Gao, L.* ; Hao, J.* ; Hua, Z.* ; Zeng, C.* ; Li, J.* ; Zeng, J.
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. ; Gronauer, T.F. ; von Toerne, C. ; Merl-Pham, J. ; König, A.-C. ; Barth, T.K.* ; Mergner, J.* ; Ludwig, C.* ; Tüshaus, J.* ; Giesbertz, P.* ; Breimann, S.* ; Schweizer, L.* ; Müller, T.* ; Kliewer, G.* ; Distler, U.* ; Gomez-Zepeda, D.* ; Popp, O.* ; Qin, D.* ; Teupser, D.* ; Cox, J.* ; Imhof, A.* ; Küster, B.* ; Lichtenthaler, S.F.* ; Krijgsveld, J.* ; Tenzer, S.* ; Mertins, P.* ; Coscia, F.* ; Hauck, S.M.
Multicenter longitudinal quality assessment of MS-based proteomics in plasma and serum.
J. Proteome Res. 24, 1017-1029 (2025)
Kardell, O. ; Gronauer, T.F. ; von Toerne, C. ; Merl-Pham, J. ; König, A.-C. ; Barth, T.K.* ; Mergner, J.* ; Ludwig, C.* ; Tüshaus, J.* ; Giesbertz, P.* ; Breimann, S.* ; Schweizer, L.* ; Müller, T.* ; Kliewer, G.* ; Distler, U.* ; Aljakouch, K.* ; Gomez‐Zepeda, D.* ; Popp, O.* ; Qin, D.* ; Teupser, D.* ; Cox, J.* ; Imhof, A.* ; Küster, B.* ; Lichtenthaler, S.F.* ; Krijgsveld, J.* ; Tenzer, S.* ; Mertins, P.* ; Coscia, F.* ; Hauck, S.M.
Correction to “Multicenter longitudinal quality assessment of MS-based proteomics in plasma and serum”.
J. Proteome Res. 24, 4862–4863 (2025)
Phlairaharn, T.* ; Shannon, A.E.* ; Zeng, X.* ; Truong, D.J.J. ; Schoof, E.M.* ; Ye, Z.* ; Searle, B.C.*
Improving proteomic dynamic range with Multiple Accumulation Precursor Mass Spectrometry. 
J. Proteome Res. 24, 5116–5126 (2025)
Geyer, P.E.* ; Hornburg, D.* ; Pernemalm, M.* ; Hauck, S.M. ; Palaniappan, K.K.* ; Albrecht, V.* ; Dagley, L.F.* ; Moritz, R.L.* ; Yu, X.* ; Edfors, F.* ; Vandenbrouck, Y.* ; Mueller-Reif, J.B.* ; Sun, Z.* ; Brun, V.* ; Ahadi, S.* ; Omenn, G.S.* ; Deutsch, E.W.* ; Schwenk, J.M.*
The circulating proteome─technological developments, current challenges, and future trends.
J. Proteome Res. 23, 5279-5295 (2024)
Blume, B. ; Schwantes, V.* ; Witting, M. ; Hayen, H.* ; Schmitt-Kopplin, P. ; Helmer, P.O.* ; Michalke, B.
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. ; von Toerne, C. ; Merl-Pham, J. ; König, A.-C. ; Blindert, M. ; Barth, T.K.* ; Mergner, J.* ; Ludwig, C.* ; Tüshaus, J.* ; Eckert, S.* ; Müller, S.A.* ; Breimann, S.* ; Giesbertz, P.* ; Bernhardt, A.M.J.* ; Schweizer, L.* ; Albrecht, V.* ; Teupser, D.* ; Imhof, A.* ; Kuster, B.* ; Lichtenthaler, S.F.* ; Mann, M.* ; Cox, J.* ; Hauck, S.M.
Multicenter collaborative study to optimize mass spectrometry workflows of clinical specimens.
J. Proteome Res. 23, 117-129 (2023)
Petrera, A. ; von Toerne, C. ; Behler, J. ; Huth, C. ; Thorand, B. ; Hilgendorff, A. ; Hauck, S.M.
