Bernd Thiede

1. Koehler, C.J., Arntzen, M.Ø., de Souza, G.A., Thiede, B. (2013) An approach for triplex-isobaric peptide termini labeling (Triplex-IPTL). Anal. Chem., 85, 2478-2485.

2. Thiede, B., Koehler, C.J., Strozynski, M., Treumann, A., Stein, R., Zimny-Arndt, U., Schmid, M., Jungblut, P.R. (2013) High resolution quantitative proteomics of HeLa cells protein species using stable isotope labeling with amino acids in cell culture (SILAC), two-dimensional gel electrophoresis (2DE) and nano-liquid chromatography coupled to an LTQ-Orbitrap mass spectrometer. Mol. Cell. Proteomics, 12, 529-538.

3. Arntzen, M.A., Boddie, P., Frick, R., Koehler, C.J., Thiede, B. (2015) Consolidation of proteomics data in the Cancer proteomics database. Proteomics, 15, 3765-3771.

4. Trung, T.T., Strozynski, M.A., Thiede, B. (2017) Quantitative phosphoproteome analysis of cisplatin-induced apoptosis in Jurkat T cells, Proteomics, 17, 1600470.

5. Trung, T.T., Bollineni, R.C., Strozynski, M.A., Koehler, C.J., Thiede, B. (2017) Identification of alternative splice variants using unique tryptic peptide sequences for database searches, J. Proteome Res., 16, 2571-2578.

6. Bollineni, R.C., Koehler, C.J., Gislefoss, R.E., Anonsen, J.H., Thiede, B. (2018) Large-scale intact glycopeptide identification by Mascot database search. Sci. Rep. 8, 2117.

• Johansen, Anette; Thiede, Bernd; Anonsen, Jan Haug & Nilsson, Göran Erik (2024). Phosphoproteomic changes in response to anoxia are tissue-specific in the anoxia-tolerant crucian carp (Carassius carassius). Frontiers in Physiology. ISSN 1664-042X. 15. doi: 10.3389/fphys.2024.1407834.
• Winiarczyk, Mateusz; Thiede, Bernd; Utheim, Tor Paaske; Kaarniranta, Kai; Winiarczyk, Dagmara & Michalak, Katarzyna [Show all 7 contributors for this article] (2024). Oxidative Stress, Persistent Inflammation and Blood Coagulation Alterations in Serum Proteome of Patients with Neovascular Age-Related Macular Degeneration. Life. ISSN 2075-1729. 14(5). doi: 10.3390/life14050624.
• Mrsa, Ago; Nardini, Greta; Halvorsen, Trine Grønhaug; Thiede, Bernd & Reubsaet, Leon (2024). One-step functionalization of paper and simplified antibody immobilization for on-the-spot immunocapture from dried serum in liquid chromatography-tandem mass spectrometry based targeted protein determination. Journal of Mass Spectrometry. ISSN 1076-5174. 59(1). doi: 10.1002/jms.4989. Show summary

  This work aimed to simplify and improve the process of binding monoclonal antibodies (mAbs) covalently to filter paper for use in dried blood spot sampling, enabling instant capture of protein biomarkers for targeted protein determination. Incorporating the necessary immunocapture sample preparation step in the initial sampling stage saves time and reduces the workload. The biomarker human chorionic gonadotropin (hCG) was used as the model analyte. The antibody-based paper samplers were prepared by functionalizing paper discs (6 mm) through a simple reaction using divinyl sulfone (DVS). After DVS activation, the paper discs were incubated with E27 hCG mAbs, followed by 0.05% tween/phosphate buffer saline to block the surface. After sample application and drying, the discs only needed to be washed before tryptic digestion and finally analysed on a nanoliquid chromatography–tandem mass spectrometry system. The finished DVS-mAbs samplers could selectively capture hCG (100 ng/mL) from human serum, with a recovery of 50%. Sample clean-up reduced the number of identified proteins from 132 to 82 before and after wash, respectively, with a 70% reduction in serum albumin signal while still retaining hCG on the sampler during the washing protocol. An evaluation of the samplers revealed excellent linearity (R2 = 0.9995) for hCG in serum with relative standard deviations below 15%. This work has presented the first ever reported paper samplers immobilized with antibodies utilizing DVS chemistry, showing promise in the future of paper-based sampling.

