2020
Bottek J, Soun C, Lill JK, Dixit A, Thiebes S, Beerlage AL, Horstmann M, Urbanek A, Heuer H, Uszkoreit J, Eisenacher M, Bracht T, Sitek B, Hoffmann F, Vijitha N, von Eggeling F, Engel DR. Spatial proteomics revealed a CX3CL1-dependent crosstalk between the urothelium and relocated macrophages through IL-6 during an acute bacterial infection in the urinary bladder. Mucosal Immunol. 2020 Feb 28. doi: 10.1038/s41385-020-0269-7. PMID: 32112048
2019
Barkovits K, Pacharra S, Pfeiffer K, Steinbach S, Eisenacher M, Marcus K, Uszkoreit J. Reproducibility, specificity and accuracy of relative quantification using spectral library-based data-independent acquisition.
Eggers B, Pacharra S, Eisenacher M, Marcus K, Uszkoreit J. Let me infuse this for you – A way to solve the first YPIC challenge. EuPA open Proteomics. Available online 16 August 2019. doi: 10.1016/j.euprot.2019.07.007
Mika T, Ladigan S, Schork K, Turewicz M, Eisenacher M, Schmiegel W, Schroers R, Baraniskin A. Monocytes-neutrophils-ratio as predictive marker for failure of first induction therapy in AML. Blood Cells Mol Dis. 2019 Jul;77:103-108. doi: 10.1016/j.bcmd.2019.04.008. Epub 2019 Apr 18. PMID: 31029023
Oertzen-Hagemann V, Kirmse M, Eggers B, Pfeiffer K, Marcus K, de Marées M, Platen P. Effects of 12 Weeks of Hypertrophy Resistance Exercise Training Combined with Collagen Peptide Supplementation on the Skeletal Muscle Proteome in Recreationally Active Men. Nutrients. 2019 May 14;11(5). pii: E1072. doi: 10.3390/nu11051072. PMID: 31091754
Schumacher H, Wenke NK, Kreye J, Höltje M, Marcus K, May C, Prüss H. IgA autoantibodies against native myelin basic protein in a patient with MS. Neurol Neuroimmunol Neuroinflamm. 2019 May 1;6(4):e569. doi: 10.1212/NXI.0000000000000569. eCollection 2019 Jul. PMID: 31355305
Guntermann A, Steinbach S, Serschnitzki B, Grotegut P, Reinehr S, Joachim SC, Schargus M, Marcus K, May C. Human tear fluid proteome dataset for usage as a spectral library and for protein modeling. Data Brief. 2019 Mar 7;23:103742. doi: 10.1016/j.dib.2019.103742. eCollection 2019 Apr. PMID: 31372408
Steinbach S, Serschnitzki B, Gerlach M, Marcus K, May C. Spiked human substantia nigra proteome data set for use as a spectral library for protein modelling and protein mapping. Data Brief. 2019 Mar 7;23:103711. doi: 10.1016/j.dib.2019.103711. eCollection 2019 Apr. PMID: 31372383
Rohm M, May C, Marcus K, Steinbach S, Theis V, Theiss C, Matschke V. The microRNA miR-375-3p and the Tumor Suppressor NDRG2 are Involved in Sporadic Amyotrophic Lateral Sclerosis. Cell Physiol Biochem. 2019;52(6):1412-1426. doi: 10.33594/000000099. PMID: 31075191
Pacharra S, Marcus K, May C. Sample Fractionation Techniques for CSF Peptide Spectral Library Generation. Methods Mol Biol. 2019;2044:69-77. doi: 10.1007/978-1-4939-9706-0_5. PMID: 31432407
Hörmann P, Barkovits K, Marcus K, Hiller K. Co-extraction for Metabolomics and Proteomics from a Single CSF Sample. Methods Mol Biol. 2019;2044:337-342. doi: 10.1007/978-1-4939-9706-0_21. PMID:31432423
Barkovits K, Tönges L, Marcus K. CSF Sample Preparation for Data-Independent Acquisition. Methods Mol Biol. 2019;2044:61-67. doi: 10.1007/978-1-4939-9706-0_4. PMID: 31432406
Mika T, Baraniskin A, Ladigan S, Wulf G, Dierks S, Haase D, Schork K, Turewicz M, Eisenacher M, Schmiegel W, Schroers R, Klein-Scory S. Digital droplet PCR-based chimerism analysis for monitoring of hematopoietic engraftment after allogeneic stem cell transplantation. Int J Lab Hematol. 2019 Jun 21. doi: 10.1111/ijlh.13073. [Epub ahead of print]
Binz PA, Shofstahl J, Vizcaíno JA, Barsnes H, Chalkley RJ, Menschaert G, Alpi E, Clauser K, Eng JK, Lane L, Seymour SL, Sánchez LFH, Mayer G, Eisenacher M, Perez-Riverol Y, Kapp EA, Mendoza L, Baker PR, Collins A, Van Den Bossche T, Deutsch EW. Proteomics Standards Initiative Extended FASTA Format (PEFF). J Proteome Res. 2019 May 13. doi: 10.1021/acs.jproteome.9b00064. [Epub ahead of print] PMID: 31081335
Köhler CU, Bonberg N, Ahrens M, Behrens T, Hovanec J, Eisenacher M, Noldus J, Deix T, Braun K, Gohlke H, Walter M, Tannapfel A, Tam Y, Sommerer F, Marcus K, Jöckel KH, Erbel R, Cantor CR, Käfferlein HU, Brüning T. Noninvasive diagnosis of urothelial cancer in urine using DNA hypermethylation signatures-Gender matters. Int J Cancer. 2019 Apr 22. doi: 10.1002/ijc.32356. [Epub ahead of print]
Hoffmann N, Rein J, Sachsenberg T, Hartler J, Haug K, Mayer G, Alka O, Dayalan S, Pearce JTM, Rocca-Serra P, Qi D, Eisenacher M, Perez-Riverol Y, Vizcaíno JA, Salek RM, Neumann S, Jones AR. mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics. Anal Chem. 2019 Mar 5;91(5):3302-3310. doi: 10.1021/acs.analchem.8b04310. Epub 2019 Feb 13 PMID: 30688441
Taleb RSZ, Moez P, Younan D, Eisenacher M, Tenbusch M, Sitek B, Bracht T. Protein Biomarker Discovery Using Human Blood Plasma Microparticles.Methods Mol Biol. 2019;1959:51-64. doi: 10.1007/978-1-4939-9164-8_4
David P, Megger DA, Kaiser T, Werner T, Liu J, Chen L, Sitek B, Dittmer U, Zelinskyy G. The PD-1/PD-L1 Pathway Affects the Expansion and Function of Cytotoxic CD8+ T Cells During an Acute Retroviral Infection. Front Immunol. 2019 Feb 5;10:54. doi: 10.3389/fimmu.2019.00054. eCollection 2019. PMID: 30804928
Witzke KE, Großerueschkamp F, Jütte H, Horn M, Roghmann F, von Landenberg N, Bracht T, Kallenbach-Thieltges A, Käfferlein H, Brüning T, Schork K, Eisenacher M, Marcus K, Noldus J, Tannapfel A, Sitek B*, Gerwert K. Integrated Fourier Transform Infrared Imaging and Proteomics for Identification of a Candidate Histochemical Biomarker in Bladder Cancer. Am J Pathol. 2019 Mar;189(3):619-631. doi: 10.1016/j.ajpath.2018.11.018. Epub 2019 Feb 12. PMID: 30770125
Perez-Riverol Y, Scrodas A, Bai J, Bernal-Llinares M, Hewapathirana S, Kundu DJ, Inuganti A, Griss J, Mayer G, Eisenacher M, Pérez E, Uszkoreit J, Pfeuffer J, Sachsenberg T, Yilmaz S, Tiwary S, Cox J, Audain E, Walzer M, Jarnuczak AF, Ternent T, Brazma A, Vizcaíno JA. The PRIDE database and related tools and resources in 2019: improving support for quantification data. Nucleic Acids Res. 2019 Jan 8. doi:10.1093/nar/gky1106. PMID: 30395289
2018
Landsberg CD, Megger DA, Hotter D, Rückborn MU, Eilbrecht M, Rashidi-Alavijeh J, Howe S, Heinrichs S, Sauter D, Sitek B, Le-Trilling VTK, Trilling M. A Mass Spectrometry-Based Profiling of Interactomes of Viral DDB1- and Cullin Ubiquitin Ligase-Binding Proteins Reveals NF-κB Inhibitory Activity of the HIV-2-Encoded Vpx. Front Immunol. 2018 Dec 19;9:2978. doi: 10.3389/fimmu.2018.02978. eCollection 2018
Zahradnik E, Janssen-Weets B, Sander I, Kendzia B, Mitlehner W, May C, Raulf M.Lower allergen levels in hypoallergenic Curly Horses? A comparison among breeds by measurements of horse allergens in hair and air samples. PLoS One. 2018 Dec 12;13(12):e0207871. doi: 10.1371/journal.pone.0207871. eCollection 2018. PMID: 30540798
Aring L, Steinbach S, Marcus K, May C. Isolation of Distinct Types of Neurons from Fresh Brain Tissue Using Laser Microdissection in Combination with High-Performance Liquid Chromatography-Mass Spectrometry. Methods Mol Biol. 2018;1723:247-260. doi: 10.1007/978-1-4939-7558-7_14. PMID: 29344865
Yao Z, Jia X, Megger DA, Chen J, Liu Y, Li J, Sitek B, Yuan Z. Label-free Proteomic Analysis of Exosomes Secreted from THP-1-derived Macrophages Treated with IFN-α Identifies Antiviral Proteins Enriched in Exosomes. J Proteome Res. 2018 Dec 14. doi: 10.1021/acs.jproteome.8b00514. [Epub ahead of print]
Xie K, Bunse C, Marcus K, Leichert L. Quantifying changes in the bacterial thiol redox proteome during host-pathogen interaction. Redox Biology, im Druck
Thomanek N, Arends J, Lindemann C, Barkovits K, Meyer H.E., Marcus K & Narberhaus F. Intricate crosstalk between lipopolysaccharide, phospholipid and fatty acid metabolism in Escherichia coli modulates proteolysis of LpxC. Front Microbiol., im Druck
Schilde LM, Kösters S, Steinbach S, Schork K, Eisenacher M, Galozzi S, Turewicz M, Barkovits K, Mollenhauer B, Marcus K, May C. Protein variability in cerebrospinal fluid and its possible implications for neurological protein biomarker research. PLoS One. 2018 Nov 29;13(11):e0206478. doi: 10.1371/journal.pone.0206478. eCollection 2018.
