743361", "labels": {"Glycoproteomics and MS Proteomics": "Technology development"}, "xrefs": [], "notes": [], "created": "2020-01-30T16:24:15.512Z", "modified": "2024-01-16T13:46:32.932Z"}, {"entity": "publication", "iuid": "cec5bda0edf54f92baf9e1594e1074dc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cec5bda0edf54f92baf9e1594e1074dc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cec5bda0edf54f92baf9e1594e1074dc"}}, "title": "Microwell-Based Live Cell Imaging of NK Cell Dynamics to Assess Heterogeneity in Motility and Cytotoxic Response.", "authors": [{"family": "Vanherberghen", "given": "Bruno", "initials": "B"}, {"family": "Frisk", "given": "Thomas", "initials": "T"}, {"family": "Forslund", "given": "Elin", "initials": "E"}, {"family": "Olofsson", "given": "Per E", "initials": "PE"}, {"family": "Guldevall", "given": "Karolin", "initials": "K"}, {"family": "\u00d6nfelt", "given": "Bj\u00f6rn", "initials": "B"}], "type": "journal article", "published": "2016-05-15", "journal": {"volume": "1441", "issn": "1940-6029", "issue": null, "pages": "87-106", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "NK cell heterogeneity has primarily been studied either on the population level, measuring average responses, or on the single cell level by flow cytometry, providing static snapshots. These approaches have certain drawbacks, not enabling dynamic observations of single cells over extended periods of time. One of the primary limitations of single cell imaging has been throughput; it has been challenging to collect data for many cells due to their dynamic nature and migrating out of the field of view. Spatially confining cells combined with automated fluorescence microscopy enables the simultaneous monitoring of many NK cells in parallel for extended periods of time (>12 h). Such an approach allows us to dissect how the sum of individual NK cell responses translates to the global average response typically observed.", "doi": "10.1007/978-1-4939-3684-7_8", "pmid": "27177659", "labels": {"Integrated Microscopy Technologies Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-05-03T12:59:22.588Z", "modified": "2021-05-24T15:33:38.402Z"}, {"entity": "publication", "iuid": "9a895951f51b49dabd4cfa2c7f7ebd3e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9a895951f51b49dabd4cfa2c7f7ebd3e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9a895951f51b49dabd4cfa2c7f7ebd3e"}}, "title": "Metagenomic approaches to disclose disease-associated pathogens: detection of viral pathogens in honeybees.", "authors": [{"family": "Granberg", "given": "Fredrik", "initials": "F"}, {"family": "Karlsson", "given": "Oskar E", "initials": "OE"}, {"family": "Bel\u00e1k", "given": "S\u00e1ndor", "initials": "S"}], "type": "journal article", "published": "2014-11-17", "journal": {"volume": "1247", "issn": "1940-6029", "issue": null, "pages": "491-511", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "Metagenomic approaches have become invaluable for culture-independent and sequence-independent detection and characterization of disease-associated pathogens. Here, the sequential steps from sampling to verification of results are described for a metagenomic-based approach to detect potential pathogens in honeybees. The pre-sequencing steps are given in detail, but due to the rapid development of sequencing technologies, all platform-specific procedures, as well as subsequent bioinformatics analysis, are more generally described. It should also be noted that this approach could, with minor modifications, be adapted for other organisms and sample matrices.", "doi": "10.1007/978-1-4939-2004-4_33", "pmid": "25399116", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [], "notes": [], "created": "2017-05-02T12:56:57.857Z", "modified": "2020-01-21T13:56:03.970Z"}, {"entity": "publication", "iuid": "27830c7f05394bbeaadc407a6b1ce591", "links": {"self": {"href": "https://publications.scilifelab.se/publication/27830c7f05394bbeaadc407a6b1ce591.json"}, "display": {"href": "https://publications.scilifelab.se/publication/27830c7f05394bbeaadc407a6b1ce591"}}, "title": "Statistical molecular design: a tool to follow up hits from small-molecule screening.", "authors": [{"family": "Lindgren", "given": "Anders E G", "initials": "AE"}, {"family": "Larsson", "given": "Andreas", "initials": "A"}, {"family": "Linusson", "given": "Anna", "initials": "A"}, {"family": "Elofsson", "given": "Mikael", "initials": "M"}], "type": "journal article", "published": "2013-12-07", "journal": {"title": "Methods Mol. Biol.", "issn": "1940-6029", "volume": "1056", "issue": null, "pages": "169-188", "issn-l": "1064-3745"}, "abstract": "In high-throughput screening (HTS) a robust assay is used to interrogate a large collection of small organic molecules in order to find