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.* ; Zhang, Y.* ; Liu, X.* ; Zhao, X.* ; Ouyang, Y.* ; Qiu, G.* ; Lv, W.* ; Zheng, F.* ; Wang, Q.* ; Lu, X.* ; Peng, X.* ; Wu, T.* ; Lehmann, R. ; Wang, C.* ; Jia, W.* ; Xu, G.*
Metabolite triplet in serum improves the diagnostic accuracy of prediabetes and diabetes screening.
J. Proteome Res. 20, 1005-1014 (2021)
Gouda, M. ; Rex, D.A.B.* ; Priya, S.E.S.* ; Modi, P.K.* ; Chanderasekaran, J.* ; Bhandary, Y.P.*
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. ; Dalke, C. ; von Toerne, C. ; Hauck, S.M. ; Azimzadeh, O.* ; Philipp, J. ; Ung, M.-C. ; Schlattl, H. ; Rößler, U.* ; Graw, J. ; Atkinson, M.J. ; Tapio, S.
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. ; Altenbuchinger, M.* ; Schultheiss, U.T.* ; Samol, C.* ; Kotsis, F.* ; Poguntke, I.* ; Sekula, P.* ; Krumsiek, J. ; Köttgen, A.* ; Spang, R.* ; Oefner, P.J.* ; Gronwald, W.*
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. ; Muschet, C. ; Wahl, S. ; Römisch-Margl, W. ; Prehn, C. ; Möller, G. ; Adamski, J.
Long-Term Stability of Human Plasma Metabolites during Storage at-80 degrees C.
J. Proteome Res. 17, 203-211 (2018)
Hoernstein, S.N.W.* ; Fode, B.* ; Wiedemann, G.* ; Lang, D. ; Niederkrüger, H.* ; Berg, B.* ; Schaaf, A.* ; Frischmuth, T.* ; Schlosser, A.* ; Decker, E.L.* ; Reski, R.*
Host cell proteome of Physcomitrella patens harbors proteases and protease inhibitors under bioproduction conditions.
J. Proteome Res. 17, 3749-3760 (2018)
Subramanian, V. ; Borchard, S. ; Azimzadeh, O. ; Sievert, W. ; Merl-Pham, J. ; Mancuso, M.* ; Pasquali, E.* ; Multhoff, G. ; Popper, B.* ; Zischka, H. ; Atkinson, M.J. ; Tapio, S.
PPARα is necessary for radiation-induced activation of noncanonical TGFβ signaling in the heart.
J. Proteome Res. 17, 1677-1689 (2018)
Lepper, M.F. ; Ohmayer, U. ; von Toerne, C. ; Maison, N. ; Ziegler, A.-G. ; Hauck, S.M.
Proteomic landscape of patient-derived CD4+T cells in recent-onset type 1 diabetes.
J. Proteome Res. 17, 618-634 (2017)
Marx, H.* ; Hahne, H.* ; Ulbrich, S.E.* ; Schnieke, A.* ; Rottmann, O.* ; Frishman, D. ; Kuster, B.*
Annotation of the domestic pig genome by quantitative proteogenomics.
J. Proteome Res. 16, 2887-2898 (2017)
Philipp, J. ; Azimzadeh, O. ; Subramanian, V. ; Merl-Pham, J. ; Lowe, D.* ; Hladik, D. ; Erbeldinger, N.* ; Ktitareva, S.* ; Fournier, C.* ; Atkinson, M.J. ; Raj, K.* ; Tapio, S.
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.* ; Adam, J. ; Adamski, J. ; Chasapi, S.A.* ; Luchinat, C.* ; Peters, A. ; Prehn, C. ; Santucci, C.* ; Spyridonidis, A.* ; Spyroulias, G.A.* ; Tenori, L.* ; Wang-Sattler, R. ; Saccenti, E.*
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. ; Seemann, I.* ; Merl-Pham, J. ; Hauck, S.M. ; Stewart, F.* ; Atkinson, M.J. ; Tapio, S. ; Azimzadeh, O.
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.* ; Gika, H.G.* ; Witting, M. ; Bletsou, A.A.* ; Athanasiadis, A.* ; Zafrakas, M.* ; Thomaidis, N.S.* ; Raikos, N.* ; Makrydimas, G.* ; Theodoridis, G.A.*
Amniotic fluid and maternal serum metabolic signatures in the second trimester associated with preterm delivery.
