Gao, L.* et al. Lipidomics atlas tracks alterations associated with deltamethrin-induced developmental neurotoxicity in embryonic zebrafish. J. Proteome Res., DOI: 10.1021/acs.jproteome.4c00779 (2025)
Kardell, O. et al. Multicenter longitudinal quality assessment of MS-based proteomics in plasma and serum. J. Proteome Res. 24, 1017-1029 (2025)
Kardell, O. et al. Correction to “Multicenter longitudinal quality assessment of MS-based proteomics in plasma and serum”. J. Proteome Res. 24, 4862–4863 (2025)
Phlairaharn, T.* et al. Improving proteomic dynamic range with Multiple Accumulation Precursor Mass Spectrometry.  J. Proteome Res. 24, 5116–5126 (2025)
Geyer, P.E.* et al. The circulating proteome─technological developments, current challenges, and future trends. J. Proteome Res. 23, 5279-5295 (2024)
Blume, B. et al. Lipidomic and metallomic alteration of Caenorhabditis elegans after acute and chronic manganese, iron and zinc exposure with link to neurodegenerative disorders.  J. Proteome Res. 22, 837–850 (2023)
Kardell, O. et al. Multicenter collaborative study to optimize mass spectrometry workflows of clinical specimens. J. Proteome Res. 23, 117-129 (2023)
Petrera, A. et al. Multiplatform approach for plasma proteomics: Complementarity of olink proximity extension assay technology to mass spectrometry-based protein profiling. J. Proteome Res. 20, 751-762 (2021)
Sun, B.* ; Smialowski, P. ; Straub, T.* & Imhof, A.* Investigation and highly accurate prediction of missed tryptic cleavages by deep learning. J. Proteome Res. 20, 3749–3757 (2021)
Wang, L.* et al. Metabolite triplet in serum improves the diagnostic accuracy of prediabetes and diabetes screening. J. Proteome Res. 20, 1005-1014 (2021)
Gouda, M. et al. Proteomics analysis revealed the importance of inflammation mediated downstream pathways and the protective role of curcumin during bleomycin-induced pulmonary fibrosis in C57BL/6 mice. J. Proteome Res. 19, 2950-2963 (2020)
Hladik, D. et al. Creb signaling mediates dose-dependent radiation response in the murine hippocampus two years after total body exposure. J. Proteome Res. 19, 337-345 (2020)
Zacharias, H.U. et al. A novel metabolic signature to predict the requirement of dialysis or renal transplantation in patients with chronic kidney disease. J. Proteome Res. 18, 1796–1805 (2019)
Haid, M. et al. Long-Term Stability of Human Plasma Metabolites during Storage at-80 degrees C. J. Proteome Res. 17, 203-211 (2018)
Hoernstein, S.N.W.* et al. Host cell proteome of Physcomitrella patens harbors proteases and protease inhibitors under bioproduction conditions. J. Proteome Res. 17, 3749-3760 (2018)
Subramanian, V. et al. PPARα is necessary for radiation-induced activation of noncanonical TGFβ signaling in the heart. J. Proteome Res. 17, 1677-1689 (2018)
Lepper, M.F. et al. Proteomic landscape of patient-derived CD4+T cells in recent-onset type 1 diabetes. J. Proteome Res. 17, 618-634 (2017)
Marx, H.* et al. Annotation of the domestic pig genome by quantitative proteogenomics. J. Proteome Res. 16, 2887-2898 (2017)
Philipp, J. et al. Radiation-induced endothelial inflammation is transferred via the secretome to recipient cells in a STAT-mediated process. J. Proteome Res. 16, 3903-3916 (2017)
Suarez-Diez, M.* et al. Plasma and serum metabolite association networks: Comparibility within and between studies using NMR and MS profiling. J. Proteome Res. 16, 2547-2559 (2017)
Subramanian, V. et al. The role of TGF beta and PPAR alpha signalling pathways in radiation response of locally exposed heart: Integrated global transcriptomics and proteomics analysis. J. Proteome Res. 16, 307-318 (2017)
Virgiliou, C.* et al. Amniotic fluid and maternal serum metabolic signatures in the second trimester associated with preterm delivery. J. Proteome Res. 16, 898-910 (2017)
Ly, A. et al. Proteomic profiling suggests central role of STAT signaling during retinal degeneration in the rd10 mouse model. J. Proteome Res. 15, 1350-1359 (2016)
Yousri, N.A.* et al. Diagnostic and prognostic metabolites identified for joint symptoms in the KORA population. J. Proteome Res. 15, 554-562 (2016)
Azimzadeh, O. et al. Integrative proteomics and targeted transcriptomics analyses in cardiac endothelial cells unravel mechanisms of long-term radiation-induced vascular dysfunction. J. Proteome Res. 14, 1203-1219 (2015)
Bakshi, M.V. et al. Total body exposure to low-dose ionizing radiation induces long-term alterations to the liver proteome of neonatally exposed mice. J. Proteome Res. 14, 366-373 (2015)
Do, K.T. et al. Network-based approach for analyzing intra- and interfluid metabolite associations in human blood, urine, and saliva. J. Proteome Res. 14, 1183-1194 (2015)
Heinzmann, S.S. & Schmitt-Kopplin, P. Deep metabotyping of the murine gastrointestinal tract for the visualization of digestion and microbial metabolism. J. Proteome Res. 14, 2267-2277 (2015)