• Storås, Andrea; Fineide, Fredrik; Magnø, Morten Schjerven; Thiede, Bernd; Chen, Xiangjun & Strumke, Inga [Show all 11 contributors for this article] (2023). Using machine learning model explanations to identify proteins related to severity of meibomian gland dysfunction. Scientific Reports. ISSN 2045-2322. 13(1). doi: 10.1038/s41598-023-50342-7. Full text in Research Archive
• Storås, Andrea; Magnø, Morten Schjerven; Fineide, Fredrik; Thiede, Bernd; Chen, Xiangjun & Strumke, Inga [Show all 9 contributors for this article] (2023). Identifying Important Proteins in Meibomian Gland Dysfunction with Explainable Artificial Intelligence. IEEE International Symposium on Computer-Based Medical Systems. ISSN 2372-9198. doi: 10.1109/CBMS58004.2023.00217. Full text in Research Archive
• Juvkam, Inga Solgård; Zlygosteva, Olga; Sitarz, Mateusz; Thiede, Bernd; Sørensen, Brita Singers & Malinen, Eirik [Show all 9 contributors for this article] (2023). Proton Compared to X-Irradiation Induces Different Protein Profiles in Oral Cancer Cells and Their Derived Extracellular Vesicles. International Journal of Molecular Sciences. ISSN 1661-6596. 24(23), p. 1–17. doi: 10.3390/ijms242316983. Full text in Research Archive
• Bogucka-Janczi, Katarzyna; Harms, Gregory; Coissieux, Marie-May; Bentires-Alj, Mohamed; Thiede, Bernd & Rajalingam, Krishnaraj (2023). ERK3/MAPK6 dictates CDC42/RAC1 activity and ARP2/3-dependent actin polymerization. eLIFE. ISSN 2050-084X. 12, p. 1–40. doi: 10.7554/eLife.85167. Full text in Research Archive
• Johansen, Anette; Thiede, Bernd; Anonsen, Jan Haug & Nilsson, Göran Erik (2023). Surviving without oxygen involves major tissue specific changes in the proteome of crucian carp (Carassius carassius). PeerJ. ISSN 2167-8359. 11, p. 1–28. doi: 10.7717/peerj.14890. Full text in Research Archive
• Meyer, Saskia; Blaas, Isaac; Bollineni, Ravi Chand; Delic-Sarac, Marina; Tran, Trung & Knetter, Cathrine [Show all 20 contributors for this article] (2023). Prevalent and immunodominant CD8 T cell epitopes are conserved in SARS-CoV-2 variants. Cell reports. ISSN 2211-1247. 42(1). doi: 10.1016/j.celrep.2023.111995. Full text in Research Archive
• Kogler, Stian; Aizenshtadt, Aleksandra; Harrison, Sean; Skottvoll, Frøydis Sved; Berg, Henriette Engen & Abadpour, Shadab [Show all 14 contributors for this article] (2022). "Organ-in-a-Column" Coupled On-line with Liquid Chromatography-Mass Spectrometry. Analytical Chemistry. ISSN 0003-2700. 94(50), p. 17677–17684. doi: 10.1021/acs.analchem.2c04530. Full text in Research Archive
• Semenova, Daria; Zabirnyk, Arsenii; Lobov, Arseniy; Boyarskaya, Nadezda; Kachanova, Olga & Uspensky, Vladimir [Show all 16 contributors for this article] (2022). Multi-omics of in vitro aortic valve calcification. Frontiers in Cardiovascular Medicine. ISSN 2297-055X. 9. doi: 10.3389/fcvm.2022.1043165. Full text in Research Archive
• Berg, Henriette Engen; Halldórsso, Skarphéðinn; Bakketeig, Eris Aas; Thiede, Bernd; Sandberg, Cecilie & Lundanes, Elsa [Show all 8 contributors for this article] (2022). Micro‐pillar array columns (µPAC): An efficient tool for comparing tissue and cultured cells of glioblastoma. Journal of chromatography open. ISSN 2772-3917. 2. doi: 10.1016/j.jcoa.2022.100047.
• Cui, Xueyan; Stavik, Benedicte; Thiede, Bernd; Sandset, Per Morten & Kanse, Sandip (2022). FSAP Protects against Histone-Mediated Increase in Endothelial Permeability In Vitro. International Journal of Molecular Sciences. ISSN 1661-6596. 23(22). doi: 10.3390/ijms232213706. Full text in Research Archive
• Berge-Seidl, Sebastian; Nielsen, Nis Valentin; Alfonso, Armando A. Rodriguez; Etscheid, Michael; Kandanur, Sai Priya Sarma & Haug, Bengt Erik [Show all 15 contributors for this article] (2022). Identification of a phage display-derived peptide interacting with the N-terminal region of factor VII activating protease (FSAP) enables characterization of zymogen activation. ACS Chemical Biology. ISSN 1554-8929. 17(9), p. 2631–2642. doi: 10.1021/acschembio.2c00538. Full text in Research Archive
• Reubsaet, Leon; Thiede, Bernd & Halvorsen, Trine Grønhaug (2022). Next generation VAMS®–Trypsin immobilization for instant proteolysis in bottom-up protein determination. . Advances in Sample Preparation. ISSN 2772-5820. 3. doi: 10.1016/j.sampre.2022.100027. Full text in Research Archive
• Nguyen, Minh Thao; Halvorsen, Trine Grønhaug; Thiede, Bernd & Reubsaet, Leon (2022). Smart proteolysis samplers for pre-lab bottom-up protein analysis – Performance of on-paper digestion compared to conventional digestion. Separation Science Plus (SSC plus). ISSN 2573-1815. 5(5), p. 171–183. doi: 10.1002/sscp.202100062. Full text in Research Archive
• Hynne, Håvard; Aqrawi, Lara A.; Jensen, Janicke Liaaen; Thiede, Bernd; Palm, Øyvind & Amdal, Cecilie Delphin [Show all 10 contributors for this article] (2022). Proteomic Profiling of Saliva and Tears in Radiated Head and Neck Cancer Patients as Compared to Primary Sjögren’s Syndrome Patients. International Journal of Molecular Sciences. ISSN 1661-6596. 23(7). doi: 10.3390/ijms23073714. Full text in Research Archive Show summary

  Patients with head and neck cancer (HNC) and patients with primary Sjögren’s syndrome (pSS) may exhibit similar symptoms of dry mouth and dry eyes, as a result of radiotherapy (RT) or a consequence of disease progression. To identify the proteins that may serve as promising disease biomarkers, we analysed saliva and tears from 29 radiated HNC patients and 21 healthy controls, and saliva from 14 pSS patients by mass spectrometry-based proteomics. The study revealed several upregulated, and in some instances overlapping, proteins in the two patient groups. Histone H1.4 and neutrophil collagenase were upregulated in whole saliva of both patient groups, while caspase-14, histone H4, and protein S100-A9 were upregulated in HNC saliva only. In HCN tear fluid, the most highly upregulated protein was mucin-like protein 1. These overexpressed proteins in saliva and tears play central roles in inflammation, host cell injury, activation of reactive oxygen species, and tissue repair. In conclusion, the similarities and differences in overexpressed proteins detected in saliva from HNC and pSS patients may contribute to the overall understanding of the different pathophysiological mechanisms inducing dry mouth. Thus, the recurring proteins identified could possibly serve as future promising biomarkers

