Song, J., Steidle, L., Steymans, I., Singh, J., Sanner, A., Böttinger, A., Winter, D., Becker, T. The mitochondrial Hsp70 controls the assembly of the F1FO-ATP synthase. Nat Commun 14, 39 (2023). https://doi.org/10.1038/s41467-022-35720-5


Griess, K., Rieck, M., Müller, N., Karsai, G., Hartwig, S., Pelligra, A., Hardt, R., Schlegel, C., Kuboth, J., Uhlemeyer, C., Trenkamp, S., Jeruschke, K., Weiss, J., Peifer-Weiss, L., Xu, W., Cames, S., Yi, X., Cnop, M., Beller, M., Stark, H., Kondadi, A.K., Reichert, A.S., Markgraf, D., Wammers, M., Häussinger, D., Kuss, O., Lehr, S., Eizirik, D., Lickert, H., Lammert, E., Roden, M., Winter, D., Al-Hasani, H., Höglinger, D., Hornemann, T., Brüning, J.C., Belgardt, B.F. Sphingolipid subtypes differentially control proinsulin processing and systemic glucose homeostasis. Nat Cell Biol (2022). https://doi.org/10.1038/s41556-022-01027-2

Singh, J., Elhabashy, H., Muthukottiappan, P., Stepath, M., Eisenacher, M., Kohlbacher, O., Gieselmann, V., Winter, D. Cross-linking of the Endolysosomal System Reveals Flotillin Structures and Putative Cargo. Nat Commun 13, 6212 (2022). https://doi.org/10.1038/s41467-022-33951-0

Karpiński, A.A.; Torres Elguera, J.C.; Sanner, A.; Konopka, W.; Kaczmarek, L.; Winter, D.; Konopka, A.; Bulska, E. Study on Tissue Homogenization Buffer Composition for Brain Mass Spectrometry-Based Proteomics. Biomedicines 2022, 10, 2466. https://doi.org/10.3390/biomedicines10102466

Richards, C.M., Jabs, S., Qiao, W., Varanese, L.D., Schweizer, M., Mosen, P.R., Riley, N.M., Klüssendorf, M., Zengel, J.R., Flynn, R.A., Rustagi, A., Widen, J.C., Peters, C.E., Ooi, Y.S., Xie, X., Shi, P., Bartenschlager, R., Puschnik, A.S., Bogyo, M., Bertozzi, C.R., Blish, C.A., Winter, D., Nagamine, C.M., Braulke, T., Carette, J.E. The human disease gene LYSET is essential for lysosomal enzyme transport and viral infection. Science 2022 Sep 8;eabn5648. https://doi.org/10.1126/science.abn5648 Online ahead of print.

Jordans, S., Hardt, R., Becker, I., Winter, D., Wang-Eckhardt, L., Eckhardt, M. Age-Dependent Increase in Schmidt-Lanterman Incisures and a Cadm4-Associated Membrane Skeletal Complex in Fatty Acid 2-hydroxylase Deficient Mice: a Mouse Model of Spastic Paraplegia SPG35. Mol Neurobiol (2022). https://doi.org/10.1007/s12035-022-02832-4


Winter, D., Becker, T. Surveying the mitochondrial proteome. Nat Cell Biol (2021). https://doi.org/10.1038/s41556-021-00801-y

Turan, F., Yilmaz, Ö., Schünemann, L., Lindenberg, T.T., Kalanithy, J.C., Harder, A., Ahmadi, S., Duman, T., MacDonald, R.B., Winter, D.Liu, C., Odermatt, B. Effect of modulating glutamate signaling on myelinating oligodendrocytes and their development—A study in the zebrafish model. J Neurosci Res. 2021; 00: 000– 000. https://doi.org/10.1002/jnr.24940

Muthukottiappana, P. and Winter, D. A proteomic view on lysosomes. Molecular Omics 2021. https://doi.org/10.1039/D1MO00205H

Mosen, P.R., Hardt, R. and Winter, D. (2021), RapiGest Precipitation Depends on Peptide Concentration. PROTEOMICS, 21, e2100129. https://doi.org/10.1002/pmic.202100129

Balboa, E., Marín, T., Oyarzún, J.E., Contreras, P.S., Hardt, R., van den Bosch, T., Alvarez, A.R., Rebolledo-Jaramillo, B., Klein, A.D.; Winter, D., Zanlungo, S. Proteomic Analysis of Niemann-Pick Type C Hepatocytes Reveals Potential Therapeutic Targets for Liver Damage. Cells 2021, 10, 2159. https://doi.org/10.3390/cells10082159

