All publications where NAPI partners and/or core facilities have contributed mass spectrometry expertise are provided below (beginning November 2020). Where NAPI partners are not included in the author list, one or more NAPI core facilities provided support in generating mass spectrometry/proteomics data contained within the manuscript.
Wang, Q. et al. UDP-glucose dehydrogenase expression is upregulated following EMT and differentially affects intracellular glycerophosphocholine and acetylaspartate levels in breast mesenchymal cell lines. Mol. Oncol. Accepted/unedited
Skottvoll, F. S. et al. Direct Electromembrane Extraction based Mass Spectrometry: A Tool for Studying Drug Metabolism Properties of Liver Organoids. Anal. Sens. Accepted/unedited
Maddirevula, S. et al. Insight into ALKBH8-related intellectual developmental disability based on the first pathogenic missense variant. Hum. Genet. doi:10.1007/s00439-021-02391-z
Hildrestrand, G. A. et al. NEIL1 and NEIL2 DNA glycosylases modulate anxiety and learning in a cooperative manner in mice. Commun. Biol. 4, 1–14
Grønningsæter, I. S. et al. Effects of the Autophagy-Inhibiting Agent Chloroquine on Acute Myeloid Leukemia Cells; Characterization of Patient Heterogeneity. J. Pers. Med. 11, 779
Waløen, K. et al. Cysteine Modification by Ebselen Reduces the Stability and Cellular Levels of 14-3-3 Proteins. Mol. Pharmacol. 100, 155–169
Farag, Y. M. et al. PeptideShaker Online: A User-Friendly Web-Based Framework for the Identification of Mass Spectrometry-Based Proteomics Data. J. Proteome Res. doi:10.1021/acs.jproteome.1c00678
Aasebø, E. et al. Proteomic Characterization of Spontaneous Stress-Induced In Vitro Apoptosis of Human Acute Myeloid Leukemia Cells; Focus on Patient Heterogeneity and Endoplasmic Reticulum Stress. Hemato 2, 607–627
Johannsen, C. et al. Comparison of LFQ and IPTL for Protein Identification and Relative Quantification. Mol. Basel Switz. 26, 5330
Myrbråten, I. S. et al. SmdA is a novel cell morphology determinant in Staphylococcus aureus. bioRxiv doi:10.1101/2021.11.23.469651.
Andersen, E. et al. Molecular Characterization of Two Homozygous Factor VII Variants Associated with Intracranial Bleeding. Thromb. Haemost. 121, 1588–1598
Vestad, B. et al. Plasma extracellular vesicles in people living with HIV and type 2 diabetes are related to microbial translocation and cardiovascular risk. Sci. Rep. 11, 21936
Skåne, A., et al. Comparative proteomic profiling reveals specific adaption of Vibrio anguillarum to oxidative stress, iron deprivation and humoral components of innate immunity. J. Proteomics 104412. doi:10.1016/j.jprot.2021.104412.
Mendel, M. et al. Splice site m6A methylation prevents binding of U2AF35 to inhibit RNA splicing. Cell 184, 3125-3142.e25
Sumabe, B. K. et al. Nucleoside Analogues Are Potent Inducers of Pol V-mediated Mutagenesis. Biomolecules 11, 843
Lirussi, L. et al. RNA Metabolism Guided by RNA Modifications: The Role of SMUG1 in rRNA Quality Control. Biomolecules 11, 76
Pinto, S. M. et al. Comparative Proteomic Analysis Reveals Varying Impact on Immune Responses in Phorbol 12-Myristate-13-Acetate-Mediated THP-1 Monocyte-to-Macrophage Differentiation. Front. Immunol. 12, 679458
Mirlashari, M. R. et al. Proteomic study of apheresis platelets made HLA class I deficient for transfusion of refractory patients. Proteomics Clin. Appl. e2100022 doi:10.1002/prca.202100022
Snapkov, I. et al. Progress and challenges in mass spectrometry-based analysis of antibody repertoires. Trends Biotechnol. doi:10.1016/j.tibtech.2021.08.006
Abudu, Y. P. et al. SAMM50 acts with p62 in piecemeal basal- and OXPHOS-induced mitophagy of SAM and MICOS components. J. Cell Biol. 220
Rye, T. K. et al. Electromembrane extraction of peptides using deep eutectic solvents as liquid membrane. Anal. Chim. Acta 1175, 338717
McKitterick, N. et al. On-line duplex molecularly imprinted solid-phase extraction for analysis of low-abundant biomarkers in human serum by liquid chromatography-tandem mass spectrometry. J. Chromatogr. A 1655, 462490
Wanichawan, P. et al. Design of a Proteolytically Stable Sodium-Calcium Exchanger 1 Activator Peptide for In Vivo Studies. Front. Pharmacol. 12, 1328