• Kallas, Pawel; Valen, Håkon; Hulander, Mats; Gadegaard, Nikolaj; Stormonth-Darling, John & O'Reilly, Padraic [Show all 9 contributors for this article] (2022). Protein-coated nanostructured surfaces affect the adhesion of Escherichia coli. Nanoscale. ISSN 2040-3364. 14(20), p. 7736–7746. doi: 10.1039/d2nr00976e. Full text in Research Archive
• Thiede, Bernd & Koehler, Christian (2021). An Approach for Triplex-IPTL. In Marcus, Katrin; Eisenacher, Martin & Sitek, Barbara (Ed.), Quantitative Methods in Proteomics. Humana Press. ISSN 978-1-0716-1023-7. p. 133–144. doi: 10.1007/978-1-0716-1024-4_10. Full text in Research Archive
• Andersen, Elisabeth; Dugarte, Maria Eugenia Chollet; Sletten, Marit; Stavik, Benedicte; Skarpen, Ellen & Backe, Paul Hoff [Show all 9 contributors for this article] (2021). Molecular Characterization of Two Homozygous Factor VII Variants Associated with Intracranial Bleeding. Thrombosis and Haemostasis. ISSN 0340-6245. 121(12), p. 1588–1598. doi: 10.1055/a-1450-8568.
• Johannsen, Christina; Koehler, Christian & Thiede, Bernd (2021). Comparison of LFQ and IPTL for Protein Identification and Relative Quantification. Molecules. ISSN 1431-5157. 26(17). doi: 10.3390/molecules26175330. Full text in Research Archive
• Malecki, Jedrzej Mieczyslaw; O'Donohue, Marie-Francoise; Kim, Yeji; Jakobsson, Magnus; Gessa, Luca & Pinto, Rita [Show all 14 contributors for this article] (2021). Human METTL18 is a histidine-specific methyltransferase that targets RPL3 and affects ribosome biogenesis and function. Nucleic Acids Research (NAR). ISSN 0305-1048. 49(6), p. 3185–3203. doi: 10.1093/nar/gkab088. Full text in Research Archive
• Krishnan, Aswini; Berthelet, Jean; Renaud, Emilie; Rosigkeit, Sebastian; Distler, Ute & Stawiski, Eric [Show all 17 contributors for this article] (2020). Proteogenomics analysis unveils a TFG-RET gene fusion and druggable targets in papillary thyroid carcinomas. Nature Communications. ISSN 2041-1723. 11. doi: 10.1038/s41467-020-15955-w. Full text in Research Archive
• Kara, Emrah; Nielsen, Nis Valentin; Eggertsdottir, Bergrun; Thiede, Bernd; Kanse, Sandip & Løset, Geir Åge (2020). Design and characterization of a new pVII combinatorial phage display peptide library for protease substrate mining using Factor VII activating protease (FSAP) as model. ChemBioChem. ISSN 1439-4227. 21(13), p. 1875–1884. doi: 10.1002/cbic.201900705. Full text in Research Archive
• Guldvik, Ingrid Jenny; Zuber, Verena; Braadland, Peder Rustøen; Grytli, Helene Hartvedt; Ramberg, Håkon Andre & Lilleby, Wolfgang [Show all 18 contributors for this article] (2020). Identification and Validation of Leucine-rich alpha-2-glycoprotein 1 as a Noninvasive Biomarker for Improved Precision in Prostate Cancer Risk Stratification. European Urology Open Science. ISSN 2666-1691. 21, p. 51–61. doi: 10.1016/j.euros.2020.08.007. Full text in Research Archive
• Perdreau-Dahl, Harmonie; Progida, Cinzia; Barfeld, Stefan Jörg; Guldsten, Hanne; Thiede, Bernd & Arntzen, Magnus Øverlie [Show all 10 contributors for this article] (2020). Sjögren syndrome/scleroderma autoantigen 1 is a direct Tankyrase binding partner in cancer cells. Communications Biology. ISSN 2399-3642. 3(1). doi: 10.1038/s42003-020-0851-2.
• Khan, Ayyad Ahmad Zartasht; Jackson, Catherine; Utheim, Tor Paaske; Reppe, Sjur; Sapkota, Dipak & Olstad, Ole Kristoffer [Show all 8 contributors for this article] (2020). Sericin-induced melanogenesis in cultured retinal pigment epithelial cells is associated with elevated levels of hydrogen peroxide and inflammatory proteins. Molecules. ISSN 1431-5157. 25(19), p. 1–20. doi: 10.3390/molecules25194395. Full text in Research Archive
• Mazagão Guerreiro, Eduarda; Øvstebø, Reidun; Thiede, Bernd; Costea, Daniela Elena; Søland, Tine Merete & Galtung, Hilde (2020). Cancer cell line-specific protein profiles in extracellular vesicles identified by proteomics. PLOS ONE. ISSN 1932-6203. 15(9), p. 1–20. doi: 10.1371/journal.pone.0238591. Full text in Research Archive
• Solhaug, Anita; Torgersen, Maria Lyngaas; Holme, Jørn Andreas; Wiik-Nielsen, Jannicke; Thiede, Bernd & Eriksen, Gunnar Sundstøl (2020). The Fusarium mycotoxin, 2-Amino-14,16-dimethyloctadecan-3-ol (AOD) induces vacuolization in HepG2 cells. Toxicology. ISSN 0300-483X. p. 433–434. doi: 10.1016/j.tox.2020.152405. Full text in Research Archive
• Riegel, Kristina; Schlöder, Janine; Sobczak, Marco; Jonuleit, Helmut; Thiede, Bernd & Schild, Hansjörg [Show all 7 contributors for this article] (2019). RAF kinases are stabilized and required for dendritic cell differentiation and function. Cell Death and Differentiation. ISSN 1350-9047. 27, p. 1300–1315. doi: 10.1038/s41418-019-0416-4. Full text in Research Archive
• Wagner, Fabienne; Kunz, Tobias C.; Chowdhury, Suvagata R.; Thiede, Bernd; Fraunholz, Martin & Eger, Debora [Show all 7 contributors for this article] (2019). Armadillo repeat-containing protein 1 is a dual localization protein associated with mitochondrial intermembrane space bridging complex. PLOS ONE. ISSN 1932-6203. 14(10), p. 1–19. doi: 10.1371/journal.pone.0218303. Full text in Research Archive
• Byskov, Kristina; M. le Gall, Sylvain; Thiede, Bernd; Camerer, Eric & Kanse, Sandip (2019). Protease activated receptors (PAR)‐1 and ‐2 mediate cellular effects of factor VII activating protease (FSAP). The FASEB Journal. ISSN 0892-6638. 34, p. 1079–1090. doi: 10.1096/fj.201801986RR. Full text in Research Archive
• Koehler, Christian & Thiede, Bernd (2019). Predominant cleavage of proteins N-terminal to serines and threonines using scandium(III) triflate. JBIC Journal of Biological Inorganic Chemistry. ISSN 0949-8257. 25, p. 61–66. doi: 10.1007/s00775-019-01733-7. Full text in Research Archive
• Aqrawi, Lara Adnan; Galtung, Hilde; Guerreiro, Eduarda; Øvstebø, Reidun; Thiede, Bernd & Utheim, Tor Paaske [Show all 11 contributors for this article] (2019). Proteomic and histopathological characterisation of sicca subjects and primary Sjögren’s syndrome patients reveals promising tear, saliva and extracellular vesicle disease biomarkers. Arthritis Research & Therapy. ISSN 1478-6354. 21, p. 1–14. doi: 10.1186/s13075-019-1961-4. Full text in Research Archive
• Itkonen, Harri; Urbanucci, Alfonso; Sara ES, Martin; Khan, Aziz; Mathelier, Anthony & Thiede, Bernd [Show all 8 contributors for this article] (2019). High OGT activity is essential for MYC-driven proliferation of prostate cancer cells. Theranostics. ISSN 1838-7640. 9(8), p. 2183–2197. doi: 10.7150/thno.30834. Full text in Research Archive
• Abudu, Yakubu Princely; Pankiv, Serhiy; Mathai, Benan John; Lystad, Alf Håkon; Bindesbøll, Christian & Brenne, Hanne Britt [Show all 14 contributors for this article] (2019). NIPSNAP1 and NIPSNAP2 act as “eat-me signal” for mitophagy. Developmental Cell. ISSN 1534-5807. 49(4), p. 509–525.e12. doi: 10.1016/j.devcel.2019.03.013. Full text in Research Archive
• Buehler, Ulrike; Schulenburg, Katharina; Yurugi, Hajime; Solman, Maja; Abankwa, Daniel & Ulges, Alexander [Show all 11 contributors for this article] (2018). Targeting prohibitins at the cell surface prevents Th17-mediated autoimmunity. EMBO Journal. ISSN 0261-4189. 37:e99429(16), p. 1–14. doi: 10.15252/embj.201899429.
• Skottvoll, Frøydis Sved; Berg, Henriette Engen; Bjørseth, Kamilla; Lund, Kaja; Roos, Norbert & Bekhradnia, Sara [Show all 13 contributors for this article] (2018). Ultracentrifugation versus kit exosome isolation: nanoLC-MS and other tools reveal similar performance biomarkers, but also contaminations. Future science OA. ISSN 2056-5623. 5(1). doi: 10.4155/fsoa-2018-0088. Full text in Research Archive
• Tran, Trung; Bollineni, Ravi Chand; Koehler, Christian & Thiede, Bernd (2018). Absolute two-point quantification of proteins using dimethylated proteotypic peptides. The Analyst. ISSN 0003-2654. 143(18), p. 4359–4365. doi: 10.1039/c8an01081a.
• Aqrawi, Lara Adnan; Chen, Xiangjun; Jensen, Janicke Liaaen; Morthen, Mathias Kaurstad; Thiede, Bernd & Utheim, Øygunn Aass [Show all 10 contributors for this article] (2018). Severity of clinical dry eye manifestations influences protein expression in tear fluid of patients with primary Sjögren's syndrome. PLOS ONE. ISSN 1932-6203. 13:e0205762(10), p. 1–14. doi: 10.1371/journal.pone.0205762. Full text in Research Archive
• Dukic, Aleksandra; Gerbaud, Pascal; Guibourdenche, Jean; Thiede, Bernd; Tasken, Kjetil & Pidoux, Guillaume (2018). Ezrin-anchored PKA phosphorylates serine 369 and 373 on connexin 43 to enhance gap junction assembly, communication, and cell fusion. Biochemical Journal. ISSN 0264-6021. 475(2), p. 455–476. doi: 10.1042/BCJ20170529. Full text in Research Archive