J. Proteome Res. 16, 898-910 (2017)
Ly, A. ; Merl-Pham, J. ; Priller, M. ; Gruhn, F. ; Senninger, N. ; Ueffing, M. ; Hauck, S.M.
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.* ; Kastenmüller, G. ; AlHaq, W.G.* ; Holle, R. ; Kääb, S.* ; Mohney, R.P.* ; Gieger, C. ; Peters, A. ; Adamski, J. ; Suhre, K. ; Arayssi, T.*
Diagnostic and prognostic metabolites identified for joint symptoms in the KORA population.
J. Proteome Res. 15, 554-562 (2016)
Azimzadeh, O. ; Sievert, W. ; Sarioglu, H. ; Merl-Pham, J. ; Yentrapalli, R. ; Bakshi, M.V. ; Janik, D. ; Ueffing, M. ; Atkinson, M.J. ; Multhoff, G. ; Tapio, S.
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. ; Azimzadeh, O. ; Barjaktarovic, Z. ; Kempf, S.J. ; Merl-Pham, J. ; Hauck, S.M. ; Buratovic, S.* ; Eriksson, P.* ; Atkinson, M.J. ; Tapio, S.
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. ; Kastenmüller, G. ; Mook-Kanamori, D.O.* ; Yousri, N.A.* ; Theis, F.J. ; Suhre, K. ; Krumsiek, J.
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. ; Mörtl, S. ; Sepe, S.* ; von Toerne, C. ; Hauck, S.M. ; Atkinson, M.J. ; Mastroberardino, P.G.* ; Tapio, S.
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. ; Sepe, S.* ; von Toerne, C. ; Janik, D. ; Neff, F. ; Hauck, S.M. ; Atkinson, M.J. ; Mastroberardino, P.G.* ; Tapio, S.
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.* ; Balluff, B.D.* ; Jones, E.A.* ; Schöne, C.D.* ; Schmitt, M.* ; Aubele, M. ; Kroep, J.R.* ; Smit, V.T.* ; Tollenaar, R.A.* ; Mesker, W.E.* ; Walch, A.K. ; McDonnell, L.A.*
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.* ; Seyfarth, K.* ; Besong Agbo, D.* ; Klafki, H.-W.* ; Rozman, J. ; Wurst, W. ; Wiltfang, J.* ; Meyer, H.E.* ; Klingenspor, M. ; Stühler, K.*
High fat diet induced isoform changes of the Parkinson’s disease protein DJ-1.
J. Proteome Res. 13, 2339-2351 (2014)
Velikova, V.B. ; Ghirardo, A. ; Vanzo, E. ; Merl, J. ; Hauck, S.M. ; Schnitzler, J.-P.
Genetic manipulation of isoprene emissions in poplar plants remodels the chloroplast proteome.
J. Proteome Res. 13, 2005-2018 (2014)
Walker, A. ; Lucio, M. ; Pfitzner, B. ; Scheerer, M.F. ; Neschen, S. ; Hrabě de Angelis, M. ; Hartmann, A. ; Schmitt-Kopplin, P.
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. ; Sievert, W.* ; Sarioglu, H. ; Yentrapalli, R. ; Barjaktarovic, Z. ; Sriharshan, A. ; Ueffing, M. ; Janik, D. ; Aichler, M. ; Atkinson, M.J. ; Multhoff, G.* ; Tapio, S.
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.* ; Hauck, S.M. ; Treutlein, G.* ; Amann, B.* ; Fröhlich, K.J.H.* ; Kremmer, E. ; Merl, J. ; Stangassinger, M.* ; Ueffing, M. ; Deeg, C. A.*
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. ; Brandner, S. ; Eberhagen, C. ; Eckardt-Schupp, F. ; Larsen, M.R.* ; Andrae, U.
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. ; Kahle-Stephan, M. ; Schäfer, A. ; Ispiryan, R. ; Blindert, M. ; Hrabě de Angelis, M. ; Neschen, S. ; Ueffing, M. ; Hauck, S.M.