compounds, hits, with a desired biological activity. The hits are then further explored by an iterative process where new compounds are designed, purchased, or synthesized, followed by an evaluation in one or more assays. Statistical molecular design (SMD) is a useful method to select a balanced, varied, and information-rich compound collection based on hits from HTS in order to create a foundation for development of optimized compounds with improved properties. In this chapter, we describe the use of SMD to explore a hit obtained from small-molecule screening.", "doi": "10.1007/978-1-62703-592-7_17", "pmid": "24306873", "labels": {"Chemical Biology Consortium Sweden": "Technology development"}, "xrefs": [], "notes": [], "created": "2019-11-11T10:02:23.491Z", "modified": "2025-10-17T13:04:30.224Z"}, {"entity": "publication", "iuid": "0fe1e59a92db484ead8642f49cef0d4b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0fe1e59a92db484ead8642f49cef0d4b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0fe1e59a92db484ead8642f49cef0d4b"}}, "title": "Stable isotope labeling methods in protein profiling.", "authors": [{"family": "Lengqvist", "given": "Johan", "initials": "J"}, {"family": "Sandberg", "given": "AnnSofi", "initials": "A"}], "type": "journal article", "published": "2013-06-15", "journal": {"volume": "1023", "issn": "1940-6029", "issue": null, "pages": "21-51", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "Mass spectrometry (MS) analysis of peptides and proteins has evolved dramatically over the last 20 years. Improvement of MS instrumentation, computational data analysis, and the availability of complete sequence databases for many species have made large-scale proteomics analyses possible. The measurement of global protein abundance by quantitative mass spectrometry has the potential to increase both speed and impact of biological and clinical research. However, to be able to detect and identify potential biomarkers, reproducible and accurate quantification is essential. The following chapter describes how to perform quantitative protein profiling using stable isotope labeling methods. Throughout, there is a focus on guidance in selection of an appropriate labeling strategy. With that in mind, we have included a section on acquisition and understanding of the liquid chromatography-mass spectrometry (LC-MS) data format. Further, we describe the different stable isotope labeling methods and their pros and cons. We start by giving an overview of the overall quantitative proteomics workflow in which extracting relevant biological information from the acquired data is the ultimate goal.", "doi": "10.1007/978-1-4614-7209-4_3", "pmid": "23765618", "labels": {"Clinical Proteomics Mass spectrometry": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:03:23.801Z", "modified": "2023-06-19T12:55:00.440Z"}, {"entity": "publication", "iuid": "2e1fe44fabcf483abdd700396ed83d4e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2e1fe44fabcf483abdd700396ed83d4e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2e1fe44fabcf483abdd700396ed83d4e"}}, "title": "Narrow-range peptide isoelectric focusing as peptide prefractionation method prior to tandem mass spectrometry analysis.", "authors": [{"family": "Pernemalm", "given": "Maria", "initials": "M", "orcid": "0000-0003-4624-031X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f15f303cb2044cfa81719700137e3603.json"}}], "type": "journal article", "published": "2013-06-15", "journal": {"volume": "1023", "issn": "1940-6029", "issue": null, "pages": "3-11", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "High sample complexity is one of the major challenges in mass spectrometry-based proteomics today. Despite massive improvement in instrumentation, sample prefractionation is still needed to reduce sample complexity and improve proteome coverage. Isoelectric focusing (IEF) has been traditionally used as a first-dimension protein separation technique in two-dimensional gel electrophoresis-based proteomics. Recently, peptide IEF has emerged as appealing alternative for anion exchange chromatography in multidimensional LC-MS/MS workflows. The rationale behind using narrow-range peptide isoelectric focusing as a prefractionation method prior to ms/ms is to reduce the complexity induced by tryptic digestion. This is done by selectively analyzing a sub-fraction of peptides with an acidic pI. The pI range is chosen as it has previously been shown that 96 % of human proteins have at least one tryptic peptide between pH 3.4 and 4.9. This ensures high proteome coverage while reducing the number of peptides with 2/3. In addition the focusing precision is optimal in this range. Therefore, by analyzing this sub-fraction of peptides the complexity of the sample can be reduced without