• Bollineni, Ravi Chand; Koehler, Christian; Gislefoss, Randi Elin; Anonsen, Jan Haug & Thiede, Bernd (2018). Large-scale intact glycopeptide identification by Mascot database search. Scientific Reports. ISSN 2045-2322. 8. doi: 10.1038/s41598-018-20331-2. Full text in Research Archive
• Pasovic, Lara; Utheim, Tor Paaske; Reppe, Sjur; Khan, Ayyad Ahmad Zartasht; Jackson, Catherine & Thiede, Bernd [Show all 8 contributors for this article] (2018). Improvement of storage medium for cultured human retinal pigment epithelial cells using factorial design. Scientific Reports. ISSN 2045-2322. 8(1). doi: 10.1038/s41598-018-24121-8. Full text in Research Archive
• Dugarte, Maria Eugenia Chollet; Andersen, Elisabeth; Skarpen, Ellen; Myklebust, Christiane Filion; Koehler, Christian & Morth, Jens Preben [Show all 12 contributors for this article] (2018). Factor VII deficiency: Unveiling the cellular and molecular mechanisms underlying Three model alterations of the enzyme catalytic domain. Biochimica et Biophysica Acta - Molecular Basis of Disease. ISSN 0925-4439. 1864(3), p. 660–667. doi: 10.1016/j.bbadis.2017.12.016.
• Imre, Gergely; Berthelet, Jean; Heering, Jan; Kehrloesser, Sebastian; Melzer, Inga Maria & Lee, Byung Il [Show all 9 contributors for this article] (2017). Apoptosis inhibitor 5 is an endogenous inhibitor of caspase-2. EMBO Reports. ISSN 1469-221X. 18(5), p. 733–744. doi: 10.15252/embr.201643744. Full text in Research Archive
• Tran, Trung; Bollineni, Ravi Chand; Strozynski, Margarita Anna; Koehler, Christian & Thiede, Bernd (2017). Identification of Alternative Splice Variants Using Unique Tryptic Peptide Sequences for Database Searches. Journal of Proteome Research. ISSN 1535-3893. 16(7), p. 2571–2578. doi: 10.1021/acs.jproteome.7b00126.
• Tran, Trung; Strozynski, Margarita Anna & Thiede, Bernd (2017). Quantitative phosphoproteome analysis of cisplatin-induced apoptosis in Jurkat T cells. Proteomics. ISSN 1615-9853. 17(11). doi: 10.1002/pmic.201600470.
• Barfeld, Stefan Jörg; Urbanucci, Alfonso; Itkonen, Harri; Fazli, Ladan; Hicks, Jessica L & Thiede, Bernd [Show all 10 contributors for this article] (2017). c-Myc antagonises the transcriptional activity of the androgen receptor in prostate cancer affecting key gene networks. EBioMedicine. ISSN 2352-3964. 18, p. 83–93. doi: 10.1016/j.ebiom.2017.04.006. Full text in Research Archive
• Stakkestad, Øystein; Lyngstadaas, Ståle Petter; Thiede, Bernd; Vondrasesek, Jiri; Skålhegg, Bjørn Steen & Reseland, Janne Elin (2017). Phosphorylation Modulates Ameloblastin Self-assembly and Ca2+ Binding. Frontiers in Physiology. ISSN 1664-042X. 8. doi: 10.3389/fphys.2017.00531. Full text in Research Archive
• Aqrawi, Lara Adnan; Galtung, Hilde; Vestad, Beate; Øvstebø, Reidun; Thiede, Bernd & Rusthen, Shermin [Show all 13 contributors for this article] (2017). Identification of potential saliva and tear biomarkers in primary Sjögren’s syndrome, utilising the extraction of extracellular vesicles and proteomics analysis. Arthritis Research & Therapy. ISSN 1478-6354. 19(1). doi: 10.1186/s13075-017-1228-x. Full text in Research Archive
• Koehler, Christian; Bollineni, Ravi Chand & Thiede, Bernd (2017). Application of the half decimal place rule to increase the peptide identification rate. Rapid Communications in Mass Spectrometry. ISSN 0951-4198. 31(2), p. 227–233. doi: 10.1002/rcm.7780. Full text in Research Archive
• Haatveit, Hanne Merethe; Wessel, Øystein; Markussen, Turhan; Lund, Morten; Thiede, Bernd & Nyman, Ingvild Berg [Show all 9 contributors for this article] (2017). Viral protein kinetics of piscine orthoreovirus infection in atlantic salmon blood cells. Viruses. ISSN 1999-4915. 9:49(3), p. 1–18. doi: 10.3390/v9030049. Full text in Research Archive
• Grundt, Kirsten; Thiede, Bernd & Østvold, Anne Carine (2017). Identification of kinases phosphorylating 13 sites in the nuclear, DNA-binding protein NUCKS. Biochimica et Biophysica Acta - Proteins and Proteomics. ISSN 1570-9639. 1865(3), p. 359–369. doi: 10.1016/j.bbapap.2016.12.009.
• Lopez Soop, Graciela; Rønningen, Torunn; Rogala, Agnieszka; Richartz, Nina; Blomhoff, Heidi Kiil & Thiede, Bernd [Show all 8 contributors for this article] (2017). AKAP95 interacts with nucleoporin TPR in mitosis and is important for the spindle assembly checkpoint. Cell Cycle. ISSN 1538-4101. 16(10), p. 947–956. doi: 10.1080/15384101.2017.1310350. Full text in Research Archive
• Fiorito, Elisa; Sharma, Yogita; Gilfillan, Siv; Wang, Shixiong; Singh, Sachin Kumar & Somisetty, Venkata Satheesh [Show all 11 contributors for this article] (2016). CTCF modulates Estrogen Receptor function through specific chromatin and nuclear matrix interactions. Nucleic Acids Research (NAR). ISSN 0305-1048. 44, p. 10588–10602. doi: 10.1093/nar/gkw785.
• Gerner, Lisa; Munack, Steffi; Temmerman, Koen; Lawrence-Dörner, Ann-Marie; Besir, Huseyin & Wilmanns, Matthias [Show all 10 contributors for this article] (2016). Data for the co-expression and purification of human recombinant CaMKK2 in complex with calmodulin in Escherichia coli. Data in Brief. ISSN 2352-3409. 8, p. 733–740. doi: 10.1016/j.dib.2016.06.033.
• Olsen, Christel Moræus; Markussen, Turhan; Thiede, Bernd & Rimstad, Espen (2016). Infectious Salmon Anaemia Virus (ISAV) RNA Binding Protein Encoded by Segment 8 ORF2 and Its Interaction with ISAV and Intracellular Proteins. Viruses. ISSN 1999-4915. 8(2). doi: 10.3390/v8020052. Full text in Research Archive
• Gerner, Lisa; Munack, Steffi; Temmerman, Koen; Lawrence-Dörner, Ann-Marie; Besir, Huseyin & Wilmanns, Matthias [Show all 9 contributors for this article] (2016). Using the fluorescent properties of STO-609 as a tool to assist structure-function analyses of recombinant CaMKK2. Biochemical and Biophysical Research Communications - BBRC. ISSN 0006-291X. 476(2), p. 102–107. doi: 10.1016/j.bbrc.2016.05.045.
• Bousquet, Paula; Sandvik, Joe Alexander; Arntzen, Magnus Øverlie; Edin, Nina Frederike J; Christoffersen, Stine & Krengel, Ute [Show all 8 contributors for this article] (2015). Hypoxia Strongly Affects Mitochondrial Ribosomal Proteins and Translocases, as Shown by Quantitative Proteomics of HeLa Cells. International Journal of Proteomics. ISSN 2090-2174. doi: 10.1155/2015/678527.
• Bollineni, Ravi Chand; Guldvik, Ingrid Jenny; Grönberg, Henrik; Wiklund, Fredrik; Mills, Ian Geoffrey & Thiede, Bernd (2015). A differential protein solubility approach for the depletion of highly abundant proteins in plasma using ammonium sulfate. The Analyst. ISSN 0003-2654. 140(24), p. 8109–8117. doi: 10.1039/c5an01560j.
• Chymkowitch, Pierre; Nguéa P, Aurélie; Aanes, Håvard; Koehler, Christian; Thiede, Bernd & Lorenz, Susanne [Show all 9 contributors for this article] (2015). Sumoylation of Rap1 mediates the recruitment of TFIID to promote transcription of ribosomal protein genes. Genome Research. ISSN 1088-9051. 25(6), p. 897–906. doi: 10.1101/gr.185793.114.
• Øverbye, Anders; Skotland, Tore; Koehler, Christian; Thiede, Bernd; Seierstad, Therese & Berge, Viktor [Show all 8 contributors for this article] (2015). Identification of prostate cancer biomarkers in urinary exosomes. OncoTarget. ISSN 1949-2553. 6(30), p. 30357–30376. doi: 10.18632/oncotarget.4851.
• Arntzen, Magnus Øverlie; Boddie, Paul; Frick, Rahel; Koehler, Christian & Thiede, Bernd (2015). Consolidation of proteomics data in the Cancer proteomics database. Proteomics. ISSN 1615-9853. 15(22), p. 3765–3771. doi: 10.1002/pmic.201500144.
• Serguienko, Anastassia; Grad, Iwona; Wennerstrøm, Anna; Meza, Leonardo Zepeda; Thiede, Bernd & Stratford, Eva Wessel [Show all 8 contributors for this article] (2015). Metabolic reprogramming of metastatic breast cancer and melanoma by Let-7a microRNA. OncoTarget. ISSN 1949-2553. 6(4), p. 2451–2465. doi: 10.18632/oncotarget.3235.
• Albrecht, Elke; Norheim, Frode; Thiede, Bernd; Holen, Torgeir; Ohashi, Tomoo & Schering, Lisa [Show all 12 contributors for this article] (2015). Irisin - A myth rather than an exercise-inducible myokine. Scientific Reports. ISSN 2045-2322. 5. doi: 10.1038/srep08889.
• Koehler, Christian; Arntzen, Magnus Øverlie & Thiede, Bernd (2015). The impact of carbon-13 and deuterium on relative quantification of proteins using stable isotope diethyl labeling. Rapid Communications in Mass Spectrometry. ISSN 0951-4198. 29(9), p. 830–836. doi: 10.1002/rcm.7170.
• Villa, Oscar ; Brookes, Steven J; Thiede, Bernd; Heijl, Lars; Lyngstadaas, Ståle Petter & Reseland, Janne Elin (2015). Subfractions of enamel matrix derivative differentially influence cytokine secretion from human oral fibroblasts. Journal of Tissue Engineering. ISSN 2041-7314. 6, p. 1–11. doi: 10.1177/2041731415575857. Full text in Research Archive Show summary