Uszkoreit J, Perez-Riverol Y, Eggers B, Marcus K, Eisenacher M. Protein Inference Using PIA Workflows and PSI Standard File Formats .J. Proteome Res. 2018 Nov 26. doi:10.1021/acs.jproteome.8b00723.
Mölleken C, Ahrens M, Schlosser A, Dietz J, Eisenacher M, Meyer HE, Schmiegel W, Holmskov U, Sarrazin C, Sorensen GL, Sitek B, Bracht T. Direct-acting antivirals-based therapy decreases hepatic fibrosis serum biomarker microfibrillar-associated protein 4 in hepatitis C patients. Clin Mol Hepatol. 2018 Nov 19. doi: 10.3350/cmh.2018.0029. [Epub ahead of print]
Zella MAS, May C, Müller T, Ahrens M, Tönges L, Gold R, Marcus K, Woitalla D. Landscape of pain in Parkinson's disease: impact of gender differences. Neurol Res. 2018 Oct 12:1-11. doi: 10.1080/01616412.2018.1531208. [Epub ahead of print]
Megger DA, Abou-Eid S, Zülch B, Sitek B. Systematic analysis of synergistic proteome modulations in a drug combination of cisplatin and MLN4924. Mol Omics. 2018 Sep 26. doi: 10.1039/c8mo00115d. [Epub ahead of print]
Barkovits K, Linden A, Galozzi S, Schilde L, Pacharra S, Mollenhauer B, Stoepel N, Steinbach S, May C, Uszkoreit J, Eisenacher M, Marcus K. Characterization of cerebrospinal fluid via data-independent acquisition mass spectrometry. J Prot Res.2018 Sep 12. doi: 10.1021/acs.jproteome.8b00308. Epub 2018 Sep 12.
Winter L, Unger A, Berwanger C, Spörrer M, Wellhausen M, Türk M, Chevessier F, Strucksberg KH, Schlötzer-Schrehardt U, Wittig I, Goldmann WH, Marcus K, Linke WA, Clemen CS, Schröder R. Imbalances in protein homeostasis caused by mutant desmin. Neuropathol Appl Neurobiol. 2018 Sep 4. doi: 10.1111/nan.12516. [Epub ahead of print]
Nwosu ZC, Battello N, Rothley M, Piorońska W, Sitek B, Ebert MP, Hofmann U, Sleeman J, Wölfl S, Meyer C, Megger DA, Dooley S. Liver cancer cell lines distinctly mimic the metabolic gene expression pattern of the corresponding human tumours. J Exp Clin Cancer Res. 2018 Sep 3;37(1):211. doi: 10.1186/s13046-018-0872-6
Willems S, Bouyssié D, Deforce D, Dorfer V, Gorshkov V, Kopczynski D, Laukens K, Locard-Paulet M, Schwämmle V, Uszkoreit J, Valkenborg D, Vaudel M, Bittremieux W. Proceedings of the EuBIC developer's meeting 2018. J proteomics 2018 Jun 2. doi: 10.1016/j.jprot.2018.05.015
Niedieker D, Großerüschkamp F, Schreiner A, Barkovits K, Kötting C, Marcus K, Gerwert K, Vorgerd M.Label-free identification of myopathological features with coherent anti-Stokes Raman scattering. Muscle Nerve. 2018 Apr 16. doi: 10.1002/mus.26140. Epub 2018 May 17.
Cortese-Krott MM, Mergia E, Kramer CM, Lückstädt W, Yang J, Wolff G, Panknin C, Bracht T, Sitek B, Pernow J, Stasch JP, Feelisch M, Koesling D, Kelm M. Identification of a soluble guanylate cyclase in RBCs: preserved activity in patients with coronary artery disease. Redox Biol. 2018 Apr;14:328-337. doi: 10.1016/j.redox.2017.08.020. Epub 2017 Sep 8.
Duarte M., Subedi P, Yilmaz E, Marcus M, Laurell T, Ekström S. Molecularly imprinted polymers synthesized via template immobilization on fumed silica nanoparticles for the enrichment of phosphopeptides. J Mol Recognit. 2018 Mar;31(3). doi: 10.1002/jmr.2677. Epub 2017 Oct 12.
Lollies A, Hartmann S, Schneider M, Bracht T, Weiß A, Arnolds J, Klein-Hitpass L, Sitek B, Hansmann ML, Küppers R, Weniger MA. An oncogenic axis of STAT-mediated BATF3 upregulation causing MYC activity in classical Hodgkin lymphoma and anaplastic large cell lymphoma. Leukemia. 2018 Jan;32(1):92-101. doi: 10.1038/leu.2017.203. Epub 2017 Jun 29.
Megger DA, Lax PM, Paauwe J, Fonseca Guerra C, Lippert B. Mixed guanine, adenine base quartets: possible roles of protons and metal ions in their stabilization. J Biol Inorg Chem. 2018 Jan;23(1):41-49. doi: 10.1007/s00775-017-1507-7. Epub 2017 Dec 7.
Baraniskin A, Chomiak M, Ahle G, Gress T, Buchholz M, Turewicz M, Eisenacher M, Margold M, Schlegel U, Schmiegel W, Hahn S, Schroers R. MicroRNA-30c as a novel diagnostic biomarker for primary and secondary B-cell lymphoma of the CNS. J Neurooncol. 2018 Jan 11. doi: 10.1007/s11060-018-2749-0. Epub 2018 Jan 11.
2017
Eckl J, Sima S, Marcus K, Lindemann C, Richter K. Hsp90-downregulation influences the heat-shock response, innate immune response and onset of oocyte development in nematodes. PLoS One. 2017 Oct 27;12(10):e0186386. doi: 10.1371/journal.pone.0186386. eCollection 2017.
Seddigh P, Bracht T, Molinier-Frenkel V, Castellano F, Kniemeyer O, Schuster M, Weski J, Hasenberg A, Kraus A, Poschet G, Hager T, Theegarte D, Opitz C, Brakhage AA, Sitek B, Hasenberg M, Gunzer M. Quantitative Analysis of Proteome Modulations in Alveolar Epithelial Type II Cells in Response to Pulmonary Aspergillus fumigatus Infection. Mol Cell Proteomics. 2017 Dec;16(12):2184-2198. doi: 10.1074/mcp.RA117.000072. Epub 2017 Sep 26.
Joachim SC, Renner M, Reinhard J, Theiss C, May C, Lohmann S, Reinehr S, Stute G, Faissner A, Marcus K. Protective effects on the retina after ranibizumab treatment in an ischemia model.Dick HB. PLoS One. 2017 Aug 11;12(8):e0182407. doi: 10.1371/journal.pone.0182407. eCollection 2017. PMID: 28800629
Taleb RSZ, Moez P, Younan D, Eisenacher M, Tenbusch M, Sitek B, Bracht T. Quantitative proteome analysis of plasma microparticles for the characterization of HCV-induced hepatic cirrhosis and hepatocellular carcinoma. Proteomics Clin Appl. 2017 Dec;11(11-12). doi: 10.1002/prca.201700014. Epub 2017 Jul 10.
Megger DA, Pott LL, Rosowski K, Zülch B, Tautges S, Bracht T, Sitek B. NHS-based Tandem Mass Tagging of Proteins at the Level of Whole Cells: A Critical Evaluation in Comparison to Conventional TMT-Labeling Approaches for Quantitative Proteome Analysis. Anal Sci. 2017;33(12):1387-1394. doi: 10.2116/analsci.33.1387.
Minakaki G, Menges S, Kittel A, Emmanouilidou E, Schaeffner I, Barkovits K, Bergmann A, Rockenstein E, Adame A, Marxreiter F, Mollenhauer B, Galasko D, Irén Buzá E, Schlötzer-Schrehardt U, Marcus K, Xiang W, Chichung Lie D, Vekrellis K, Masliah E, Winkler J, Klucken J. Autophagy inhibition promotes alpha-synuclein release and transfer via extracellular vesicles with a hybrid autophago/exosome-like phenotype. Autophagy. 2017 Dec 4:1-61. doi: 10.1080/15548627.2017.1395992. Epub 2018 Jan 15.
Mora MI, Molina M, Odriozola L, Elortza F, Mato JM, Sitek B, Zhang P, He F, Latasa MU, Avila M, Corrales F. Prioritizing Popular Proteins in Liver Cancer: Remodelling One-Carbon Metabolism. J Proteome Res. 2017 Dec 1;16(12):4506-4514. doi: 10.1021/acs.jproteome.7b00390. Epub 2017 Oct 2.