significant loss of proteome coverage. As the theoretical pI of peptides can be calculated, the pI of the identified peptides can be used to validate the peptide sequence (identified peptides with pI outside the pH range 3.4-4.9 are more likely to be false positives). In addition, this approach is compatible with iTRAQ labelling as the different iTRAQ labels migrate similarly in IEF.", "doi": "10.1007/978-1-4614-7209-4_1", "pmid": "23765616", "labels": {"Clinical Proteomics Mass spectrometry": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:03:24.100Z", "modified": "2021-07-08T11:36:54.632Z"}, {"entity": "publication", "iuid": "2e42e8d0491849e18636a9542a65ef10", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2e42e8d0491849e18636a9542a65ef10.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2e42e8d0491849e18636a9542a65ef10"}}, "title": "Protein quantification by peptide quality control (PQPQ) of shotgun proteomics data.", "authors": [{"family": "Forshed", "given": "Jenny", "initials": "J"}], "type": "journal article", "published": "2013-06-15", "journal": {"volume": "1023", "issn": "1940-6029", "issue": null, "pages": "149-158", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "This chapter describes how to improve quantitative accuracy and precision in shotgun proteomics by PQPQ (protein quantification by peptide quality control). The method is based on the assumption that the quantitative pattern of peptides derived from one protein will correlate over several samples. Dissonant patterns are assumed to arise either from mismatched peptides or due to the presence of different protein species. PQPQ identifies and excludes outliers and detects the existence of different protein species by correlation analysis. Alternative protein species can then be quantified separately. PQPQ can handle shotgun proteomics data from several MS instruments, data from different kinds of labeling, and label-free data. We have previously shown that data processing by PQPQ improves the information output from shotgun proteomics by validating the algorithm on seven datasets related to different cancer studies (Forshed et al., Mol Cell Proteomics 10(10):M111.010264, 2011). Data from two labeling procedures and three different instrumental platforms was included in the evaluation. With this unique method using both peptide sequence data and quantitative data, we can improve the quantitative accuracy and precision on the protein level and detect different protein species (Forshed et al., Mol Cell Proteomics 10(10):M111.010264, 2011).", "doi": "10.1007/978-1-4614-7209-4_9", "pmid": "23765624", "labels": {"Clinical Proteomics Mass spectrometry": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:03:23.206Z", "modified": "2017-05-30T12:42:45.953Z"}, {"entity": "publication", "iuid": "afd562f281744bc99a19b35dbd0c972d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/afd562f281744bc99a19b35dbd0c972d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/afd562f281744bc99a19b35dbd0c972d"}}, "title": "Comprehensive analysis of MHC ligands in clinical material by immunoaffinity-mass spectrometry.", "authors": [{"family": "Kasuga", "given": "Kie", "initials": "K"}], "type": "journal article", "published": "2013-06-15", "journal": {"volume": "1023", "issn": "1940-6029", "issue": null, "pages": "203-218", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "Major histocompatibility complexes (MHC) are expressed on antigen-presenting cells (APC) that display peptide antigens. This is a crucial step to activate a T-cell response. Since immunogenic ligand of MHC is closely related with autoimmunity, inflammatory diseases, and cancer, comprehensive analysis of MHC ligands (the so-called Ligandome) is essential to unveil disease pathogenesis. Recently, immunotherapies such as vaccination have been focused on as new therapies of cancer, HIV, and infectious diseases. Therefore, the importance of comprehensive analysis of MHC ligands is increasing. Mass spectrometry has been the core technology of ligand identification since the 1990s. The sensitivity of mass spectrometers has been improved dramatically in recent years; thus, it enables to identify MHC ligands in clinical materials. This chapter lays out the workflow of MHC ligand identification in clinical materials, especially human bronchoalveolar (BAL) cells. MHC-ligand complexes are enriched by immunoaffinity extraction and captured ligand peptides are identified by LC-MS/MS. MHC class II ligand in BAL cells is described in this text; however, this approach is applicable to MHC class I and other clinical materials such as tissues.", "doi": "10.1007/978-1-4614-7209-4_14", "pmid": "23765629", "labels": {"Clinical Proteomics Mass