  Enamel matrix derivative is used to promote periodontal regeneration during the corrective phase of the treatment of periodontal defects. Our main goal was to analyze the bioactivity of different molecular weight fractions of enamel matrix derivative. Enamel matrix derivative, a complex mixture of proteins, was separated into 13 fractions using size-exclusion chromatography and characterized by sodium dodecyl sulfate–polyacrylamide gel electrophoresis and liquid chromatography–electrospray ionization–tandem mass spectrometry. Human periodontal ligament fibroblasts were treated with either enamel matrix derivative or the different fractions. Proliferation and cytokine secretion to the cell culture medium were measured and compared to untreated cells. The liquid chromatography–electrospray ionization–tandem mass spectrometry analyses revealed that the most abundant peptides were amelogenin and leucine-rich amelogenin peptide related. The fractions containing proteins above 20 kDa induced an increase in vascular endothelial growth factor and interleukin-6 secretion, whereas lower molecular weight fractions enhanced proliferation and secretion of interleukin-8 and monocyte chemoattractant protein-1 and reduced interleukin-4 release. The various molecular components in the enamel matrix derivative formulation might contribute to reported effects on tissue regeneration through their influence on vascularization, the immune response, and chemotaxis.

• Albrecht, Elke; norheim, frode; Thiede, Bernd; Lee, Sindre; Holen, Torgeir & Ohashi,, Tomoo [Show all 12 contributors for this article] (2015). Irisin – a myth rather than an exercise-inducible myokine. Scientific Reports. ISSN 2045-2322. doi: 10.1038/srep08889.
• Glowinski, Frithjof; Holland, Carsten; Thiede, Bernd; Jungblut, Peter R. & Meyer, Thomas (2014). Analysis of T4SS-induced signaling by H. pylori using quantitative phosphoproteomics. Frontiers in Microbiology. ISSN 1664-302X. 5(JULY). doi: 10.3389/fmicb.2014.00356.
• Haaland, Ingvild; Opsahl, Jill Anette; Berven, Frode; Reikvam, Håkon; Fredly, Hanne Kristin & Haugse, Ragnhild [Show all 11 contributors for this article] (2014). Molecular mechanisms of nutlin-3 involve acetylation of p53, histones and heat shock proteins in acute myeloid leukemia. Molecular Cancer. ISSN 1476-4598. 13(1:116). doi: 10.1186/1476-4598-13-116. Full text in Research Archive
• Frank, Matthias Johannes; Walter, Martin Sebastian; Rubert, Marina; Thiede, Bernd; Monjo Cabrer, Marta & Reseland, Janne Elin [Show all 8 contributors for this article] (2014). Cathodic polarization coats titanium based implant materials with enamel matrix derivate (EMD). Materials. ISSN 1996-1944. 7(3), p. 2210–2228. doi: 10.3390/ma7032210. Full text in Research Archive Show summary