Di Lorenzo, G., Westermann, L.M., Yorgan, T.A.,  Stürznickel, J., Ludwig, N.F., Ammer, L.S., Baranowsky, A., Ahmadi, S., Pourbarkhordariesfandabadi, E., Breyer, S.R., Board, T.N., Foster, A. , Mercer, J., Tylee, K., Voltolini Velho, R.,  Schweizer, M., Renné, T., Braulke, T., Randon, D.N., Sperb-Ludwig, F., Lapagesse de Camargo Pinto, L., Araujo Moreno, C., Cavalcanti, D.P., Amling, M., Kutsche, K., Winter, D., Muschol, N.M., Schwartz, I.V.D, Rolvien, T., Danyukova, T., Schinke, T., Pohl, S. Pathogenic variants in GNPTAB and GNPTG encoding distinct subunits of GlcNAc-1-phosphotransferase differentially impact bone resorption in patients with mucolipidosis type II and III. Genet Med (2021). https://doi.org/10.1038/s41436-021-01285-9

Singh, J., Ponnaiyan, S., Gieselmann, V., Winter, D. Generation of Antibodies Targeting Cleavable Cross-Linkers. Anal Chem. 2021, 93, 8, 3762–3769 Publication Date:February 16, 2021. https://pubmed.ncbi.nlm.nih.gov/33591729/

Mosen, P., Sanner, A., Singh, J., Winter, D. Targeted Quantification of the Lysosomal Proteome in Complex Samples. Proteomes 2021, 9(1), 4; https://doi.org/10.3390/proteomes9010004


Akter, F., Ponnaiyan S., Kögler-Mohrbacher, B., Bleibaum, F., Damme, M., Renard, B.Y., Winter, D. Multi cell line analysis of lysosomal proteomes reveals unique features and novel lysosomal proteins. . https://doi.org/10.1101/2020.12.21.423747 - PREPRINT

Hardt, R., Jordans, S., Winter, D., Gieselmann, V., Wang-Eckhardt, L., Eckhardt, M. Decreased turnover of the CNS myelin protein Opalin in a mouse model of hereditary spastic paraplegia 35. Human Molecular Genetics, ddaa246, https://doi.org/10.1093/hmg/ddaa246 Published: 20 November 2020

Contreras, P., Tapia, P., González-Hódar, L., Peluso, I., Soldati, C., Napolitano, G., Matarese, M., Las Heras, M., Valls, C., Martinez, A., Balboa, E., Castro, J., Leal, N., Platt, F., Sobota, A., Winter, D., Klein, A., Medina, D., Ballabio, A.,  Alvarez, A., Zanlungo, S.  c-Abl Inhibition Activates TFEB and Promotes Cellular Clearance in a Lysosomal Disorder. iScience, Volume 23, Issue 11, 20 November 2020, 101691 https://doi.org/10.1016/j.isci.2020.101691

Goebel, T., Mausbach, S., Tuermer, A., Eltahir, H., Winter, D., Gieselmann, V., Thelen, M. Proteaphagy in Mammalian Cells Can Function Independent of ATG5/ATG7. Molecular & Cellular Proteomics April 16, 2020, mcp.RA120.001983; https://doi.org/10.1074/mcp.RA120.001983

Ponnaiyan, S., Akter, F., Singh, J., Winter, D. Comprehensive Draft of the Mouse Embryonic Fibroblast Lysosomal Proteome by Mass Spectrometry Based Proteomics. Sci Data. 7 (1), 68 2020 Feb 26 DOI: 10.1038/s41597-020-0399-5

Erjaee, Z., Shekarforoush, S.S., Hosseinzadeh, S., Dheghani, A., Winter, D. Identification of Antifungal Intracellular Proteins of Endophytic Bacillus pumilus by LC–MS/MS Analysis. Int J Pept Res Ther (2020). https://doi.org/10.1007/s10989-020-10040-8

Singh, J., Kaade. E., Muntel, J., Bruderer, R., Reiter, L., Thelen, M., Winter, D. Systematic comparison of strategies for the enrichment of lysosomes by data independent acquisition. J. Proteome Res. 2020, 19, 1, 371-381 DOI: 10.1021/acs.jproteome.9b00580 


Rehorst, W.A., Thelen, M.P., Nolte, H., Türk, C., Cirak, S., Peterson, J.M., Wong, G.W., Wirth, B., Krüger, M., Winter, D., Kye, M.J. Muscle regulates mTOR dependent axonal local translation in motor neurons via CTRP3 secretion: implications for a neuromuscular disorder, spinal muscular atrophy. Acta Neuropathol Commun. 2019 Oct 15;7(1):154. doi: 10.1186/s40478-019-0806-3.