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.* ; Hammer, E.* ; Gesell-Salazar, M.* ; Völker, U.* ; Stangl, K.* ; Meiners, S.
Low dose proteasome inhibition affects alternative splicing.
J. Proteome Res. 11, 3947-3954 (2012)
Gündisch, S.* ; Hauck, S.M. ; Sarioglu, H. ; Schott, C.* ; Viertler, C.* ; Kap, M.* ; Schuster, T.* ; Reischauer, B.* ; Rosenberg, R.* ; Verhoef, C.* ; Mischinger, H.-J.* ; Riegman, P.* ; Zatloukal, K.* ; Becker, K.-F.*
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. ; Nitsche, U.* ; Balluff, B. ; Elsner, M. ; Rauser, S. ; Schöne, C. ; Nipp, M. ; Maak, M.* ; Feith, M.* ; Ebert, M.P.* ; Friess, H.* ; Langer, R.* ; Höfler, H. ; Zitzelsberger, H. ; Rosenberg, R.* ; Walch, A.K.
Tumor classification of six common cancer types based on proteomic profiling by MALDI imaging.
J. Proteome Res. 11, 1996-2003 (2012)
Chen, J.* ; Zhang, X.Y.* ; Cao, R.* ; Lu, X.* ; Zhao, S.M.* ; Fekete, A. ; Huang, Q.* ; Schmitt-Kopplin, P. ; Wang, Y.S.* ; Xu, Z.L.* ; Wan, X.P.* ; Wu, X.H.* ; Zhao, N.Q.* ; Xu, C.J.* ; Xu, G.W.*
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. ; Barjaktarovic, Z. ; Aubele, M. ; Calzada-Wack, J. ; Sarioglu, H. ; Atkinson, M.J.* ; Tapio, S.
Formalin-fixed paraffin-embedded (FFPE) proteome analysis using gel-free and gel-based proteomics.
J. Proteome Res. 9, 4710-4720 (2010)
Balluff, B. ; Elsner, M. ; Kowarsch, A. ; Rauser, S. ; Meding, S. ; Schuhmacher, C.* ; Feith, M.* ; Herrmann, K.* ; Röcken, C.* ; Schmid, R.M.* ; Höfler, H. ; Walch, A.K. ; Ebert, M.P.*
Classification of HER2/neu status in gastric cancer using a breast-cancer derived proteome classifier.
J. Proteome Res. 9, 6317-6322 (2010)
Ergin, B.* ; Meding, S. ; Langer, R.* ; Kap, M.* ; Viertler, C.* ; Schott, C.* ; Ferch, U.* ; Riegman, P.* ; Zatloukal, K.* ; Walch, A.K. ; Becker, K.F.*
Proteomic analysis of PAXgene-fixed tissues.
J. Proteome Res. 9, 5188-5196 (2010)
Gloeckner, C.J. ; Boldt, K. ; von Zweydorf, F. ; Helm, S. ; Wiesent, L. ; Sarioglu, H. ; Ueffing, M.
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. ; Marquardt, C. ; Balluff, B. ; Deininger, S.O.* ; Albers, C.* ; Belau, E.* ; Hartmer, R.* ; Suckau, D.* ; Specht, K.* ; Ebert, M.P.* ; Schmitt, M.* ; Aubele, M. ; Höfler, H. ; Walch, A.K.
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. ; Böllner, C. ; Thomas, G.* ; Atkinson, M.J. ; Esposito, I. ; Höfler, H. ; Aubele, M.
Identification of differentially expressed proteins in triple-negative breast carcinomas using DIGE and mass spectrometry.
J. Proteome Res. 8, 3430-3438 (2009)
Werner, T.* ; Hoermannsperger, G.* ; Schuemann, K.* ; Hölzlwimmer, G. ; Tsuji, S.* ; Haller, D.*
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.* ; Hauck, S.M. ; Schoeffmann, S. ; Amann, B.* ; Stangassinger, M.* ; Ueffing, M. ; Deeg, C.A.*
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. ; Schoeffmann, S. ; Amann, B.* ; Stangassinger, M.* ; Gerhards, H.* ; Ueffing, M. ; Deeg , C.A.*
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)