  The idea of a bioactive surface coating that enhances bone healing and bone growth is a strong focus of on-going research for bone implant materials. Enamel matrix derivate (EMD) is well documented to support bone regeneration and activates growth of mesenchymal tissues. Thus, it is a prime candidate for coating of existing implant surfaces. The aim of this study was to show that cathodic polarization can be used for coating commercially available implant surfaces with an immobilized but functional and bio-available surface layer of EMD. After coating, XPS revealed EMD-related bindings on the surface while SIMS showed incorporation of EMD into the surface. The hydride layer of the original surface could be activated for coating in an integrated one-step process that did not require any pre-treatment of the surface. SEM images showed nano-spheres and nano-rods on coated surfaces that were EMD-related. Moreover, the surface roughness remained unchanged after coating, as it was shown by optical profilometry. The mass peaks observed in the matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy (MALDI-TOF MS) analysis confirmed the integrity of EMD after coating. Assessment of the bioavailability suggested that the modified surfaces were active for osteoblast like MC3M3-E1 cells in showing enhanced Coll-1 gene expression and ALP activity.

• Pavlovic-Kozjak, Vera; Prell, F; Thiede, Bernd; Gotz, M; Wosiek, D & Ott, C [Show all 7 contributors for this article] (2014). C1orf163/RESA1 is a novel mitochondrial intermembrane space protein connected to respiratory chain assembly. Journal of Molecular Biology (JMB). ISSN 0022-2836. 426(4), p. 908–920. doi: 10.1016/j.jmb.2013.12.001.
• Oldenburg Ruppelt, Anja; Delbarre, Erwan; Thiede, Bernd; Vigouroux, Corinne & Collas, Philippe (2014). Deregulation of Fragile X-related protein 1 by the lipodystrophic lamin A p.R482W mutation elicits a myogenic gene expression program in preadipocytes. Human Molecular Genetics. ISSN 0964-6906. 23(5), p. 1151–1162. doi: 10.1093/hmg/ddt509.
• Callaway, A.; Kostrzewa, M.; Willershausen, B.; Schmidt, F.; Thiede, Bernd & Küpper, H. [Show all 7 contributors for this article] (2013). Identification of Lactobacilli from Deep Carious Lesions by Means of Species-Specific PCR and MALDI-TOF Mass Spectrometry. Clinical Laboratory. ISSN 1433-6510. 59(11-12), p. 1373–1379. doi: 10.7754/Clin.Lab.2013.121225.
• Størvold, Gro Leite; Landskron, Johannes; Strozynski, Margarita Anna; Arntzen, Magnus; Koehler, Christian & Kalland, Maria Elisabeth [Show all 8 contributors for this article] (2013). Quantitative profiling of tyrosine phosphorylation revealed changes in the activity of the T cell receptor signaling pathway upon cisplatin-induced apoptosis. Journal of Proteomics. ISSN 1874-3919. 91, p. 344–357. doi: 10.1016/j.jprot.2013.07.019.
• Arczewska, Katarzyna; Tomazella, Gisele Guicardi; Lindvall, Jessica M.; Kassahun, Henok; Maglioni, Silvia & Torgovnick, Alessandro [Show all 17 contributors for this article] (2013). Active Transcriptomic and Proteomic Reprogramming in the C. elegans Nucleotide Excision Repair Mutant xpa-1. Nucleic Acids Research (NAR). ISSN 0305-1048. 41(10), p. 5368–5381. doi: 10.1093/nar/gkt225.
• Murrell, Wayne; Palmero, Emily Herrera; Bianco, John; Stangeland, Biljana; Joel, Mrinal & Paulson, Linda Marie [Show all 16 contributors for this article] (2013). Expansion of Multipotent Stem Cells from the Adult Human Brain. PLOS ONE. ISSN 1932-6203. 8(8). doi: 10.1371/journal.pone.0071334.

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• Dugarte, Maria Eugenia Chollet; Harrison, Sean; Baumgarten, Saphira Felicitas; de la Morena-Barrio, Maria Eugenia; Bravo-Pérez, Carlos & Mowinckel, Marie-Christine [Show all 12 contributors for this article] (2022). Human iPSC-derived hepatic organoids – a model for blood coagulation research and therapy. Human Gene Therapy. ISSN 1043-0342. doi: 10.1089/hum.2022.29225.abstracts.
• Bakketeig, Eris Aas; Olsen, Christine; Berg, Henriette Engen; Nyman, Tuula Anneli; Thiede, Bernd & Lundanes, Elsa [Show all 8 contributors for this article] (2021). Optimization of concatenation of fractions in comprehensive two dimensional liquid chromatography bottom-up proteomics. Show summary

  Two dimensional liquid chromatography (2D-LC) has long been a commonly used technique in bottom-up proteomics, and is as relevant today as ever [1, 2]. To maximize the number of protein identifications, analytical chemists have strived to obtain 2D-LC systems with a high degree of orthogonality, which is needed to reach the required high peak capacities. A system utilizing reversed-phase chromatography (RP) in both column dimensions with a large difference in pH has proven to yield a higher peak capacity for peptides, even with a lower degree of orthogonality compared to other combinations [3]. The present study is based on Reubsaet, et al. [4]. The study is a comprehensive offline RPRP 2D-LC system with high pH (>9) in the first dimension and low pH (3) in the second dimension. The method’s purpose is to maximise protein identifications from one trypsinated protein sample. To achieve maximum identifications, Reubsaet incorporated the concept of concatenation of fractions. In practice, concatenation is applied through collecting the column output from the first dimension in eight numbered vials, where the 1st, 9th, 17th, … fractions are collected in the first vial, the 2nd, 10th, 18th, … are collected in the second, etc. [4]. In the present study, the fractionation scheme is examined by changing the total number of vials in which samples are concatenated, the number of fractions in each vial, and the collection time for each fraction. As the method demands high precision and is very timeconsuming, automatization is practically essential. Automatization is achieved with the spider fractionation scheme, proposed and shown by Kulak, et al.[5]. Here, a 10-port injector connects the first dimension column to each sample vial, and switches between them automatically, reducing the strain on the operator drastically, while removing human errors. The optimization of the concatenation will lead to higher numbers of identified proteins in proteomics.