Schoor, C., Brocke‐Ahmadinejad, N., Gieselmann, V., Winter, D., Investigation of Oligodendrocyte Precursor Cell Differentiation by Quantitative Proteomics. PROTEOMICS 2019 Jun 19:e1900057. doi: 10.1002/pmic.201900057.

Ahmadi, S., Winter, D., Identification of unexpected protein modifications by mass spectrometry based proteomics. Methods in molecular biology, “Functional Proteomics” (Clifton, N.J.) 2019, 1871: 225-251

Khundadze, M., Ribaudo, F., Hussain, A., Rosentreter, J., Nietzsche, S., Thelen, M., Winter, D., Hoffmann, B., Afzal, M.A., Hermann, T., de Heus, C., Piskor, E.M., Kosan, C., Franzka, P., von Kleist, L., Stauber, T., Klumperman, J., Damme, M., Proikas-Cezanne, T., Hübner, C.A. A mouse model for SPG48 reveals a block of autophagic flux upon disruption of adaptor protein complex five. Neurobiology of Disease 2019, July; 127: 419-431.


Di Lorenzo, G., Velho, R.V., Winter, D., Thelen, M., Ahmadi, S., Schweizer, M., De Pace, R., Cornils, K., Yorgan, T.A., Grüb, S. and Hermans-Borgmeyer, I., Schinke, T., Müller-Loennies, S., Braulke, T., Pohl, S. Lysosomal proteome and secretome analysis identifies missorted enzymes and their non-degraded substrates in mucolipidosis III mouse cells. Molecular & Cellular Proteomics, August 1, 2018, First published on May 17, 2018, 17 (8) 1612-1626; https://doi.org/10.1074/mcp.RA118.000720

Ahmadi, S. and Winter, D. Identification of Poly(ethylene glycol) and Poly(ethylene glycol)-Based Detergents Using Peptide Search Engines. Analytical Chemistry 2018, Jun 5;90(11):6594-6600

Course, M.M., Scott, A.I., Schoor, C., Hsieh, C.H., Papakyrikos, A.M., Winter, D., Cowan, T.M. and Wang, X., 2018. Phosphorylation of MCAD selectively rescues PINK1 deficiencies in behavior and metabolism. Mol Biol Cell. 2018 May 15;29(10):1219-1227.  doi: 10.1091/mbc.E18-03-0155.

Dehghani, A., Godderz, M. and Winter, D., Tip-Based Fractionation of Batch-Enriched Phosphopeptides Facilitates Easy and Robust Phosphoproteome Analysis. Journal of Proteome Research 17:46-54.

Tsai, P.-I., Lin, C.-H., Hsieh, C.-H., Papakyrikos A.M., Kim M.J., Napolioni, V., Schoor, C., Couthouis, J., Wu, R.-M., Wszolek, Z.K., Winter, D., Greicius, M.D., Ross, O.A. and Wang, X. PINK1 Phosphorylates MIC60/Mitofilin to Control Structural Plasticity of Mitochondrial Crista Junctions. Mol Cell. 2018 Mar 1;69(5):744-756.e6.  doi: 10.1016/j.molcel.2018.01.026.

Hardt, R., Winter, D., Gieselmann, V. and Eckhardt, M. Identification of progesterone receptor membrane component-1 as an interaction partner and possible regulator of fatty acid 2-hydroxylase. Biochemical Journal. 2018, 475(5):853-871, doi: 10.1042/bcj20170963


Thelen, M., Winter, D., Markmann, S., Braulke, T., and Gieselmann, V. (2017) SILAC-based comparative proteomic analysis of lysosomes from mammalian cells using LC-MS/MS. Methods Mol Biol. 2017;1594:1-18.  doi: 10.1007/978-1-4939-6934-0_1.

Müller, T. and Winter, D. Systematic Evaluation of Protein Reduction and Alkylation Reveals Massive Unspecific Side Effects by Iodine-containing Reagents. Molecular & Cellular Proteomics 16:1173-1187.

Peng, B., Weintraub, S.T., Coman, C., Ponnaiyan, S., Sharma, R., Tews, B., Winter, D. and Ahrends, R. A Comprehensive High-Resolution Targeted Workflow for the Deep Profiling of Sphingolipids. Analytical Chemistry 89:12480-12487.