spectrometry": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:03:23.503Z", "modified": "2017-05-30T12:42:50.697Z"}, {"entity": "publication", "iuid": "f1a748adc53d487b9c3cf711b8237af8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f1a748adc53d487b9c3cf711b8237af8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f1a748adc53d487b9c3cf711b8237af8"}}, "title": "Highly multiplexed antibody suspension bead arrays for plasma protein profiling.", "authors": [{"family": "Drobin", "given": "Kimi", "initials": "K"}, {"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": "2013-06-15", "journal": {"volume": "1023", "issn": "1940-6029", "issue": null, "pages": "137-145", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "Alongside the increasing availability of affinity reagents, antibody microarrays have become a powerful tool to screen for target proteins in complex samples. Applying directly labeled samples onto arrays instead of using sandwich assays offers an approach to facilitate a systematic, high-throughput, and flexible exploration of protein profiles in body fluids such as serum or plasma. As an alternative to planar arrays, a system based on color-coded beads for the creation of antibody arrays in suspension has become available to offer a microtiter plate-based option for screening larger number of samples with variable sets of capture reagents. A procedure was established for analyzing biotinylated samples without the necessity to remove excess labeling substance. We have shown that this assay system allows detecting proteins down into lower pico-molar and higher pg/ml levels with dynamic ranges over three orders of magnitude. Presently, this workflow enables the profiling of 384 samples for up to 384 proteins per assay.", "doi": "10.1007/978-1-4614-7209-4_8", "pmid": "23765623", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:37.784Z", "modified": "2021-07-08T12:07:34.315Z"}, {"entity": "publication", "iuid": "32d051b055a54dd2b0d572969e20db54", "links": {"self": {"href": "https://publications.scilifelab.se/publication/32d051b055a54dd2b0d572969e20db54.json"}, "display": {"href": "https://publications.scilifelab.se/publication/32d051b055a54dd2b0d572969e20db54"}}, "title": "Employment of complementary dissociation techniques for body fluid characterization and biomarker discovery.", "authors": [{"family": "Good", "given": "David M", "initials": "DM"}, {"family": "Rutishauser", "given": "Dorothea", "initials": "D"}], "type": "journal article", "published": "2013-04-30", "journal": {"volume": "1002", "issn": "1940-6029", "issue": null, "pages": "223-232", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "Proteomic analysis of biological fluids has become the de facto method for biomarker discovery over the past half decade. Mass spectrometry, in particular, has emerged as the premier technology to perform such analysis. This shift in the prevailing choice of analytical method is primarily due to the rapid evolution of mass spectrometry technology, with advances in acquisition speed, increased resolving power and mass accuracy, and the development of novel fragmentation methods. The benefits of using one of these new fragmentation methods, electron-transfer dissociation, as a complement to the traditional dissociation technique (i.e., collision-activated dissociation) have been thoroughly illustrated. Detailed here is a method for proteomic analysis of a readily obtainable and often investigated biological fluid, blood plasma, which takes advantage of these complementary dissociation techniques and employs the most recent advances in mass spectrometry technology.", "doi": "10.1007/978-1-62703-360-2_18", "pmid": "23625407", "labels": {"Advanced Mass Spectrometry Proteomics": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:02:43.372Z", "modified": "2017-05-30T12:33:28.974Z"}, {"entity": "publication", "iuid": "1ffdcc71b4b048d4b6e82279e3a06bca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1ffdcc71b4b048d4b6e82279e3a06bca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1ffdcc71b4b048d4b6e82279e3a06bca"}}, "title": "Identification and verification of microRNAs by high-throughput sequencing.", "authors": [{"family": "H\u00e4llman", "given": "Jimmie", "initials": "J"}, {"family": "Avesson", "given": "Lotta", "initials": "L"}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "S\u00f6derbom", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2013-03-16", "journal": {"volume": "983", "issn": "1940-6029", "issue": null, "pages": "125-138", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "High-throughput sequencing methods have become invaluable for detection and analysis of small RNAs. The results are millions of sequences that need to be carefully analyzed by computational methods and preferentially verified by different experimental techniques. Here we