• Hanson, Ingunn; Pitman, Kathinka Elinor; Thiede, Bernd; Cai, Yiqing & Edin, Nina Frederike Jeppesen (2021). Proteomic Analysis of Low Dose-Rate Primed Cells and Extracellular Exosomes.
• Dugarte, Maria Eugenia Chollet; andersen, elisabeth; de la Morena-Barrio, Maria Eugenia; Bravo-Perez, Carlos; Mowinckel, Marie-Christine & Myklebust, Christiane Fillion [Show all 12 contributors for this article] (2020). Characterizing Coagulation FVII from iPSC-Hepatocytes-like Cells: Setting the Basis for Cell Therapy Development. Blood. ISSN 0006-4971. 136. doi: 10.1182/blood-2020-139211.
• Hanson, Ingunn; Edin, Nina Frederike J; Thiede, Bernd & Altanerova, Ursula (2020). Communication of radioprotective efects by TGF-β3.
• Hanson, Ingunn; Altanerova, Ursula; Thiede, Bernd & Edin, Nina Frederike J (2020). Radioprotector TGF-β3 is secreted in exosomes and activated by LDR priming. Show summary

  The biological effects of ionizing radiation in the low-dose region is important for diagnostic imaging, healthy tissue in radiation therapy and environmental radiation. For a majority of tested cell lines, the low dose hyper-radiosensitive (HRS) response has been shown to be default. We have previously shown that cells primed with a low dose-rate (⁓0.3 Gy/h) ionizing radiation permanently loses the HRS response. We have also shown that the transforming growth factor (TGF)-β3 is responsible for this effect. Here, we investigated the secretion mechanism of TGF-β3 from LDR primed cells, and theorize regarding the way it is activated. Exosomes were isolated from LDR primed cells, and were shown to remove HRS in reporter cells when co-cultured with these. Adding a TGF-β3 inhibitor to the medium restored the HRS response in reporter cells, confirming that TGF-β3 was the factor in the exosomes responsible for removing HRS. Mass spectrometry was performed on the content of exosomes from primed and control cells. Proteomic analysis confirmed the presence of exosome-specific proteins in exosomes from primed and control groups. TGF-β3 along with latency-associated protein (LAP), the protein that TGF-β3 is bound to in its inactive form, was present in similar amounts in both groups, indicating that TGF-β3 was secreted in its inactive form, regardless of LDR priming. Three proteins were significantly upregulated in the primed exosomes. These proteins will be investigated further in future experiments. We conclude that TGF-β3 is secreted in its inactive form in exosomes from LDR primed and unprimed cells, and that the priming is responsible for its activation. We will further investigate three significantly upregulated proteins with regards to their role in the activation of TGF-β3.

• Berg, Henriette Engen; Halldórsson, Skarphéðinn; Thiede, Bernd; Vik-Mo, Einar O.; Lundanes, Elsa & Wilson, Steven Ray Haakon (2020). Micro pillar array columns for comprehensive proteomics. Show summary

  Pillar array nano liquid chromatography columns can potentially replace packed nano liquid chromatography (nLC) columns for analyses of complex samples due to high chromatographic performance and low backpressure. In our study, pillar array columns are used for the detection of potential biomarkers in Glioblastoma Multiforme (GBM), which is the most aggressive form of brain cancer in adults. Pillar array columns consist of several micropillars etched into silicon wafers using lithographic micromachining. The interest of these columns in nLC format has increased as an option to packed nLC columns as the chromatographic efficiency could outperform nLC columns packed with sub-2 µm particles while maintaining the sensitivity [1]. In contrast to packed columns, where eddy dispersion is the main source of band broadening due to irregular flow paths between the particles, the perfectly ordered pillars in pillar array columns eliminate the eddy dispersion to a minimum. The low backpressure of pillar array columns compared to that of packed columns also permits the use of exceptionally long columns, increasing the chromatographic performance further. Using pillar array columns, plate numbers over 1 million and reduced plate heights (h) even <1 µm have been achieved [2-4]. High chromatographic performance is especially important in comprehensive proteomics. Pre-fractionation (using e.g. gel electrophoresis) is often added in proteomic protocols to increase the throughput [5]. However, performing pre-fractionation can be time-consuming in addition to the highly increased instrument time required. Recently, a micro-Chip pillar array nLC column (µPACTM) compatible with standard nLC instrumentation has been commercialized (Figure 1) [6]. Our question was; could the use of µPAC nLC columns reduce the need for pre-fractionation in comprehensive proteomics of GBM biopsies?

• Berg, Henriette Engen; Skottvoll, Frøydis Sved; Bjørseth, Kamilla; Sæterdal, Kristina Erikstad; Brandtzaeg, Ole Kristian & Vehus, Tore [Show all 11 contributors for this article] (2018). Development of nanoLC column technology for proteomic studies . Show summary

  Background NanoLC has emerged as a major technique in proteomics due to improved sensitivity, which enables analysis of small sample volumes and low concentrations. In our group (Bioanalytical chemistry, BACH) we focus on the development of column technology, including porous layer open tubular (PLOT) columns and self-packing of columns for proteomic applications. Methods The PLOT columns were used for both on-line digestion (enzyme reactors) and separations (10 µm ID, PS-DVB with ODS). Enzyme reactors (20 µm ID and multi-PLOT columns (~8 µm ID)) were immobilized with trypsin and Lys-C for protein digestion. We also compared self-packed columns of 50 µm ID (2.6 µm C18 core-shell particles) to a commercial column (75 µm ID). The columns were used for detection of CYP27a1 in MDA-MB-231 (breast cancer) cells, and biomarker candidates in MDA-MB-231 and glioblastoma multiforme (brain cancer) exosomes. For exosome isolation (cell culture medium), ultracentrifugation (“golden standard”) was compared to a Total Exosome Isolation Reagent from Thermo Fisher regarding protein yield and purity. Results Our PLOT columns were successfully employed for proteins, metabolites and peptides with attogram detection limits and peak capacities around 250 [1]. The enzyme reactors provided sufficient digestion in ~5 minutes compared to overnight digestions (common in off-line protocols) [2]. Furthermore, a quantitative method of the neurotoxin ricin was developed using the multi-PLOT to reduce manual sample handling [3] . The self-packed columns obtained peak capacities comparable to the commercial nanoLC column for peptide separations [4]. The self-packed columns were used for the targeted detection of CYP27A1 (potential breast cancer biomarker) in MDA-MB-231 cells. In the recent exosome study, exosomes were present and biomarker candidates were identified. However, the characterization techniques are in our hands not satisfactory. Conclusions We have successfully developed sensitive nanoLC column formats for proteomic applications.