Konopka, A., Winter, D., Konopka, W., Busto, M. E. D., Nunez, S., Goenaga-Infante, H., Fisicaro, P., and Lehmann, W. D. (2016) Sec-to-Cys selenoprotein - a novel type of recombinant, full-length selenoprotein standard for quantitative proteomics. Journal of Analytical Atomic Spectrometry 31, 1929-1938

Ditgen, D., Anandarajah, E. M., Hansmann, J., Winter, D., Schramm, G., Erttmann, K. D., Liebau, E., and Brattig, N. W. (2016) Multifunctional Thioredoxin-Like Protein from the Gastrointestinal Parasitic Nematodes Strongyloides ratti and Trichuris suis Affects Mucosal Homeostasis. Journal of Parasitology Research 2016, 17

Jalaei, J., Fazeli, M., Rajaian, H., Ghalehsoukhteh, S. L., Dehghani, A., and Winter, D. (2016) In vitro antihistamine-releasing activity of a peptide derived from wasp venom of Vespa orientalis. Asian Pacific Journal of Tropical Biomedicine 6, 259-264


Winter, D., Dehghani, A., and Steen, H. (2015) Optimization of Cell Lysis and Protein Digestion Protocols for Protein Analysis by LC-MS/MS. Methods in molecular biology (Clifton, N.J.) 1295, 259-273

Shahraz, A., Kopatz, J., Mathy, R., Kappler, J., Winter, D., Kapoor, S., Schutza, V., Scheper, T., Gieselmann, V., and Neumann, H. (2015) Anti-inflammatory activity of low molecular weight polysialic acid on human macrophages. Scientific Reports 5


Prabakaran, S., Hemberg, M., Chauhan, R., Winter, D., Tweedie-Cullen, R. Y., Dittrich, C., Hong, E., Gunawardena, J., Steen, H., Kreiman, G., and Steen, J. A. (2014) Quantitative profiling of peptides from RNAs classified as noncoding. Nat Commun. 2014 Nov 18;5:5429.  doi: 10.1038/ncomms6429. 

Singh, S.*, Winter, D.*, Kirchner, M.*, Chauchan, R.*, Ahmed, S., Ozlu, N., Tzur, A., Steen, J. A., and Steen, H. (2014) Co-regulation proteomics reveals substrates and mechanisms of APC/C-dependent degradation. EMBO J. 2014 Feb 18;33(4):385-99.  doi: 10.1002/embj.201385876. *shared first authorship


Eichhorn, T., Winter, D., Buchele, B., Dirdjaja, N., Frank, M., Lehmann, W. D., Mertens, R., Krauth-Siegel, R. L., Simmet, T., Granzin, J., and Efferth, T. (2013) Molecular interaction of artemisinin with translationally controlled tumor protein (TCTP) of Plasmodium falciparum. Biochemical Pharmacology 85, 38-45


Renard, B. Y., Xu, B., Kirchner, M., Zickmann, F., Winter, D., Korten, S., Brattig, N. W., Tzur, A., Hamprecht, F. A., and Steen, H. (2012) Overcoming Species Boundaries in Peptide Identification with Bayesian Information Criterion-driven Error-tolerant Peptide Search (BICEPS). Molecular & Cellular Proteomics 11

Singh, S. A., Winter, D., Bilimoria, P. M., Bonni, A., Steen, H., and Steen, J. A. (2012) FLEXIQinase, a mass spectrometry-based assay, to unveil multikinase mechanisms. Nature Methods 9, 504-U134

Weeraratne, S. D., Amani, V., Teider, N., Pierre-Francois, J., Winter, D., Kye, M. J., Sengupta, S., Archer, T., Remke, M., Bai, A. H. C., Warren, P., Pfister, S. M., Steen, J. A. J., Pomeroy, S. L., and Cho, Y. J. (2012) Pleiotropic effects of miR-183 similar to 96 similar to 182 converge to regulate cell survival, proliferation and migration in medulloblastoma. Acta Neuropathologica 123, 539-552

Winter, D., Hung, C. W., Jaskolla, T. W., Karas, M., and Lehmann, W. D. (2012) Enzyme-cleavable tandem peptides for quantitative studies in MS-based proteomics. PROTEOMICS 12, 3470-3474


Seidler, J., Zinn, N., Haaf, E., Boehm, M. E., Winter, D., Schlosser, A., and Lehmann, W. D. (2011) Metal ion-mobilizing additives for comprehensive detection of femtomole amounts of phosphopeptides by reversed phase LC-MS. Amino Acids 41, 311-320