Deutsch EW, Orchard S, Binz PA, Bittremieux W, Eisenacher M, Hermjakob H, Kawano S, Lam H, Mayer G, Menschaert G, Perez-Riverol Y, Salek RM, Tabb DL, Tenzer S, Vizcaíno JA, Walzer M, Jones AR. Proteomics Standards Initiative: Fifteen Years of Progress and Future Work. J Proteome Res. 2017 Dec 1;16(12):4288-4298. doi: 10.1021/acs.jproteome.7b00370. Epub 2017 Sep 15.
Turewicz M, Kohl M, Ahrens M, Mayer G, Uszkoreit J, Naboulsi W, Bracht T, Megger DA, Sitek B, Marcus K, Eisenacher M. BioInfra.Prot: A Comprehensive Proteomics Workflow Including Data Standardization, Protein Inference, Expression Analysis and Data Publication. J Biotechnol. 2017 Nov 10;261:116-125. doi: 10.1016/j.jbiotec.2017.06.005. Epub 2017 Jun 9.
Rieder V, Schork KU, Kerschke L, Blank-Landeshammer B, Sickmann A, Rahnenführer J. Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra.J. Proteome Res. 2017 16 (11), 4035-4044. doi: 10.1021/acs.jproteome.7b00427. Epub 2017 Sep 29.
Drees SL, Klinkert B, Helling S, Beyer DF, Marcus K, Narberhaus F, Lübben M. One Gene, two proteins: Coordinated production of a copper chaperone by differential transcript formation and translational frameshifting in Escherichia coli. Mol Microbiol. 2017 Nov;106(4):635-645. doi: 10.1111/mmi.13841. Epub 2017 Oct 6.
Mayer G, Quast C, Felden J, Lange M, Prinz M, Pühler A, Lawerenz C, Scholz U, Glöckner FO, Müller W, Marcus K, Eisenacher M. A generally applicable lightweight method for calculating a value structure for tools and services in bioinformatics infrastructure projects. Brief Bioinform. 2017 Oct 30. doi: 10.1093/bib/bbx140. [Epub ahead of print]
Trezzi JP, Galozzi S, Jaeger C, Barkovits K, Brockmann K, Maetzler W, Berg D, Marcus K, Betsou F, Hiller K, Mollenhauer B. Distinct metabolomic signature in cerebrospinal fluid in early parkinson's disease. Mov Disord. 2017 Oct;32(10):1401-1408. doi: 10.1002/mds.27132. Epub 2017 Aug 26.
Megger DA, Philipp J, Le-Trilling VTK, Sitek B, Trilling M. Deciphering of the Human Interferon-Regulated Proteome by Mass Spectrometry-Based Quantitative Analysis Reveals Extent and Dynamics of Protein Induction and Repression. Front. Immunol. 2017 Sept 14. doi: 10.3389/fimmu.2017.01139.
Nwosu ZC, Megger DA, Hammad S, Sitek B, Roessler S, Ebert MP, Meyer C, Dooley S. Identification of the Consistently Altered Metabolic Targets in Human Hepatocellular Carcinoma. Cell Mol Gastroenterol Hepatol. 2017 May 31;4(2):303-323.e1. doi: 10.1016/j.jcmgh.2017.05.004. eCollection 2017 Sept.
da Veiga Leprevost F, Grüning BA, Alves Aflitos S, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Vera Alvarez R, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192.
Renner M, Reinhard J, Theiss C, May C, Lohmann S, Reinehr S, Stute G, Faissner A, Marcus K, Dick HB. Protective effects on the retina after ranibizumab treatment in an ischemia model. PLoS One. 2017 Aug 11;12(8):e0182407. doi: 10.1371/journal.pone.0182407. eCollection 2017.
Vizcaíno JA, Mayer G, Perkins S, Barsnes H, Vaudel M, Perez-Riverol Y, Ternent T, Uszkoreit J, Eisenacher M, Fischer L, Rappsilber J, Netz E, Walzer M, Kohlbacher O, Leitner A, Chalkley RJ, Ghali F, Martínez-Bartolomé S, Deutsch EW, Jones AR. The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics. Mol Cell Proteomics. 2017 Jul;16(7):1275-1285. doi: 10.1074/mcp.M117.068429. Epub 2017 May 17.
Vizcaíno JA, Walzer M, Jiménez RC, Bittremieux W, Bouyssié D, Carapito C, Corrales F, Ferro M, Heck AJR, Horvatovich P, Hubalek M, Lane L, Laukens K, Levander F, Lisacek F, Novak P, Palmblad M, Piovesan D, Pühler A, Schwämmle V, Valkenborg D, van Rijswijk M, Vondrasek J, Eisenacher M, Martens L, Kohlbacher O. A community proposal to integrate proteomics activities in ELIXIR. F1000Res. 2017 Jun 13;6. pii: ELIXIR-875. doi: 10.12688/f1000research.11751.1. eCollection 2017.
Kälsch J, Padden J, Bertram S, Pott LL, Reis H, Westerwick D, Schaefer CM, Sowa JP, Möllmann D, Fingas C, Dechȇne A, Sitek B, Eisenacher M, Canbay A, Ahrens M, Baba HA. Annexin A10 optimally differentiates between intrahepatic cholangiocarcinoma and hepatic metastases of pancreatic ductal adenocarcinoma: a comparative study of immunohistochemical markers and panels. Virchows Arch. 2017 May;470(5):537-543. doi: 10.1007/s00428-017-2114-2. Epub 2017 Mar 29.
Willems S, Bouyssié D, David M, Locard-Paulet M, Mechtler K, Schwämmle V, Uszkoreit J, Vaudel M, Dorfer V. Proceedings of the EuBIC Winter School 2017. J Proteomics. 2017 May 24;161:78-80. doi: 10.1016/j.jprot.2017.04.001. Epub 2017 Apr 4.
Lindemann C, Thomanek N, Hundt FC, Lerari T, Meyer HE, Wolters D, Marcus K. Strategies in relative and absolute quantitative mass spectrometry based proteomics. Biol Chem. 2017 May 1;398(5-6):687-699. doi: 10.1515/hsz-2017-0104.
Sydor S, Sowa JP, Megger DA, Schlattjan M, Jafoui S, Wingerter L, Carpinteiro A, Baba HA, Bechmann LP, Sitek B, Gerken G, Gulbins E, Canbay A. Acid sphingomyelinase deficiency in Western diet-fed mice protects against adipocyte hypertrophy and diet-induced liver steatosis. Mol Metab. 2017 Mar 12;6(5):416-427. doi: 10.1016/j.molmet.2017.03.002. eCollection 2017 May
Nöbauer K, Hummel K, Mayrhofer C, Ahrens M, Setyabudi FMC, Schmidt-Heydt M, Eisenacher M, Razzazi-Fazeli E. Comprehensive proteomic analysis of Penicillium verrucosum. Proteomics. 2017 May;17(9). doi: 10.1002/pmic.201600467.
Bittremieux W, Walzer M, Tenzer S, Zhu W, Salek RM, Eisenacher M, Tabb DL. The Human Proteome Organization-Proteomics Standards Initiative Quality Control Working Group: Making Quality Control More Accessible for Biological Mass Spectrometry. Anal Chem. 2017 Apr 18;89(8):4474-4479. doi: 10.1021/acs.analchem.6b04310. Epub 2017 Mar 30.
Megger DA, Rosowski K, Radunsky C, Kösters J, Sitek B, Müller J. Structurally related hydrazone-based metal complexes with different antitumor activities variably induce apoptotic cell death. Dalton Trans. 2017 Apr 5;46(14):4759-4767. doi: 10.1039/c6dt04613d.
Großerueschkamp F, Bracht T, Diehl HC, Kuepper C, Ahrens M, Kallenbach-Thieltges A, Mosig A, Eisenacher M, Marcus K, Behrens T, Brüning T, Theegarten D, Sitek B, Gerwert K. Spatial and molecular resolution of diffuse malignant mesothelioma heterogeneity by integrating label-free FTIR imaging, laser capture microdissection and proteomics. Sci Rep. 2017 Mar 30;7:44829. doi: 10.1038/srep44829.
Jia X, Chen J, Megger DA, Zhang X, Kozlowski M, Zhang L, Fang Z, Li J, Chu Q, Wu M, Li Y, Sitek B, Yuan Z. Label-free Proteomic Analysis of Exosomes Derived from Inducible Hepatitis B Virus-Replicating HepAD38 Cell Line. Mol Cell Proteomics. 2017 Apr;16(4 suppl 1):S144-S160. doi: 10.1074/mcp.M116.063503. Epub 2017 Feb 27.
Kälsch J, Pott LL, Takeda A, Kumamoto H, Möllmann D, Canbay A, Sitek B, Baba HA. Bathing in carbon dioxide-enriched water alters protein expression in keratinocytes of skin tissue in rats. Int J Biometeorol. 2017 Apr;61(4):739-746. doi: 10.1007/s00484-016-1252-6. Epub 2016 Oct 5.
Megger DA, Rosowski K, Ahrens M, Bracht T, Eisenacher M, Schlaak JF, Weber F, Hoffmann AC, Meyer HE, Baba HA, Sitek B. Tissue-based quantitative proteome analysis of human hepatocellular carcinoma using tandem mass tags. Biomarkers. Biomarkers. 2017 Mar;22(2):113-122. doi: 10.1080/1354750X.2016.1210678. Epub 2016 Jul 28.
Lindemann C, Thomanek N, Kuhlmann K, Meyer HE, Marcus K, Narberhaus F. Next-generation trapping of protease substrates by label-free proteomics. Microbial Proteomics, Methods and Protocolls. in press
Trezzi JP, Jäger C, Galozzi S, Barkovits K, Marcus K, Mollenhauer B, Hiller K. Metabolic profiling of body fluids and multivariate data analysis. MethodsX. 2017 Feb 20;4:95-103. doi: 10.1016/j.mex.2017.02.004. eCollection 2017.