Reigada, I. et al. Surfaceome and Exoproteome Dynamics in Dual-Species Pseudomonas aeruginosa and Staphylococcus aureus Biofilms. Front. Microbiol. 12, 1571
Borowicz, P. et al. Tyr192 Regulates Lymphocyte-Specific Tyrosine Kinase Activity in T Cells. J. Immunol. 207, 1128–1137
Holm, S. et al. Immune complexes, innate immunity, and NETosis in ChAdOx1 vaccine-induced thrombocytopenia. Eur. Heart J. doi:10.1093/eurheartj/ehab506
Wollen, K. L. et al. ALKBH3 partner ASCC3 mediates P-body formation and selective clearance of MMS-induced 1-methyladenosine and 3-methylcytosine from mRNA. J. Transl. Med. 19, 287
Savijoki, K. et al. Surface-Shaving Proteomics of Mycobacterium marinum Identifies Biofilm Subtype-Specific Changes Affecting Virulence, Tolerance, and Persistence. mSystems 6, e005002
Lorentzen, S. B. et al. Genomic and Proteomic Study of Andreprevotia ripae Isolated from an Anthill Reveals an Extensive Repertoire of Chitinolytic Enzymes. J. Proteome Res. 20, 4041–4052
Jensen, S. et al. Endozoicomonadaceae symbiont in gills of Acesta clam encodes genes for essential nutrients and polysaccharide degradation. FEMS Microbiol. Ecol. 97
Mehta, S. et al. ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework. F1000Research 10, 103
Mehta, S. et al. Updates on metaQuantome Software for Quantitative Metaproteomics. J. Proteome Res. 20, 2130–2137
Skagen, C. et al. Chronic treatment with terbutaline increases glucose and oleic acid oxidation and protein synthesis in cultured human myotubes. Curr. Res. Pharmacol. Drug Discov. 2, 100039
Alves, C. R. R. et al. Cancer-induced muscle atrophy is determined by intrinsic muscle oxidative capacity. FASEB J. Off. Publ. Fed. Am. Soc. Exp. Biol. 35, e21714
Halvorsen, T. G. et al. Matrix-Assisted Ionization and Tandem Mass Spectrometry Capabilities in Protein Biomarker Characterization—An Initial Study Using the Small Cell Lung Cancer Biomarker Progastrin Releasing Peptide as a Model Compound. J. Am. Soc. Mass Spectrom. 32, 611–614
Alswady-Hoff, M. et al. Long-Term Exposure to Nanosized TiO2 Triggers Stress Responses and Cell Death Pathways in Pulmonary Epithelial Cells. Int. J. Mol. Sci. 22, 5349
Hernandez-Valladares, M. et al. Proteomic Studies of Primary Acute Myeloid Leukemia Cells Derived from Patients Before and during Disease-Stabilizing Treatment Based on All-Trans Retinoic Acid and Valproic Acid. Cancers 13, 2143
Halvorsen, T. G. et al. Affinity capture in bottom-up protein analysis – Overview of current status of proteolytic peptide capture using antibodies and molecularly imprinted polymers. Anal. Chim. Acta 338714. doi:10.1016/j.aca.2021.338714
Aasebø, E. et al. Proteomic Comparison of Bone Marrow Derived Osteoblasts and Mesenchymal Stem Cells. Int. J. Mol. Sci. 22, 5665
Koehler, C. J. & Thiede, B. An Approach for Triplex-IPTL. Methods Mol. Biol. Clifton NJ 2228, 133–144.
Małecki, J. M. et al. Human METTL18 is a histidine-specific methyltransferase that targets RPL3 and affects ribosome biogenesis and function. Nucleic Acids Res. 49, 3185–3203
Pizzi, E. et al. Next-Generation Dried Blood Spot Samplers for Protein Analysis: Describing Trypsin-Modified Smart Sampling Paper. Separations 8, 66
Berzaghi, R. et al. Secretion rates and protein composition of extracellular vesicles released by cancer-associated fibroblasts after radiation. J. Radiat. Res. doi:10.1093/jrr/rrab018
Olinski, R. et al. Genomic Uracil and Aberrant Profile of Demethylation Intermediates in Epigenetics and Hematologic Malignancies. Int. J. Mol. Sci. 22, 4212.
Røberg-Larsen, H. et al. Liquid chromatography, a key tool for the advancement of single-cell omics analysis. Anal. Chim. Acta 338551. doi:10.1016/j.aca.2021.338551.
Nthiga, T. M. et al. Regulation of Golgi turnover by CALCOCO1-mediated selective autophagy. J. Cell Biol. 220
Wirth, M. et al. Phosphorylation of the LIR domain of SCOC modulates ATG8 binding affinity and specificity. J. Mol. Biol. 166987–166987. doi:10.1016/j.jmb.2021.166987.
Ramberg, H. et al. Proteomic analyses Identify Major Vault Protein as a Prognostic Biomarker for Fatal Prostate Cancer. Carcinogenesis. doi:10.1093/carcin/bgab015.