describe how to use high-throughput sequencing followed by bioinformatics and northern blot to identify one particular class of small RNA, microRNAs.", "doi": "10.1007/978-1-62703-302-2_7", "pmid": "23494305", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:58:04.217Z", "modified": "2021-07-07T15:22:42.686Z"}, {"entity": "publication", "iuid": "758b525b3955477e8f58d7cc2c603d38", "links": {"self": {"href": "https://publications.scilifelab.se/publication/758b525b3955477e8f58d7cc2c603d38.json"}, "display": {"href": "https://publications.scilifelab.se/publication/758b525b3955477e8f58d7cc2c603d38"}}, "title": "Structural genetic variation in the context of somatic mosaicism.", "authors": [{"family": "Dumanski", "given": "Jan P", "initials": "JP"}, {"family": "Piotrowski", "given": "Arkadiusz", "initials": "A"}], "type": "journal article", "published": "2012-01-10", "journal": {"volume": "838", "issn": "1940-6029", "issue": null, "pages": "249-272", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "Somatic mosaicism is the result of postzygotic de novo mutation occurring in a portion of the cells making up an organism. Structural genetic variation is a very heterogeneous group of changes, in terms of numerous types of aberrations that are included in this category, involvement of many mechanisms behind the generation of structural variants, and because structural variation can encompass genomic regions highly variable in size. Structural variation rapidly evolved as the dominating type of changes behind human genetic diversity, and the importance of this variation in biology and medicine is continuously increasing. In this review, we combine the evidence of structural variation in the context of somatic cells. We discuss the normal and disease-related somatic structural variation. We review the recent advances in the field of monozygotic twins and other models that have been studied for somatic mutations, including other vertebrates. We also discuss chromosomal mosaicism in a few prime examples of disease genes that contributed to understanding of the importance of somatic heterogeneity. We further highlight challenges and opportunities related to this field, including methodological and practical aspects of detection of somatic mosaicism. The literature devoted to interindividual variation versus papers reporting on somatic variation suggests that the latter is understudied and underestimated. It is important to increase our awareness about somatic mosaicism, in particular, related to structural variation. We believe that further research of somatic mosaicism will prove beneficial for better understanding of common sporadic disorders.", "doi": "10.1007/978-1-61779-507-7_12", "pmid": "22228016", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:01:02.848Z", "modified": "2020-01-21T13:56:03.060Z"}, {"entity": "publication", "iuid": "2759f61b2b44435d8c551e4ed8476e7b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2759f61b2b44435d8c551e4ed8476e7b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2759f61b2b44435d8c551e4ed8476e7b"}}, "title": "Antibody suspension bead arrays.", "authors": [{"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": "2011-03-04", "journal": {"volume": "723", "issn": "1940-6029", "issue": null, "pages": "29-36", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "Alongside the increasing availability of affinity reagents, antibody microarrays have been developed to become a powerful tool to screen for target proteins in complex samples. Besides multiplexed sandwich immunoassays, the application of directly applying labeled sample onto arrays with immobilized capture reagents offers an approach to facilitate a systematic, high-throughput analysis of body fluids such as serum or plasma. An alternative to commonly used planar arrays has become available in form of a system based on color-coded beads for the creation of antibody arrays in suspension. The assay procedure offers an uncomplicated option to screen larger numbers of serum or plasma samples with variable sets of capture reagents. In addition, the established procedure of whole sample biotinylation circumvents the purification steps, which are generally required to remove excess labeling substance. We have shown that this assay system allows detecting proteins down into lower pico-molar and higher picogram per milliliter levels with dynamic ranges over three orders of magnitude. Presently, this workflow enables the profiling of 384 clinical samples for up to 100 proteins per assay.", "doi": "10.1007/978-1-61779-043-0_3", "pmid": "21370057", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-10-30T10:37:50.048Z", "modified": "2021-07-08T12:07:34.021Z"}], "created": "2017-05-09T09:12:52.813Z", "modified": "2020-11-27T13:14:08.320Z"}