Jash B, Scharf P, Sandmann N, Fonseca Guerra C, Megger DA, Müller J. A metal-mediated base pair that discriminates between the canonical pyrimidine nucleobases. Chem. Sci., 2017,8, 1337-1343 doi: 10.1039/C6SC03482A. Epub 2016 Oct 10.
Pott LL, Hagemann S, Reis H, Lorenz K, Bracht T, Herold T, Skryabin BV, Megger DA, Kälsch J, Weber F, Sitek B, Baba HA. Eukaryotic elongation factor 2 is a prognostic marker and its kinase a potential therapeutic target in HCC. Oncotarget. 2017 Feb 14;8(7):11950-11962. doi: 10.18632/oncotarget.14447.
Güttsches AK, Brady S, Krause K, Maerkens A, Uszkoreit J, Eisenacher M, Schreiner A, Galozzi S, Mertens-Rill J, Tegenthoff M, Holton JL, Harms MB, Lloyd TE, Vorgerd M, Weihl CC, Marcus K, Kley R. Proteomics of rimmed vacuoles define new risk allele in inclusion body myositis. Ann Neurol. 2017 Feb;81(2):227-239. doi: 10.1002/ana.24847. Epub 2017 Jan 27.
Herrfurth L, Theis V, Matschke V, May C, Marcus K, Theiss C. Morphological plasticity of emerging Purkinje cells in response to exogenous VEGF. Front Mol Neurosci. 2017 Jan 30;10:2. doi: 10.3389/fnmol.2017.00002. eCollection 2017.
Megger DA, Padden J, Rosowski K, Uszkoreit J, Bracht T, Eisenacher M, Gerges C, Neuhaus H, Schumacher B, Schlaak JF, Sitek B. One Sample, One Shot - Evaluation of sample preparation protocols for the mass spectrometric proteome analysis of human bile fluid without extensive fractionation. Journal of Proteomics. 2017 Jan 10. doi.org/10.1016/j.jprot.2016.11.021
Audain E, Uszkoreit J, Sachsenberg T, Pfeuffer J, Liang X, Hermjakob H, Sanchez A, Eisenacher M, Reinert K, Tabb DL, Kohlbacher O, Perez-Riverol Y. In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics. J Proteomics. 2017 Jan 6;150:170-182. doi: 10.1016/j.jprot.2016.08.002. Epub 2016 Aug 4.
Witzke K, Rosowski K, Müller C, Ahrens M, Eisenacher M, Megger DA, Knobloch J, Koch A, Bracht T, Sitek B. Quantitative Secretome Analysis of Activated Jurkat Cells using Click Chemistry-Based Enrichment of Secreted Glycoproteins. J Proteome Res. 2017 Jan 6;16(1):137-146. doi: 10.1021/acs.jproteome.6b00575. Epub 2016 Oct 19.
Nieser M, Henopp T, Brix J, Stoß L, Sitek B, Naboulsi W, Anlauf M, Schlitter AM, Klöppel G, Gress T, Moll R, Bartsch DK, Heverhagen AE, Knoefel WT, Kaemmerer D, Haybaeck J, Fend F, Sperveslage J, Sipos B. Loss of Chromosome 18 in Neuroendocrine Tumors of the Small Intestine: The Enigma Remains. Neuroendocrinology. 2017;104(3):302-312. doi: 10.1159/000446917. Epub 2016 May 25.
2016
Arends J, Thomanek N, Kuhlmann K, Marcus K, Narberhaus F. In vivo trapping of FtsH substrates by label-free quantitative proteomics. Proteomics. 2016 Dec;16(24):3161-3172. doi: 10.1002/pmic.201600316.
Kolbe K, Bukhari H, Loosse C, Leonhardt G, Glotzbach A, Pawlas M, Hess K, Theiss C, Müller T. Extensive nuclear sphere generation in the human Alzheimer's brain. Neurobiol Aging. 2016 Dec;48:103-113. doi: 10.1016/j.neurobiolaging.2016.08.016. Epub 2016 Aug 26.
Stratmann B, Engelbrecht B, Espelage BC, Klusmeier N, Tiemann J, Gawlowski T, Mattern Y, Eisenacher M, Meyer HE, Rabbani N, Thornalley PJ, Tschoepe D, Poschmann G, Stühler K. Glyoxalase 1-knockdown in human aortic endothelial cells - effect on the proteome and endothelial function estimates. Sci Rep. 2016 Nov 29;6:37737. doi: 10.1038/srep37737.
Plum S, Steinbach S, Attems J, Keers S, Riederer P, Gerlach M, May C, Marcus K. Proteomic characterization of neuromelanin granules isolated from human substantia nigra by laser-microdissection. Sci Rep. 2016 Nov 14;6:37139. doi: 10.1038/srep37139.
Chen J, Shinde S, Subedi P, Wierzbicka C, Sellergren B, Helling S, Marcus K. Validation of molecularly imprinted polymers for side chain selective phosphopeptide enrichment. J Chromatogr A. 2016 Nov 4;1471:45-50. doi: 10.1016/j.chroma.2016.10.018. Epub 2016 Oct 11.
Pattky M, Barkovits K, Marcus K, Weiergräber OH, Huhn C. Statically Adsorbed Coatings for High Separation Efficiency and Resolution in CE-MS Peptide Analysis: Strategies and Implementation. Methods Mol Biol. 2016;1483:53-75. doi: 10.1007/978-1-4939-6403-1_4.
Kumar G, Hummel K, Ahrens M, Menanteau-Ledouble S, Welch TJ, Eisenacher M, Razzazi-Fazeli E, El-Matbouli M. Shotgun proteomic analysis of Yersinia ruckeri strains under normal and iron-limited conditions. Vet Res. 2016 Oct 6;47(1):100.
Winter L, Wittig I, Peeva V, Eggers B, Heidler J, Chevessier F, Kley RA, Barkovits K, Strecker V, Berwanger C, Herrmann H, Marcus K, Kornblum C, Kunz WS, Schröder R, Clemen CS. Mutant desmin substantially perturbs mitochondrial morphology, function and maintenance in skeletal muscle tissue. Acta Neuropathol. 2016 Sep;132(3):453-73. doi: 10.1007/s00401-016-1592-7. Epub 2016 Jul 8.
Dinter E, Saridaki T, Nippold M, Plum S, Diederichs L, Komnig D, Fensky L, May C, Marcus K, Voigt, A, Schulz J.B, Falkenburger B.H. Rab7 induces clearance of α-synuclein aggregates. J Neurochem. 2016 Sep;138(5):758-74. doi: 10.1111/jnc.13712. Epub 2016 Aug 4.
Naboulsi W, Bracht T, Megger DA, Reis H, Ahrens M, Turewicz M, Eisenacher M, Tautges S, Canbay AE, Meyer HE, Weber F, Baba HA, Sitek B. Quantitative proteome analysis reveals the correlation between endocytosis-associated proteins and hepatocellular carcinoma dedifferentiation. Biochim Biophys Acta. 2016 Nov;1864(11):1579-85. doi: 10.1016/j.bbapap.2016.08.005. Epub 2016 Aug 9
Bukhari H, Kolbe K, Leonhardt G, Loosse C, Schröder E, Knauer S, Marcus K, Müller T. Membrane tethering of APP c-terminal fragments is a prerequisite for T668 phosphorylation preventing nuclear sphere generation. Cell Signal. 2016 Nov;28(11):1725-34. doi: 10.1016/j.cellsig.2016.08.007. Epub 2016 Aug 14.
Recke A, Oei A, Hübner F, Fechner K, Graf J, Hagenah J, May C, Woitalla D, Salmen A, Zillikens D, Gold R, Schlumberger W, Schmidt E. Parkinson's disease and multiple sclerosis are not associated with autoantibodies against structural proteins of the dermal-epidermal junction. Br J Dermatol. 2016 Aug;175(2):407-9. doi: 10.1111/bjd.14538. Epub 2016 May 18.
Henriques AG, Müller T, Oliveira JM, Cova M, da Cruz E Silva CB, da Cruz E Silva OA. Altered protein phosphorylation as a resource for potential AD biomarkers. Sci Rep. 2016 Jul 28;6:30319. doi: 10.1038/srep30319.
Perez-Riverol Y, Gatto L, Wang R, Sachsenberg T, Uszkoreit J, da Veiga Leprevost F, Fufezan C, Ternent T, Eglen SJ, Katz DS, Pollard TJ, Konovalov A, Flight RM, Blin K, Vizcaino JA. Ten Simple Rules for Taking Advantage of Git and GitHub. PLoS Comput Biol 12(7): e1004947. 14 July 2016; doi:10.1371/journal.pcbi.1004947. PMID: 27415786
Bracht T, Molleken C, Ahrens M, Poschmann G, Schlosser A, Eisenacher M, Stühler K, Meyer HE, Schmiegel WH, Holmskov U, Sorensen GL, Sitek B. Evaluation of the biomarker candidate MFAP4 for non-invasive assessment of hepatic fibrosis in hepatitis C patients. Journal of Translational Medicine. 2016 Jul 4. doi: 10.1186/s12967-016-0952-3.
Bertram S, Padden J, Kälsch J, Ahrens M, Pott L, Canbay A, Weber F, Fingas C, Hoffmann AC, Vietor A, Schlaak JF, Eisenacher M, Reis H, Sitek B, Baba HA. Novel immunohistochemical markers differentiate intrahepatic cholangiocarcinoma from benign bile duct lesions. J Clin Pathol. 2016 Jul;69(7):619-26. doi: 10.1136/jclinpath-2015-203418. Epub 2016 Jan 4.