Quiles-Jiménez, A. et al. DNA glycosylase Neil3 regulates vascular smooth muscle cell biology during atherosclerosis development. Atherosclerosis. doi:10.1016/j.atherosclerosis.2021.02.023.
Oveland, E. et al. Cuprizone and EAE mouse frontal cortex proteomics revealed proteins altered in multiple sclerosis. Sci. Rep. 11, 7174
Aasebø, E. et al. The Constitutive Extracellular Protein Release by Acute Myeloid Leukemia Cells—A Proteomic Study of Patient Heterogeneity and Its Modulation by Mesenchymal Stromal Cells. Cancers 13, 1509
Kavli, B. et al. RPA2 winged-helix domain facilitates UNG-mediated removal of uracil from ssDNA; implications for repair of mutagenic uracil at the replication fork. Nucleic Acids Res. doi:10.1093/nar/gkab195.
Askarian, F. et al. The lytic polysaccharide monooxygenase CbpD promotes Pseudomonas aeruginosa virulence in systemic infection. Nat. Commun. 12, 1230
Skogvold, H. B. et al. Bridging the polar and hydrophobic metabolome in single-run untargeted liquid chromatography-mass spectrometry dried blood spot metabolomics for clinical purposes. medRxiv doi:10.1101/2021.03.22.21254119.
Bossche, T. V. D. et al. Critical Assessment of Metaproteome Investigation (CAMPI): A Multi-Lab Comparison of Established Workflows. bioRxiv doi:10.1101/2021.03.05.433915.
Martinez-Val, A. et al. Spatial-proteomics reveal in-vivo phospho-signaling dynamics at subcellular resolution. bioRxiv doi:10.1101/2021.02.02.425898.
Bascuñana, P., Brackhan, M. & Pahnke, J. Machine Learning-Supported Analyses Improve Quantitative Histological Assessments of Amyloid-β Deposits and Activated Microglia. J. Alzheimers Dis. 79, 597–605.
Namasivayam, V. et al. C@PA: Computer-Aided Pattern Analysis to Predict Multitarget ABC Transporter Inhibitors. J. Med. Chem. (2021) doi:10.1021/acs.jmedchem.0c02199.
Mosleth, E. F. et al. ‘Cerebrospinal fluid proteome shows disrupted neuronal development in multiple sclerosis’, Scientific reports, 11(1), p. 4087.
Roberg-Larsen, H., Wilson, S. R. and Lundanes, E. ‘Recent advances in on-line upfront devices for sensitive bioanalytical nano LC methods’, Trends in analytical chemistry: TRAC, 136, p. 116190.
Skottvoll, F. S. et al. ‘Electromembrane Extraction and Mass Spectrometry for Liver Organoid Drug Metabolism Studies’, Analytical chemistry, 93(7), pp. 3576–3585.
Stamnaes, J. et al. ‘In Well-Treated Celiac Patients Low-Level Mucosal Inflammation Predicts Response to 14-day Gluten Challenge’, Advancement of science, 8(4), p. 2003526.
Zawadzka, M. et al. ‘Searching for a UV-filter in the eyes of high-flying birds’, Scientific reports, 11(1), p. 273.
Burger, B., Vaudel, M. and Barsnes, H. ‘Importance of Block Randomization When Designing Proteomics Experiments’, Journal of proteome research, 20(1), pp. 122–128.
Kogler, S. et al. “Organoid-in-a-column” coupled on-line with liquid chromatography-mass spectrometry. bioRxiv 2020.09.08.282756 (2020) doi:10.1101/2020.09.08.282756.
Harrison, S. P. et al. Scalable production of tissue-like vascularised liver organoids from human PSCs. bioRxiv 2020.12.02.406835 (2020) doi:10.1101/2020.12.02.406835.
Hernandez-Valladares, M. et al. Biological characteristics of aging in human acute myeloid leukemia cells: the possible importance of aldehyde dehydrogenase, the cytoskeleton and altered transcriptional regulation. Aging 12, 24734–24777
Louwe, M. C. et al. Absence of NLRP3 Inflammasome in Hematopoietic Cells Reduces Adverse Remodeling After Experimental Myocardial Infarction. JACC Basic Transl. Sci. 5, 1210–1224
Tadele, D. S. et al. A cell competition–based small molecule screen identifies a novel compound that induces dual c-Myc depletion and p53 activation. J. Biol. Chem. 296, 100179
Nymark, M. et al. Functional studies of CpSRP54 in diatoms show that the mechanism of thylakoid protein insertion differs from plants and green algae. Plant J. doi:10.1111/tpj.15149
Tsjokajev, A. et al. Mass spectrometry-based measurements of cyclic adenosine monophosphate in cells, simplified using reversed phase liquid chromatography with a polar characterized stationary phase. J. Chromatogr. B 1160, 122384
Michalak, L. et al. Microbiota-directed fibre activates both targeted and secondary metabolic shifts in the distal gut. Nat. Commun. 11, 5773