• Eriksen, Gunnar Sundstøl; Thiede, Bernd & Solhaug, Anita (2018). Effects of an emerging Fusarium mycotoxin on hepatocytes.
• Khan, Ayyad Ahmad Zartasht; Jackson, Catherine; Reppe, Sjur; Utheim, Tor Paaske; Olstad, Ole Kristoffer & Thiede, Bernd [Show all 7 contributors for this article] (2018). Sericin-Induced Melanogenesis in Cultured Retinal Pigment Epithelium is Associated with Elevated Levels of Hydrogen Peroxide.
• Bollineni, Ravi Chand; Koehler, Christian; Gislefoss, Randi Elin; Anonsen, Jan Haug & Thiede, Bernd (2018). Author Correction: Large-scale intact glycopeptide identification by Mascot database search. Scientific Reports. ISSN 2045-2322. 8. doi: 10.1038/s41598-018-28147-w.
• López-Soop, Graciela; Rønningen, Torunn; Rogala, Agnieszka; Richartz, Nina; Blomhoff, Heidi Kiil & Thiede, Bernd [Show all 8 contributors for this article] (2017). AKAP95 interacts with nucleoporin TPR in mitosis and is important for the spindle assembly checkpoint. Cell Cycle. ISSN 1538-4101. 16(10), p. 947–956. doi: 10.1080/15384101.2017.1310350..
• Sved Skottvoll, Frøydis; Lund, Kaja; Røberg-Larsen, Hanne; Berg, Henriette Sjånes; Thiede, Bernd & Lundanes, Elsa [Show all 7 contributors for this article] (2017). Diagnostic potential of exosomes: The purification issue.
• Jensen, Janicke Liaaen; Utheim, Øygunn Aass; Chen, Xiangjun; Thiede, Bernd; Aqrawi, Lara Adnan & Rusthen, Shermin [Show all 9 contributors for this article] (2016). Searching for Disease Biomarkers for Primary Sjögren’s Syndrome Based on Oral and Ocular Patient Examinations.
• Jungblut, Peter R.; Thiede, Bernd & Schluter, H (2016). Towards deciphering proteomes via the proteoform, protein speciation, moonlighting and protein code concepts. Journal of Proteomics. ISSN 1874-3919. 134, p. 1–4. doi: 10.1016/j.jprot.2016.01.012.
• Lopez Soop, Graciela; Reiner, Andrew Henry; Thiede, Bernd; Collas, Philippe & Küntziger, Thomas Michel (2015). Regulation of Normal Mitotic Progression by A-kinase Anchoring Protein 95 (AKAP95).
• Perdreau, Harmonie; Guldsten, Hanne; Progida, Cinzia; Thiede, Bernd; Bakke, Oddmund & Morth, Jens Preben (2014). Molecular and Structural Characterization of Sjögren syndrome/scleroderma autoantigen 1 (SSSCA1).
• Bousquet, Paula; Abshiru, Nebiyu; Sandvik, Joe Alexander; Pettersen, Erik O; Thiede, Bernd & Woods, Robert [Show all 8 contributors for this article] (2014). Anti-tumor antibodies and hypoxia.
• Arntzen, Magnus & Thiede, Bernd (2013). Cell Death Proteomics.
• Bousquet, Paula; Abshiru, Nebiyu; Johansen, Rune Forstrøm; Bjørås, Magnar; Sandvik, Joe Alexander & Pettersen, Erik O [Show all 10 contributors for this article] (2013). A structural and functional study of anti-ganglioside antibodies. International Journal of Molecular Medicine. ISSN 1107-3756. 32, p. S42–S42. Show summary

  NeuGc GM3 is considered an attractive target for cancer immunotherapy since it is a tumor-associated antigen present in several types of cancer such as breast carcinoma, melanoma and non-small cell lung cancer (NSCLC) while being effectively absent in healthy human tissues. The monoclonal antibody (mAb) 14F7 is specific for NeuGc GM3 and does not cross-react with NeuAc GM3, a ganglioside found in healthy tissues, even though these two glycolipids have highly similar structures. 14F7 treatment has shown to induce complement-dependent cytotoxicity (CDC) and antibody-dependent cell-mediated cytotoxicity (ADCC), but has in addition the ability to directly kill tumor cells without involving the complement system. We employed a mass spectrometry-based approach and SPR analysis for the characterization of the binding interactions between 14F7 and the NeuGc GM3 ganglioside or the anti-idiotypic antibody generated from 14F7, 4G9, respectively. In order to understand the mechanism by which the antibody kills the cells, we then performed stable isotope labeling with amino acids in cell culture (SILAC) combined with proteomics to identify and quantify proteins after antibody treatment. SILAC was also employed to investigate the protein expression in HeLa cells under hypoxic conditions. The combination of MS, SPR and SILAC analyses employed here have allowed us to gain a significantly improved understanding of the molecular interactions and functions of a highly promising antibody for cancer immunotherapies.

• Berg, Henriette Engen; Wilson, Steven Ray Haakon; Lundanes, Elsa; Thiede, Bernd & Vik-Mo, Einar Osland (2022). Exploring miniaturized chromatography formats and sample preparation methods for shotgun proteomics in limited biological samples. Department of Chemistry, Faculty of Mathematics and Natural Sciences, University of Oslo. ISSN 1501-7710. 2022(2522). Show summary

  A significant challenge in medical diagnostics is the development of simple but efficient tools for the detection/quantification of several biomarkers simultaneously using non-invasive sampling techniques. In this regard, the analysis of proteins (proteomics) is essential for understanding cellular processes and biomarker discovery. However, proteins vary greatly in terms of concentration levels and chemical properties in biological materials. Further, low sample sizes of modern biological models (e.g., patient-derived cell cultures, exosomes, and organoids) remain a big analytical challenge. The present work has focused on the brain cancer glioblastoma, which is in great need of increased knowledge and non-invasive sampling techniques. In addition, human organoids, which could act as a future in vitro model for disease modeling and personalized medicine, have been investigated. We have used high-resolution mass spectrometry for protein identification, exploring a selection of miniaturized liquid chromatography formats (for separation) and sample preparation techniques. By implementing these techniques, we have been able to study exosomes, 2D/3D cell cultures, and organoids, identifying over 6300 proteins in a single run using less than 5 µg of protein. The work has provided important insight into the possibilities and challenges of several novel models. It represents a development toward deeper proteomic profiling focusing on maintaining a high protein yield and time efficiency.

• Bakketeig, Eris Aas; Wilson, Steven Ray Haakon; Lundanes, Elsa; Berg, Henriette Engen; Olsen, Christine & Reubsaet, Leon [Show all 8 contributors for this article] (2021). The setup and optimization of a complete global proteomics two-dimensional liquid chromatography system, using Spider Fractionation. Universitetet i Oslo.
• Köhler, Christian Jeffrey; Thiede, Bernd; Lundanes, Elsa & Greibrokk, Tyge (2013). Isobaric peptide termini labeling (IPTL) - An alternative approach for quantitative proteomics. Universitetet i Oslo.

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