Broering R, Trippler M, Werner M, Real CI, Megger DA, Bracht T, Schweinsberg V, Sitek B, Eisenacher M, Meyer HE, Baba HA, Weber F, Hoffmann AC, Gerken G, Schlaak JF. Hepatic expression of proteasome subunit alpha type-6 is upregulated during viral hepatitis and putatively regulates the expression of ISG15 ubiquitin-like modifier, a proviral host gene in hepatitis C virus infection. J Viral Hepat. 2016 May;23(5):375-86. doi: 10.1111/jvh.12508. Epub 2016 Feb 1.
Turewicz M, Ahrens M, May C, Marcus K, Eisenacher M. PAA: an R/bioconductor package for biomarker discovery with protein microarrays. Bioinformatics. 2016 May 15;32(10):1577-9. doi: 10.1093/bioinformatics/btw037. Epub 2016 Jan 22.
Mayer G, Marcus K, Eisenacher M, Kohl M. Boolean modeling techniques for protein co-expression networks in systems medicine. Expert Rev Proteomics. 2016 Jun;13(6):555-69. doi: 10.1080/14789450.2016.1181546. Epub 2016 May 6.
Schrötter A, Park YM, Marcus K, Martins-de-Souza D, Nilsson P, Magraoui FE, Meyer HE, Grinberg LT. Key players in neurodegenerative disorders in focus-New insights into the proteomic profile of Alzheimer's disease, schizophrenia, ALS, and multiple sclerosis-24th HUPO BPP Workshop: September 29, 2015, Vancouver, Canada. Proteomics. 2016 Apr;16(7):1047-50. doi: 10.1002/pmic.201600047.
Köhler J, Schuler M, Gauler TC, Nöpel-Dünnebacke S, Ahrens M, Hoffmann AC, Kasper S, Nensa F, Gomez B, Hahnemann M, Breitenbuecher F, Cheufou D, Özkan F, Darwiche K, Hoiczyk M, Reis H, Welter S, Eberhardt WEE, Martin Eisenacher, Teschler H, Stamatis G, Schmiegel W, Hahn SA, Baraniskin A. ‘Circulating U2 Small Nuclear RNA Fragments as a Diagnostic and Prognostic Biomarker in Lung Cancer Patients’. J Cancer Res Clin Oncol. 2016 Apr;142(4):795-805. doi: 10.1007/s00432-015-2095-y. Epub 2015 Dec 19.
Manitz MP, Plümper J, Demir S, Ahrens M, Eßlinger M, Wachholz S, Eisenacher M, Juckel G, Friebe A.
Flow cytometric characterization of microglia in the offspring of PolyI:C treated mice.
Brain Res. Brain Res 2016 Apr 1;1636:172-82. doi: 10.1016/j.brainres.2016.02.004. Epub 2016 Feb 10.
Mölleken C, Poschmann G, Bonella F, Costabel U, Sitek B, Stühler K, Meyer HE, Schmiegel WH, Marcussen N, Helmer M, Nielsen O, Hansen S, Schlosser A, Holmskov U, Sorensen GL. MFAP4: a candidate biomarker for hepatic and pulmonary fibrosis? Sarcoidosis Vasc Diffuse Lung Dis. 2016 Mar 29;33(1):41-50.
Padden J, Ahrens M, Kälsch J, Bertram S, Megger DA, Bracht T, Eisenacher M, Kocabayoglu P, Meyer HE, Sipos B, Baba HA, Sitek B. Immunohistochemical Markers Distinguishing Cholangiocellular Carcinoma from Pancreatic Ductal Adenocarcinoma Discovered by Proteomic Analysis of Microdissected Cells. Mol Cell Proteomics. 2016 Mar;15(3):1072-82. doi: 10.1074/mcp.M115.054585. Epub 2015 Dec 7.
Peters M, Guidato PM, Peters K, Megger DA, Sitek B, Classen B, Heise EM, Bufe A. Allergy-Protective Arabinogalactan Modulates Human Dendritic Cells via C-Type Lectins and Inhibition of NF-κB. J Immunol. 2016 Feb 15;196(4):1626-35. doi: 10.4049/jimmunol.1502178. Epub 2016 Jan 8.
Maerkens A, Olivé M, Schreiner A, Feldkirchner S, Schessl J, Uszkoreit J, Barkovits K, Güttsches AK, Theis V, Eisenacher M, Tegenthoff M, Goldfarb LG, Schröder R, Schoser B, van der Ven PF, Fürst DO, Vorgerd M, Marcus K, Kley RA New insights into the protein aggregation pathology in myotilinopathy by combined proteomic and immunolocalization analyses. 2016 Feb 3;4(1):8. doi: 10.1186/s40478-016-0280-0.
Casadei N, Sood P, Ulrich T, Fallier-Becker P, Kieper N, Helling S, May C, Glaab E, Chen J, Nuber S, Marcus K, Rapaport D, Ott T, Riess O, Krüger R, Fitzgerald JC. Mitochondrial defects and neurodegeneration in mice overexpressing wild-type or G399S mutant HtrA2. Hum Mol Genet. 2016 Feb 1;25(3):459-71. doi: 10.1093/hmg/ddv485. Epub 2015 Nov 24.
Le-Trilling VT, Megger DA, Katschinski B, Landsberg CD, Rückborn MU, Tao S, Krawczyk A, Bayer W, Drexler I, Tenbusch M, Sitek B, Trilling M. Broad and potent antiviral activity of the NAE inhibitor MLN4924. Sci Rep. 2016 Feb 1;6:19977. doi: 10.1038/srep19977.
Loosse C., Pawlas M., Bukhari H.S., Maghnouj A., Hahn S., Marcus K., Müller T. 'Nuclear spheres modulate the expression of BEST1 and GADD45G.' Cell Signal. 2016 Jan;28(1):100-9. doi: 10.1016/j.cellsig.2015.10.019. Epub 2015 Oct 28.
Perez-Riverol Y, Xu QW, Wang R, Uszkoreit J, Griss J, Sanchez A, Reisinger F, Csordas A, Ternent T, Del-Toro N, Dianes JA, Eisenacher M, Hermjakob H, Vizcaino JA. PRIDE Inspector Toolsuite: moving towards a universal visualization tool for proteomics data standard formats and quality assessment of ProteomeXchange datasets. Mol Cell Proteomics. 2016 Jan;15(1):305-17. doi: 10.1074/mcp.O115.050229. Epub 2015 Nov 6.
Naboulsi W, Megger DA, Bracht T, Kohl M, Turewicz M, Eisenacher M, Voss DM, Schlaak JF, Hoffmann AC, Weber F, Baba HA, Meyer HE, Sitek B. Quantitative tissue proteomics analysis reveals versican as potential biomarker for early-stage hepatocellular carcinoma. J Proteome Res. 2016 Jan 4;15(1):38-47.doi:10.1021/acs.jproteome.5b00420. Epub 2015 Dec 18.
Vizcaíno JA, Csordas A, Del-Toro N, Dianes JA, Griss J, Lavidas I, Mayer G, Perez-Riverol Y, Reisinger F, Ternent T, Xu QW, Wang R, Hermjakob H. 2016 update of the PRIDE database and its related tools, Nucleic Acids Res. 2016 Jan 4;44(D1):D447-56. doi: 10.1093/nar/gkv1145. Epub 2015 Nov 2.
Henkel S, Wellhausen R, Woitalla D, Marcus K, May C. Epitope Mapping Using Peptide Microarray in Autoantibody Profiling. Methods Mol Biol. 2016;1368:209-24. doi: 10.1007/978-1-4939-3136-1_15.
2015
Mayer G., Stephan C., Meyer H.E., Kohl M., Marcus K., Eisenacher M. 'ProCon- PROteomics CONversion tool', J Proteomics. 2015 Nov 3;129:56-62. doi: 10.1016/j.jprot.2015.06.015. Epub 2015 Jul 13.
Montesinos-Rongen M., Purschke F.G., Brunn A., May C., Nordhoff E., Marcus K., Deckert M. 'Primary Central Nervous System (CNS) Lymphoma B Cell Receptors Recognize CNS Proteins.' J Immunol. 2015, 195(3):1312-9.
Chevessier F., Schuld J., Orfanos Z., Plank A.C., Wolf L., Maerkens A., Unger A., Schlötzer-Schrehardt U., Kley R.A., von Hörsten S., Marcus K., Linke W.A., Vorgerd M., van der Ven P.F., Fürst D.O., Schröder R. 'Myofibrillar instability exacerbated by acute exercise in filaminopathy.' Hum Mol Genet. 2015 pii: ddv421.
Haghikia A., Jörg S., Duscha A., Berg J. Manzel A., Waschbisch A., Hammer A.2, Lee D.H., May C., Wilck N., Balogh A., Ostermann A.I., Schebb N.H., Akkad D.A., Grohme D.A., Kleinewietfeld M., Kempa S., Thöne J., Demir S., Müller D.N., Gold R., Linker R.A. 'Dietary Fatty Acids Directly Impact Central Nervous System Autoimmunity via the Small Intestine.' Immunity. 2015 Oct 20;43(4):817-29. doi: 10.1016/j.immuni.2015.09.007.
Plum S, Steinbach S, Abel L, Marcus K, Helling S, May C. Proteomics in neurodegenerative diseases: Methods for obtaining a closer look at the neuronal proteome. Proteomics Clin Appl. 2015 Oct;9(9-10):848-71. doi: 10.1002/prca.201400030. Epub 2014 Nov 10.
Walker A., Skibbe K., Steinmann E., Pfaender S., Kuntzen T., Megger D.A., Groten S., Sitek B., Lauer G.M., Kim A.Y., Pietschmann T., Allen T.M., Timm J. 'Distinct escape pathway by HCV genotype 1a from a dominant CD8+ T cell response by selection of altered epitope processing.' J Virol. 2015 Oct 7;90(1):33-42. doi: 10.1128/JVI.01993-15.
