The Global Proteomics and Proteogenomics unit at SciLifeLab in Stockholm (at Karolinska Institutet), Glycoproteomics and MS Proteomics unit at SciLifeLab in Gothenburg (at Gothenburg University), and the Clinical Proteomics unit at SciLifeLab in Lund (at Lund University) all specialize in MS-based protein and peptide analysis using cutting-edge technologies. We welcome all areas in medicine, natural sciences, planetary biology and all other biology disciplines.
MS-based protein analysis, at all units
Analysis of proteins in all ranges from complex biological samples such as tissue, fluid to single cells, enabling protein profiling and comprehensive insights into protein function, disease and regulatory mechanisms.
Protein identification, expression and quantification
Proteogenomics is rapidly developing field in biological mass spectrometry that combines proteomics information with sample specific genomic and transcriptomics information. Applications in proteogenomics include discovery of novel protein coding regions to improve genome annotation; detection of variant and mutated proteins based on DNA and/or RNA sequence data; discovery of cancer neoantigens and evaluation of the impact of genomic changes (e.g. copy number alterations, SNPs, mutations, hyper methylation) on the proteome. The facility also provides service in broad range of MS-based proteomics applications to encompass the needs of the Swedish life science community, including quantitative proteomics and proteome profiling, in-depth proteomics, interaction studies by immunoprecipition MS (IP-MS) and post-translational modification (PTM) analysis.
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Services
Personalized proteomics Individual sequence based search database generation for variant analysis at the protein level coupled with in-depth quantitative proteome analysis.
Disease state/Variant proteomics Database supplemented with all known SNPs and disease causing genetic alterations. (Can be used when sample specific sequence data is not available.)
Unbiased proteogenomics in any species with a sequenced genome Six frame translation of genome generated database searches for protein coding genome annotation.
XenoProteomics Database supplemented with peptides from disease causing pathogens.
Meta proteomics Proteogenomics analysis based on metagenomics database generation
Plasma proteomics In-depth global MS-based plasma proteomics
Start-up meeting and Experimental planning Our long experience in applied proteomics provide us with a unique opportunity to assist users and in many instances refine the original experimental plan. For this reason we always offer a start-up meeting to go through the user request in detail.
Analysis of low cell numbers (100-1000)
Services during holidays:
The core unit is not engaging/handling any new requests/projects during summer and Christmas holidays:
Midsummer – second week of Aug (~7 weeks)
Christmas Eve – first week of Jan (~3 weeks)
Equipment
Mass spectrometers
MS Orbitrap Astral, Thermo Scientific
MS Orbitrap Astral, Thermo Scientific
MS Q Exactive HF, Thermo Scientific
MS Q Exactive HF, Thermo Scientific.
MS Orbitrap Exploris 480, Thermo Scientific.
MS Tims-TOF Pro, Bruker
MS TimsTOF HT incl Evoep, Bruker
MS Tims-TOF SCP incl Evosep, Bruker
MS Acquity Premier Offline UPLC, Waters
Peptide separation technologies
HiRIEF (High Resolution Isoelectric Focusing)
Thermo Vanquish Neo LC
Robots
Ettan Digester (modified Gilson 215), GE Healthcare Life Science
Biomek i7 (Beckman Coulter) robot for automated sample preparation
Addresses
SciLifeLab Masspektrometri, alfa plan 1 Tomtebodavägen 23 B 171 65 Solna Sweden
SciLifeLab Proteogenomics Tomtebodav 23A 171 65 Solna Sweden
The Proteomics Core Facility (PCF) at the University of Gothenburg provides advanced mass spectrometry services and expert support for proteomic and glycoproteomic research. We assist researchers from sample preparation through to data analysis, offering deep insights into protein expression and modification.
Our facility handles a wide range of biological materials, including tissues, cells, plasma, CSF, urine, exosomes, and proteins from immunoprecipitation, BioID, or recombinant expression. This flexibility allows us to support diverse research needs, from basic science to clinical studies.
We specialize in global quantitative proteomics, enabling the identification and quantification of up to 10,000 proteins in a single experiment. This approach reveals critical molecular mechanisms and dynamic changes in biological systems. For quantification, we offer two main strategies: Tandem Mass Tag (TMT™) labelling for multiplexed analysis of up to 18 samples, and label-free quantification using data-independent acquisition (DIA), ideal for large-scale and clinical studies within precision medicine. We have recently implemented Biognosys' P2 Enrichment technology, enabling quantification of up to 7,000 plasma proteins—a major leap from previous capabilities.