Kempf, S.J. et al. Low-dose ionizing radiation rapidly affects mitochondrial and synaptic signaling pathways in murine hippocampus and cortex. J. Proteome Res. 14, 2055-2064 (2015)
Kempf, S.J. et al. Neonatal irradiation leads to persistent proteome alterations involved in synaptic plasticity in the mouse hippocampus and cortex. J. Proteome Res. 14, 4674-4686 (2015)
Dekker, T.J.* et al. Multicenter Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging (MALDI MSI) identifies proteomic differences in breast-cancer-associated stroma. J. Proteome Res. 13, 4730-4738 (2014)
McDonnell, L.A.* ; Walch, A.K. ; Stoeckli, M.* & Corthals, G.L.* MSiMass list: A public database of identifications for protein MALDI MSI. J. Proteome Res. 13, 1138–1142 (2014)
Poschmann, G.* et al. High fat diet induced isoform changes of the Parkinson’s disease protein DJ-1. J. Proteome Res. 13, 2339-2351 (2014)
Velikova, V.B. et al. Genetic manipulation of isoprene emissions in poplar plants remodels the chloroplast proteome. J. Proteome Res. 13, 2005-2018 (2014)
Walker, A. et al. The importance of sulfur-containing metabolites in discriminating fecal extracts between normal and type 2 diabetic mice. J. Proteome Res. 13, 4220-4231 (2014)
Azimzadeh, O. et al. PPAR alpha: A novel radiation target in locally exposed Mus musculus heart revealed by quantitative proteomics. J. Proteome Res. 12, 2700-2714 (2013)
Degroote, R.L.* et al. Expression changes and novel interaction partners of talin 1 in effector cells of autoimmune uveitis. J. Proteome Res. 12, 5812–5819 (2013)
Merl, J. ; Deeg, C.A.* ; Swadzba, M.E.* ; Ueffing, M. & Hauck, S.M. Identification of autoantigens in body fluids by combining pull-downs and organic precipitations of intact immune complexes with quantitative label-free mass spectrometry. J. Proteome Res. 12, 5656-5665 (2013)
Schulz, M. et al. Quantitative phosphoproteomic analysis of early alterations in protein phosphorylation by 2,3,7,8-tetrachlorodibenzo-p-dioxin. J. Proteome Res. 12, 866-882 (2013)
von Toerne, C. et al. Apoe, Mbl2 and Psp plasma protein levels correlate with diabetic phenotype in NZO mice - an optimized rapid workflow for SRM-based quantification. J. Proteome Res. 12, 1331-1343 (2013)
Bieler, S.* et al. Low dose proteasome inhibition affects alternative splicing. J. Proteome Res. 11, 3947-3954 (2012)
Gündisch, S.* et al. Variability of protein and phosphoprotein levels in clinical tissue specimens during the preanalytical phase. J. Proteome Res. 11, 5748-5762 (2012)
Krumsiek, J. ; Suhre, K. ; Illig, T. ; Adamski, J. & Theis, F.J. Bayesian independent component analysis recovers pathway signatures from blood metabolomics data. J. Proteome Res. 11, 4120-4131 (2012)
Meding, S. et al. Tumor classification of six common cancer types based on proteomic profiling by MALDI imaging. J. Proteome Res. 11, 1996-2003 (2012)
Chen, J.* et al. Serum 27-nor-5β-Cholestane-3,7,12,24,25 pentol glucuronide discovered by metabolomics as potential diagnostic biomarker for epithelium ovarian cancer. J. Proteome Res. 10, 2625-2632 (2011)
Azimzadeh, O. et al. Formalin-fixed paraffin-embedded (FFPE) proteome analysis using gel-free and gel-based proteomics. J. Proteome Res. 9, 4710-4720 (2010)
Balluff, B. et al. Classification of HER2/neu status in gastric cancer using a breast-cancer derived proteome classifier. J. Proteome Res. 9, 6317-6322 (2010)
Ergin, B.* et al. Proteomic analysis of PAXgene-fixed tissues. J. Proteome Res. 9, 5188-5196 (2010)
Gloeckner, C.J. et al. Phosphopeptide analysis reveals two discrete clusters of phosphorylation in the N-terminus and the Roc domain of the Parkinson-disease associated protein kinase LRRK2. J. Proteome Res. 9, 1738-1745 (2010)
Rauser, S. et al. Classification of HER2 receptor status in breast cancer tissues by MALDI imaging mass spectrometry. J. Proteome Res. 9, 1854-1863 (2010)
Antonov, A.V. ; Dietmann, S. ; Wong, P. ; Igor, R. & Mewes, H.-W. PLIPS, an automatically collected database of protein lists reported bMIPS: curated databasesy proteomics studies. J. Proteome Res. 8, 1193-1197 (2009)
Schulz, D.M. et al. Identification of differentially expressed proteins in triple-negative breast carcinomas using DIGE and mass spectrometry. J. Proteome Res. 8, 3430-3438 (2009)
Werner, T.* et al. Intestinal epithelial cell proteome from wild-type and TNF{Delta}ARE/WT mice: Effect of iron on the development of chronic ileitis. J. Proteome Res. 8, 3252-3264 (2009)
Zipplies, J.K.* et al. Serum PEDF levels are decreased in a spontaneous animal model for human autoimmune uveitis. J. Proteome Res. 8, (Sp. Iss. SI), 992-998 (2009)
Hauck, S.M. et al. Retinal Mueller Glial Cells Trigger the Hallmark Inflammatory Process in Autoimmune Uveitis. J. Proteome Res. 6, 2121-2131 (2007)
Alge, C.S.* ; Hauck, S.M. ; Priglinger, S.G.* ; Kampik, A.* & Ueffing, M. Differential protein profiling of primary versus immortalized human RPE cells identifies expression patterns associated with cytoskeletal remodeling and cell survival. J. Proteome Res. 5, 862-878 (2006)