Rattay S, Trilling M, Megger DA,Sitek, B, Meyer HE, Hengel H, Le-Trilling VT. 'The Canonical Immediate-Early 3 Gene Product pIE611 of Mouse Cytomegalovirus Is Dispensable for Viral Replication, but Mediates Transcriptional and Post-transcriptional Regulation of Viral Gene Products.' J Virol. 2015 Aug;89(16):8590-8. doi: 10.1128/JVI.01234-15. Epub 2015 Jun 10.
Chen J, Shinde S, Koch MH, Eisenacher M, Galozzi S, Lerari T, Barkovits K, Subedi P, Krüger R, Kuhlmann K, Sellergren B, Helling S, Marcus K (2015) Low-bias phosphopeptide enrichment from scarce samples using plastic antibodies. Sci Rep. 2015 Jul 1;5:11438. doi: 10.1038/srep11438.
Reis H., Padden J., Ahrens M., Pütter C., Bertram S., Pott L.L., Reis A.C., Weber F., Juntermanns B., Hoffmann A.C., Eisenacher M., Schlaak J.F., Canbay A., Meyer H.E., Sitek B., Baba H.A. 'Differential proteomic and tissue expression analyses identify valuable diagnostic biomarkers of hepatocellular differentiation and hepatoid adenecarcinomas' Pathology. 2015 Oct;47(6):543-50. doi: 10.1097/PAT.0000000000000298.
Galozzi S., Marcus K., Barkovits K. 'Amyloid-β as a biomarker for Alzheimer's disease: quantification methods in body fluids', Expert Rev. o Proteomics, August 2015, Vol.12, No. 4 : Pages 343-354; doi:10.1586/14789450.2015.1065183.
Peng J., Alam S., Radhakrishnan K., Mariappan M., Rudolph M.G., May C., Dierks T., von Figura K., and Schmidt B. 'Eukaryotic Formylglycine-Generating Enzyme Catalyzes a Monooxygenase Type of Reaction', FEBS J, 2015 Sep;282(17):3262-74. doi: 10.1111/febs.13347. Epub 2015 Jul 7.
Molina M., Steinbach Y., Park M., Yun S.Y., Di Lorenzo alho A.T., Heinsen H., Grinberg L.T., Marcus K., Leite R.E., and May C. 'Enrichment of Single Neurons and Defined Brain Regions from Human Brain Tissue Samples for Subsequent Proteome Analysis', J Neural Transm, 2015 Jul;122(7):993-1005. doi: 10.1007/s00702-015-1414-4. Epub 2015 Jun 30.
Reis H, Pütter C, Megger DA, Bracht T, Weber F, Hoffmann AC, Bertram S, Wohlschläger J, Hagemann S, Eisenacher M, Scherag A, Schlaak JF, Canbay A, Meyer HE, Sitek B, Baba HA. A structured proteomic approach identifies 14-3-3Sigma as a novel and reliable protein biomarker in panel based differential diagnostics of liver tumors. Biochim Biophys 2015 Jun;1854(6):641-50. doi: 10.1016/j.bbapap.2014.10.024. Epub 2014 Nov 5.
Uszkoreit J., Maerkens A., Perez-Riverol Y., Meyer H.E., Marcus K., Stephan C., Kohlbacher O., Eisenacher M. 'PIA - An intuitive protein inference engine with a web-based user interface.' J. Proteome Res. 2015 Jul 2;14(7):2988-97. doi: 10.1021/acs.jproteome.5b00121. Epub 2015 Jun 10.
Brosseron F1, Marcus K, May C. Isolating peripheral lymphocytes by density gradient centrifugation and magnetic cell sorting. Methods Mol Biol. 2015;1295:33-42. doi: 10.1007/978-1-4939-2550-6_3.
Sitek B., Meyer HE., Kondo T. Editorial Medical Proteomics. Biochim Biophys Acta. 2015 Feb 18. pii: S1570-9639(15)00042-4. doi: 10.1016/j.bbapap.2015.02.006. Epub 2015 Feb 18.
Deutsch E.W., Albar J.P., Binz P.A., Eisenacher M., Jones A.R., Mayer G., Omenn G.S., Orchard S., Vizcaíno J.A., Hermjakob H. Development of Data Representation Standards by the Human Proteome Organization Proteomics Standards Initiative. J Am Med Inform Assoc. 2015 May;22(3):495-506. doi: 10.1093/jamia/ocv001. Epub 2015 Feb 28.
Pienimaeki-Roemer A, Kuhlmann K, Böttcher A, Konovalova T, Black A, Orsó E, Liebisch G, Ahrens M, Eisenacher M, Meyer HE, Schmitz G (2014). Lipidomic and proteomic characterization of platelet extracellular vesicle subfractions from senescent platelets. Transfusion 2015 Mar;55(3):507-21. doi: 10.1111/trf.12874. Epub 2014 Oct 21.
Barkovits K., Helling S., Marcus K. MS-based methods for biomarkers of Parkinson's disease: what is the future? Bioanalysis 2015, 7(2):149-51. doi: 10.4155/bio.14.273.
Schoenebeck B. & May C., Mollenhauer B., Meyer H.E., Güldner C., Respondek G., Höglinger G., Marcus K. Improved preparation of nasal lavage fluid (NLF) as a noninvasive sample for proteomic biomarker discovery. BBA – Proteins and Proteomics 2015 Feb 10. doi: 10.1016/j.bbapap.2015.01.015. Epub 2015 Feb 10.
Weiß F., Schnabel A., Planatscher H., van den Berg B.H., Serschnitzki B., Nuessler A.K., Thasler W.E., Weiss T.S., Reuss M., Stoll D., Templin M.F., Joos T.O., Marcus K., Poetz O. Indirect protein quantification of drug-transforming enzymes using peptide group-specific immunoaffinity enrichment and mass spectrometry. Sci Rep. 2015 Mar 4;5:8759. doi: 10.1038/srep08759.
Schrötter A., Magraoui F.E., Marcus K., Park Y.M., Meyer H.E., Grinberg L.T. New Milestones in the Development of Characterization Tools for Neurodegenerative Diseases in Proteomics: 22nd HUPO BPP Workshop 7 October 2014, Madrid, Spain. Proteomics 2015, 15(4), 627-629. doi: 10.1002/pmic.201570035.
Looße C., Galozzi S., Debor L., Julsing M.K., Bühler B., Schmid A., Barkovits K., Müller T., Marcus K. Direct infusion-SIM for absolute protein quantification in complex samples: simple, fast, robust. EuPA Open Proteomics 2015
Bracht T, Schweinsberg V, Trippler M, Kohl M, Ahrens M, Padden J, Naboulsi W, Barkovits K, Megger DA, Eisenacher M, Borchers CH, Schlaak JF, Hoffmann AC, Weber F, Baba HA, Meyer HE, Sitek B. Analysis of disease-associated protein expression using quantitative proteomics - Fibulin-5 is expressed in association with hepatic fibrosis. J Proteome Res. 2015 Mar 25. doi: 10.1021/acs.jproteome.5b00053. Epub 2015 Apr 6
Diehl H, Beine B, Elm J, Ahrens M, Trede D, Eisenacher M, Marcus K, Meyer HE, Henkel C. The challenge of on-tissue digestion for MALDI-MSI – a comparison of different protocols to improve imaging experiments. Anal Bioanal Chem. 2015 Mar;407(8):2223-43. doi: 10.1007/s00216-014-8345-z. Epub 2015 Feb 17.
Geisler, C. Gaisa, N. T. Pfister, D. Fuessel, S. Kristiansen, G. Braunschweig, T. Gostek, S. Beine, B. Diehl, H. C. Jackson, A. M. Borchers, C. Heidenreich, A. Meyer, H. E. Knüchel, R. Henkel, C. Identification and Validation of Potential New Biomarkers for Prostate Cancer Diagnosis and Prognosis Using 2D-DIGE and MS. Biomed Research International 2015(-) (2015) 1-23. DOI: 10.1155/2015/454256. Epub 2015 Jan 15.
Reidick, C. El Magraoui, F. Meyer, H. E. Stenmark, H. Platta, H. Regulation of the Tumor-suppressor function of the Class III phosphatidylinositol 3-kinase complex by Ubiquitin and SUMO. Cancers 7(1) (2015) 1-29. DOI: 10.3390/cancers7010001
Ahrens M, Turewicz M, Marcus K, Meyer HE, May C, Eisenacher M, and Rahnenführer J FSOL - a workflow for the detection of patient subgroups and affected molecular features in high-throughput omics data. (accepted on pre-print server of PeerJ group as Proceedings of the German Conference on Bioinformatics, Dortmund, Germany 2015)
2014
Waldera-Lupa, D. M. Kalfalah, F. Florea, A.-M. Sass, S. Kruse, F. Rieder, V. Tigges, J. Fritsche, E. Krutmann, J. Busch, H. Boerries, M. Meyer, H. E. Boege, F. Theis, F. Reifenberger, G. Stühler, K. Proteome-wide analysis reveals an age-associated cellular phenotype of in situ aged human fibroblasts. Aging 6(10) (2014) 856-878.
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. Journal of Proteome Research 13(5) (2014) 2339-2351. DOI: 10.1021/pr401157k. Epub 2014 Mar 28.
Ma, X. Sickmann, A. Pietsch, J. Wildgruber, R. Weber, G. Infanger, M. Bauer, J. Grimm, D. Proteomic differences between microvascular endothelial cells and the EA.hy926 cell line forming three-dimensional structures. Proteomics 14(6) (2014) 689-698. DOI: 10.1002/pmic.201300453. Epub 2013 Feb 20.