Wang, X., Winter, D., Ashrafi, G., Schlehe, J., Wong, Y. L., Selkoe, D., Rice, S., Steen, J., Lavoie, M. J., and Schwarz, T. L. (2011) PINK1 and Parkin Target Miro for Phosphorylation and Degradation to Arrest Mitochondrial Motility. Cell 147, 893-906

Winter, D., and Steen, H. (2011) Optimization of cell lysis and protein digestion protocols for the analysis of HeLa S3 cells by LC-MS/MS. PROTEOMICS 11, 4726-4730


Winter, D., Seidler, J., Hahn, B., and Lehmann, W. D. (2010) Structural and Mechanistic Information on c (1) Ion Formation in Collision-Induced Fragmentation of Peptides. Journal of the American Society for Mass Spectrometry 21, 1814-1820

Winter, D., Seidler, J., Kugelstadt, D., Derrer, B., Kappes, B., and Lehmann, W. D. (2010) Minimally permutated peptide analogs as internal standards for relative and absolute quantification of peptides and proteins. PROTEOMICS 10, 1510-1514

Zinn, N., Winter, D., and Lehmann, W. D. (2010) Recombinant isotope labeled and selenium quantified proteins for absolute protein quantification. Analytical Chemistry 82, 2334-2340


Brenner, D., Brechmann, M., Rohling, S., Tapernoux, M., Mock, T., Winter, D., Lehmann, W. D., Kiefer, F., Thome, M., Krammer, P. H., and Arnold, R. (2009) Phosphorylation of CARMA1 by HPK1 is critical for NF-kappa B activation in T cells. Proceedings of the National Academy of Sciences of the United States of America 106, 14508-14513

Renard, B. Y., Kirchner, M., Monigatti, F., Ivanov, A. R., Rappsilber, J., Winter, D., Steen, J. A. J., Hamprecht, F. A., and Steen, H. (2009) When less can yield more - Computational preprocessing of MS/MS spectra for peptide identification. PROTEOMICS 9, 4978-4984

Schilling, M., Maiwald, T., Hengl, S., Winter, D., Kreutz, C., Kolch, W., Lehmann, W. D., Timmer, J., and Klingmuller, U. (2009) Theoretical and experimental analysis links isoform-specific ERK signalling to cell fate decisions. Molecular Systems Biology 5, 334

Winter, D., Kugelstadt, D., Seidler, J., Kappes, B., and Lehmann, W. D. (2009) Protein phosphorylation influences proteolytic cleavage and kinase substrate properties exemplified by analysis of in vitro phosphorylated Plasmodium falciparum glideosome-associated protein 45 by nano-ultra performance liquid chromatography-tandem mass spectrometry. Analytical Biochemistry 393, 41-47

Winter, D., and Lehmann, W. D. (2009) Individual b (2) ion fragmentation profiles combined with AspN digestion improve N-terminal peptide sequencing. Analytical and Bioanalytical Chemistry 393, 1587-1591

Winter, D., and Lehmann, W. D. (2009) Sequencing of the thirteen structurally isomeric quartets of N-terminal dipeptide motifs in peptides by collision-induced dissociation. PROTEOMICS 9, 2076-2084

Winter, D., Pipkorn, R., and Lehmann, W. D. (2009) Separation of peptide isomers and conformers by ultra performance liquid chromatography. Journal of Separation Science 32, 1111-1119

Winter, D., Seidler, J., Ziv, Y., Shiloh, Y., and Lehmann, W. D. (2009) Citrate Boosts the Performance of Phosphopeptide Analysis by UPLC-ESI-MS/MS. Journal of Proteome Research 8, 418-424

Winter, D., Seidler, J., Ziv-Lehrman, S., Shiloh, Y., and Lehmann, W. D. (2009) Simultaneous Identification and Quantification of Proteins by Differential O-16/O-18 Labeling and UPLC-MS/MS Applied to Mouse Cerebellar Phosphoproteome Following Irradiation. Anticancer Research 29, 4949-4958


Winter, D., Shiloh, Y., and Lehmann, W. D. (2008) Phosphopeptide Isomer Analysis by Ultra Performance Liquid Chromatography-Tandem Mass Spectrometry. American Laboratory On-Line June 2008, 21-24


Kugelstadt, D., Winter, D., Pluckhahn, K., Lehmann, W. D., and Kappes, B. (2007) Raf kinase inhibitor protein affects activity of Plasmodium falciparum calcium-dependent protein kinase 1. Molecular and Biochemical Parasitology 151, 111-117


Winter D, Lehmann WD, Minimal Permutated Analoga (MIPA) as internal Peptide Standards for Quantitative Proteomics. EU patent EP 07112749.2, US patent 12/669,406