Our glycoproteomics support focuses on characterizing glycosylated proteins, proteoglycans, glycosphingolipids etc. Using enrichment techniques, optimized ionization, and advanced bioinformatics, we can identify glycan structures and their specific attachment sites on peptides—essential for understanding the role of glycosylation in health and disease.
Using the unit
When you are planning a project for analyses at PCF, please contact us via pcf@gu.se. We are happy recommending suitable methodology and study design in order to create results of high quality and scientific impact. After filling in our sample submission form you are welcome to deliver your samples to our facility.
Services
Protein identification
Quantitative or targeted proteomics
Interaction proteomics after affinity-based approaches
High-throughput data-independent proteomics of large cohorts
Global and relative quantification and identification of glycopeptides
Structural characterization of N- and O-linked glycopeptides
Screening of released N-linked and O-linked oligosaccharides and liberated glycans from glycolipids for comparative glycomics.
Characterization of N-linked and O-linked oligosaccharides and liberated glycans from glycolipids using exoglycosidases
Identification and relative quantification of phosphopeptides
Custom-made biological mass spectrometry
Equipment
Automated sample preparation
Beckman Coulter Biomek i7
KingFisher Apex
Cellenion CellenONE
MassSpectrometers
Bruker timsTOF SCP
Bruker timsTOF HT
Thermo Orbitrap Astral
Thermo Orbitrap Eclipse Tribrid
Thermo Orbitrap Fusion Lumos Tribrid
Thermo Orbitrap Fusion Tribrid
Thermo QExactiveHF
Thermo LTQ Orbitrap
Peptide Separation
Online: Thermo Easy nLC1200 systems
Online: Evosep One nLC systems
Online: Thermo Vanquish Neo HPLCs
Offline: high pH UPLC fractionation: Thermo Dionex Ultimate 3000
Addresses
Proteomics Core Facility University of Gothenburg Medicinaregatan 19 41390 Göteborg
(for parcels)
University of Gothenburg Proteomics Core Facility Medicinaregatan 9E (pavilion) 41390 Göteborg
The Clinical Proteomics Unit within SciLifeLab is part of the Swedish National Infrastructure for Biological Mass Spectrometry (BioMS). The clinical proteomics effort is distributed across Lund University, University of Gothenburg and Karolinska Institutet. Our mission is to advance precision medicine through state-of-the-art biological mass spectrometry (MS).
Clinical proteomics makes it possible to measure thousands of proteins, their variants, and post-translational modifications directly from clinical samples—going far beyond traditional single-marker assays. With the latest generation of mass spectrometers (Orbitrap Astral, ion mobility TOF) and automated, high-throughput workflows, our unit provides unique opportunities to:
Identify clinically relevant biomarkers
Stratify patients with greater precision
Support translational and clinical research with robust, reproducible data
The unit builds on strong local collaborations with healthcare and the university hospital regions, as well as extensive expertise in biomarker development, and translational clinical studies. From our base in Lund, and with mirrored instrumentation also established at GU and KI, we enable synchronized, large-scale, and prospective analyses across Sweden—supporting national clinical trials and biobank studies.
Using the unit
We encourage researchers from academia, healthcare, and industry to contact us early in the project planning phase. Our team can advise on study design, sample handling, and method selection to ensure high-quality and clinically relevant results.
Requests for service can be initiated by contacting us via biomslund@epic.lu.se, or pcf@gu.se or proteomicscore@scilifelab.se. Our expert staff will contact you to plan the project and discuss the next steps. After filling in a sample submission form, you are welcome to deliver your samples to our unit.
Services
We provide access to state-of-the-art MS-based proteomics technologies and expert support for clinical and translational projects. Our main services include:
Global proteome profiling – quantitative analysis of thousands of proteins across tissues, cells, plasma, CSF, urine, and other clinical materials.
Large-scale cohort analysis – high-throughput, harmonized workflows for biobank studies and multi-center clinical trials.
Disease-focused applications – tailored analyses to support cancer research, cardiovascular disease, infectious disease, and other clinical studies.
Equipment
Clinical Proteomics Lund hosts part of the mirrored national instrument setup also established at Gothenburg and Stockholm. This mirrored setup enables reproducible, synchronized analyses across the three sites, uniquely positioning Sweden for population-scale clinical proteomics.
Mirrored instrumentation:
Mass spectrometers
Bruker timsTOF HT – for high-throughput analyses
Bruker timsTOF SCP – for single-cell and low-input analysis
Liquid chromatography systems
Evosep One LC – for rapid clinical workflows
Automatedsample preparation
Beckman Coulter Biomek i7 liquid handler
Additional instrumentation:
Instruments not mirrored nationally but available at Lund for specialized applications.
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