Zahedi, R. P. Ueffing, M. Sickmann, A. Proteomics - moving from inventory to personalized medicine? Proteomics 14(17-18) (2014) 1953-1953. DOI: 10.1002/pmic.201470133.
Krumm, C. Harmuth, S. Hijazi, M. Neugebauer, B. Kampmann, A.-L. Geltenpoth, H. Sickmann, A. Tiller, J. C. Biologisch schaltbare antimikrobielle Poly(2-methyloxazoline) auf Grundlage des Satellitengruppeneffekts. Angewandte Chemie-International Edition 126(15) (2014) 3908-3913. DOI: 10.1002/ange.201311150
Tinnefeld, V. Sickmann, A. Ahrends, R. Catch me if you can: challenges and applications of cross-linking approaches. European Journal of Mass Spectrometry (EUR J MASS SPECTROM) 20(1) (2014) 99-116. DOI: 10.1255/ejms.1259
Krumm, C. Harmuth, S. Hijazi, M. Neugebauer, B. Kampmann, A.-L. Gelthenpoth, H. Sickmann, A. Tiller, J. C. Antimicrobial Poly(2-methyloxazoline)s with Bioswitchable Activity through Satellite Group Modification. Angewandte Chemie-International Edition 53(15) (2014) 3830-3834. DOI: 10.1002/anie.201311150. Epub 2014 Mar 5.
Mossmann, D. Vögtle, F. N. Taskin, A. A. Teixeira, P. F. Ring, J. Pinho, C. M. Burkhart, J. M. Burger, N. Loreth, D. Graff, C. Metzger, F. Sickmann, A. Kretz, O. Wiedemann, N. Zahedi, R. P. Madeo, F. Glaser, E. Meisinger, C. Amyloid-? Peptide Induces Mitochondrial Dysfunction by Inhibition of Preprotein Maturation. Cell Metabolism 20(4) (2014) 662-669. DOI: 10.1016/j.cmet.2014.07.024. Epub 2014 Aug 28.
Burkhart, J.M. Gambaryan, S. Watson, S. Jurk, K. Walter, U. Sickmann, A. Heemskerk, J.W. Zahedi, R.P. What can proteomics tell us about platelet dysfunction? Circulation Research 114(7) (2014) 1204-1219. DOI: 10.1161/CIRCRESAHA.114.301598. Epub 2013 Mar 28.
Vizcaíno JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Ríos D, Dianes JA, Sun Z, Farrah T, Bandeira N, Binz PA, Xenarios I, Eisenacher M, Mayer G, Gatto L, Campos A, Chalkley RJ, Kraus HJ, Albar JP, Martinez-Bartolomé S, Apweiler R, Omenn GS, Martens L, Jones AR, Hermjakob H (2014). ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat Biotechnol 2014 Mar 10;32(3):223-6. doi: 10.1038/nbt.2839.
Kuhlmann K, Tschapek A, Wiese H, Eisenacher M, Meyer HE, Hatt HH, Oeljeklaus S, Warscheid B (2014). The Membrane Proteome of Sensory Cilia to the Depth of Olfactory Receptors. Mol Cell Proteomics 2014 Jul;13(7):1828-43. doi: 10.1074/mcp.M113.035378. Epub 2014 Apr 18.
El Magraoui F, Eisenacher M, Schrötter A, Kuhlmann K, Heinsen H, Andrén P, Nilsson P, Häggmark A, Schmitz G, Verhaert P, Borchers C, Yoo JS, Lee BH, Meyer HE, Grinberg LT (2014). Developing New Methods to Answer Old and New Questions in Neurodegenerative Diseases: 21(st) Workshop of the HUPO Brain Proteome Project (HBPP) 23-24 January 2014, Honolulu, Hawaii. Proteomics 2014 Jun;14(11):1308-10. doi: 10.1002/pmic.201470083. Epub 2014 Apr 22.
Geillinger KE, Kuhlmann K, Eisenacher M, Giesbertz P, Meyer HE, Daniel H, Spanier B (2014). Intestinal Amino Acid Availability via PEPT-1 Affects TORC1/2 Signaling and the Unfolded Protein Response. J Proteome Res 2014 Aug 1;13(8):3685-92. doi: 10.1021/pr5002669. Epub 2014 Jul 16.
Seymour SL, Farrah T, Binz PA, Chalkley RJ, Cottrell JS, Searle BC, Tabb DL, Vizcaíno JA, Prieto G, Uszkoreit J, Eisenacher M, Martínez-Bartolomé S, Ghali F, Jones AR (2014). A standardized framing for reporting protein identifications in mzIdentML 1.2. Proteomics 2014 Nov;14(21-22):2389-99. doi:10.1002/pmic.201400080. Epub 2014 Sep 23.
Uszkoreit J, Plohnke N, Rexroth S, Marcus K, Eisenacher M (2014). The bacterial proteogenomic pipeline. BMC Genomics 2014 Dec 8;15 Suppl 9:S19. doi: 10.1186/1471-2164-15-S9-S19. Epub 2014 Dec 8.
Wiese H, Kuhlmann K, Wiese S, Stoepel NS, Pawlas M, Meyer HE, Stephan C, Eisenacher M, Drepper F, Warscheid B. Comparison of Alternative MS/MS and Bioinformatics Approaches for Confident Phosphorylation Site Localization. J Proteome Res. 2013 Dec 23. Doi: 10.1021/pr400402s. Epub 2014 Jan 03.
Santos M, Domingues SC, Costa P, Muller T, Galozzi S, Marcus K, da Cruz E Silva EF, da Cruz E Silva OA, Rebelo S. Identification of a Novel Human LAP1 Isoform That Is Regulated by Protein Phosphorylation. PLoS One. 2014 Dec 2;9(12):e113732. doi: 10.1371/journal.pone.0113732. eCollection 2014.
El Magraoui F., Brinkmeier R., Schrötter A., Girzalsky W., Müller T., Marcus K., Meyer H.E., Erdmann R., Platta H.W., Distinct Ubiquitination Cascades Act on the Peroxisomal Targeting Signal Type 2 Co-receptor Pex18p, Traffic 2013, 14(12), 1290-1301 doi: 10.1111/tra.12120. Epub 2013 Oct 7.
El Magraoui F., Schrötter A., Brinkmeier R., Kunst L., Mastalski T., Müller T., Marcus K., Meyer H.E., Girzalsky W., Erdmann R., Platta H.W., The Cytosolic Domain of Pex22p Stimulates the Pex4p-Dependent Ubiquitination of the PTS1-Receptor, PloS One. 2014, 9(8), e105894. doi: 10.1371/journal.pone.0105894. eCollection 2014.
Overkamp K.E., Langklotz S., Aras M., Helling S., Marcus K., Bandow J.E., Hoef Emden K., Frankenberg-Dinkel N., Chromophore composition of the phycobiliprotein Cr-PC577 from the cryptophyte Hemiselmis pacifica, Photosynth Res. 2014 Dec;122(3):293-304. doi: 10.1007/s11120-014-0029-1. Epub 2014 Aug 19.
Nel I, Baba HA, Weber F, Sitek B, Eisenacher M, Meyer HE, Schlaak JF, Hoffmann AC. IGFBP1 in epithelial circulating tumor cells as a potential response marker to selective internal radiation therapy in hepatocellular carcinoma. Biomark Med. 2014 Jun;8(5):687-98. doi: 10.2217/bmm.14.23.
Ul-Hussain M, Olk S, Schoenebeck B, Wasielewski B, Meier C, Prochnow N, May C, Galozzi S, Marcus K, Zoidl G, Dermietzel R, Internal Ribosomal Entry Site (IRES) Activity Generates Endogenous Carboxyl-terminal Domains of Cx43 and Is Responsive to Hypoxic Conditions. J Biol Chem. 2014 Jul 25;289(30):20979-20990. Epub 2014 May 28.
Schrötter A, El Magraoui F, Gröttrup B, Heinsen H, Marcus K, Meyer HE, Park YM, Grinberg LT, Frontiers in neurodegeneration--new insights and prospects--20th HUPO BPP Workshop: 15 September 2013, Yokohama, Japan. Proteomics. 2014 Jun;14(11):1305-7. doi: 10.1002/pmic.201470084.
Sirajuddin S, Barupala D, Helling S, Marcus K, Stemmler TL, Rosenzweig AC, Effects of Zinc on Particulate Methane Monooxygenase Activity and Structure. J Biol Chem. 2014, 289(31), 21782-21794. doi: 10.1074/jbc.M114.581363. Epub 2014 Jun 18.
Padden J, Megger DA, Bracht T, Reis H, Ahrens M, Kohl M, Eisenacher M, Schlaak JO, Canbay AE, Weber F, Hoffmann AC, Kuhlmann K, Meyer HE, Baba HA, Sitek B. Identification of Novel Biomarker Candidates for the Immunohistochemical Diagnosis of Cholangiocellular Carcinoma. Mol Cell Proteomics. 2014 Oct;13(10):2661-72. doi: 10.1074/mcp.M113.034942. Epub 2014 Jul 17.
Megger DA, Naboulsi W, Meyer HE, Sitek B. Proteome Analyses of Hepatocellular Carcinoma. Journal of Clinical and Transnational Hepatology 2014 vol. 2, Pages: 23-30. Doi: 10.14218/JCTH.2013.00022.
Alkatout I, Friemel J, Sitek B, Anlauf M, Eisenach PA, Stühler K, Scarpa A, Perren A, Meyer HE, Knoefel WT, Klöppel G, Sipos B. Novel prognostic markers revealed by a proteomic approach separating benign from malignant insulinomas. Mod Pathol. 2015 Jan 28. doi: 10.1038/modpathol.2014.82. Epub 2014 Jun 20.
Bracht T, Hagemann S, Loscha M, Megger DA, Padden J, Eisenacher M, Kuhlmann K, Meyer HE, Baba HA, Sitek B. Proteome Analysis of a Hepatocyte-Specific BIRC5 (Survivin)-Knockout Mouse Model during Liver Regeneration.
J Proteome Res. 2014 Jun 6;13(6):2771-82. doi: 10.1021/pr401188r. Epub 2014 May 27.
Diepenbroek M, Casadei N, Esmer H, Saido TC, Takano J, Kahle PJ, Nixon RA, Rao MV, Melki R, Pieri L, Helling S, Marcus K, Krueger R, Masliah E, Riess O, Nuber S. Overexpression of the Calpain-specific Inhibitor Calpastatin reduces human alpha-Synuclein Processing, Aggregation and Synaptic Impairment in [A30P]αSyn transgenic mice. Hum Mol Genet. 2014 Aug 1;23(15):3975-89. doi: 10.1093/hmg/ddu112. Epub 2014 Mar 11.
Abel L, Kutschki S, Turewicz M, Eisenacher M, Stoutjesdijk J, Meyer HE, Woitalla D, May C. Autoimmune profiling with protein microarrays in clinical applications. Biochim Biophys Acta. 2014 May;1844(5):977-87. doi: 10.1016/j.bbapap.2014.02.023. Epub 2014 Mar 7.
May C, Nordhoff E, Casjens S, Turewicz M, Eisenacher M, Gold R, Brüning T, Pesch B, Stephan C, Woitalla D, Penke B, Janáky T, Virók D, Siklós L, Engelhardt JI, Meyer HE. Highly Immunoreactive IgG Antibodies Directed against a Set of Twenty Human Proteins in the Sera of Patients with Amyotrophic Lateral Sclerosis Identified by Protein Array. PLoS One. 2014 Feb 26;9(2):e89596. doi: 10.1371/journal.pone.0089596. eCollection 2014.
Harbauer AB, Zahedi RP, Sickmann A, Pfanner N, Meisinger C. The Protein Import Machinery of Mitochondria-A Regulatory Hub in Metabolism, Stress, and Disease. Cell Metab. 2014 Mar 4;19(3):357-72. doi: 10.1016/j.cmet.2014.01.010. Epub 2014 Feb 20.
Baraniskin A, Nöpel-Dünnebacke S, Schumacher B, Gerges C, Bracht T, Sitek B, Meyer HE, Gerken G, Dechene A, Schlaak JF, Schroers R, Pox C, Schmiegel W, Hahn SA. Analysis of U2 Small Nuclear RNA Fragments in the Bile Differentiates Cholangiocarcinoma from Primary Sclerosing Cholangitis and Other Benign Biliary Disorders. Dig Dis Sci. 2014 Jul;59(7):1436-41. doi: 10.1007/s10620-014-3034-5. Epub 2014 Jan 31.
Nensa FM, Neumann MH, Schroetter A, Przyborski A, Mastalski T, Susdalzew S, Loosse C, Helling S, El Magraoui F, Erdmann R, Meyer HE, Uszkoreit J, Eisenacher M, Suh J, Guenette SY, Roehner N, Koegel D, Theiss C, Marcus K, Mueller T. Amyloid Beta A4 Precursor Protein-binding Family B Member 1 (FE65) Interactomics Revealed Synaptic Vesicle Glycoprotein 2A (SV2A) and Sarcoplasmic/Endoplasmic Reticulum Calcium ATPase 2 (SERCA2) as New Binding Proteins in the Human Brain. Mol Cell Proteomics. 2014 Feb;13(2):475-88. doi: 10.1074/mcp.M113.029280. Epub 2013 Nov 27.
Eisenacher M, Stephan C. Computational proteomics in the post-identification era. Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):1. doi: 10.1016/j.bbapap.2013.10.012. No abstract available.
Beck F, Geiger J, Gambaryan S, Veit J, Vaudel M, Nollau P, Kohlbacher O, Martens L, Walter U, Sickmann A, Zahedi RP. Time-resolved characterization of cAMP/PKA-dependent signaling reveals that platelet inhibition is a concerted process involving multiple signaling pathways. Blood. 2014 Jan 30;123(5):e1-e10. doi: 10.1182/blood-2013-07-512384. Epub 2013 Dec 9.
Meckel H, Stephan C, Bunse C, Krafzik M, Reher C, Kohl M, Meyer HE, Eisenacher M. The amino acid's backup bone - storage solutions for proteomics facilities. Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):2-11. doi: 10.1016/j.bbapap.2013.05.018. Epub 2013 May 27.
Kohl M, Megger DA, Trippler M, Meckel H, Ahrens M, Bracht T, Weber F, Hoffmann AC, Baba HA, Sitek B, Schlaak JF, Meyer HE, Stephan C, Eisenacher M. A practical data processing workflow for multi-OMICS projects. Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):52-62. doi: 10.1016/j.bbapap.2013.02.029. Epub 2013 Mar 15.
Mayer G, Jones AR, Binz PA, Deutsch EW, Orchard S, Montecchi-Palazzi L, Vizcaíno JA, Hermjakob H, Oveillero D, Julian R, Stephan C, Meyer HE, Eisenacher M. Controlled vocabularies and ontologies in proteomics: overview, principles and practice. Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):98-107. doi: 10.1016/j.bbapap.2013.02.017. Epub 2013 Feb 19.
Vaudel M, Sickmann A, Martens L. Introduction to Opportunities and Pitfalls in Functional Mass Spectrometry Based Proteomics. Biochim Biophys Acta. 2 2014 Jan;1844(1 Pt A):12-20. doi: 10.1016/j.bbapap.2013.06.019. Epub 2013 Jul 9.
2013
Bauer, S. Endres, M. Lange, M. Schmidt, T. Schumbrutzki, C. Sickmann, A. Beier, D. Novel function assignment to a member of the essential HP1043 response regulator family of epsilon-proteobacteria. Microbiology-SGM 159(5) (2013) 880-889. DOI: 10.1099/mic.0.066548-0. Epub Mar 8.
Mihlan, S. Reiß, C. Thalheimer, P. Herterich, S. Gaetzner, S. Kremerskothen, J. Pavenstädt, H. J. Lewandrowski, U. Sickmann, A. Butt, E. Nuclear import of LASP-1 is regulated by phosphorylation and dynamic protein-protein interactions. Oncogene 32(-) (2013) 2107-2113. DOI: 10.1038/onc.2012.216. Epub 2013 Apr 18.
Megger DA, Pott LL, Ahrens M, Padden J, Bracht T, Kuhlmann K, Eisenacher M, Meyer HE, Sitek B. Comparison of label-free and label-based strategies for proteome analysis of hepatoma cell lines. Biochim Biophys Acta. 2014 May;1844(5):967-76. doi: 10.1016/j.bbapap.2013.07.017. Epub 2013 Aug 14.
Real CI, Megger DA, Sitek B, Jahn-Hofmann K, Ickenstein LM, John MJ, Walker A, Timm J, Kuhlmann K, Eisenacher M, Meyer HE, Gerken G, Broering R, Schlaak JF., Identification of Proteins that Mediate the Pro-viral Functions of the Interferon Stimulated Gene 15 in Hepatitis C Virus Replication. Antiviral Res. 2013 Oct 24. pii: S0166-3542(13)00299-4. doi: 10.1016/j.antiviral.2013.10.009. Epub 2013 Dec.
Korrodi-Gregório L, Abrantes J, Muller T, Melo-Ferreira J, Marcus K, da Cruz E Silva OA, Fardilha M, Esteves. Not so pseudo: the evolutionary history of protein phosphatase 1 regulatory subunit 2 and related pseudogenes. BMC Evol Biol. 2013 Nov 6;13:242. doi: 10.1186/1471-2148-13-242.
Ahrens M, Turewicz M, Casjens S, May C, Pesch B, Stephan C, Woitalla D, Gold R, Brüning T, Meyer HE, Rahnenführer J, Eisenacher M. Detection of patient subgroups with differential expression in omics data: a comprehensive comparison of univariate measures. PLoS One. 2013 Nov 22;8(11):e79380. doi: 10.1371/journal.pone.0079380.
Schrötter A, Magraoui FE, Gröttrup B, Wiltfang J, Heinsen H, Marcus K, Meyer HE, Grinberg LT, Park YM. Early Diagnosis of Neurodegenerative Diseases - The Long Awaited Holy Grail and Bottleneck of Modern Brain Research - 19th HUPO BPP Workshop: May 22-24, 2013, Dortmund, Germany. Proteomics. 2013 Oct;13(20):2938-2941. doi: 10.1002/pmic.201370164.
Schober D., Mayer G., Moing A., Eisenacher M., Neumann S., Ontological analysis of controlled vocabularies used in PSI/MSI supported XML standards, Workshop: ODLS 2013, GI-Edition Lecture Notes in Informatics, Proceedings of the Jahrestagung der Gesellschaft für Informatik 2013, Matthias Horbach (Hrsg.), Koblenz, Germany, 16.-20. September 2013, p. 1875-1888.
Besong Agbo D, Klafki H, Poschmann G, Seyfarth K, Genius J, Janßen C, Stühler K, Wurst W, Meyer HE, Klingenspor M, Wiltfang J. Development of a Capillary Isoelectric Focusing Immunoassay to Measure DJ-1 Isoforms in Biological Samples. Anal Biochem. 2013 Dec 15;443(2):197-204. doi: 10.1016/j.ab.2013.09.013. Epub 2013 Sep 17.
Kötter S, Gout L, Von Frieling-Salewsky M, Müller AE, Helling S, Marcus K, Dos Remedios C, Linke WA, Krüger M. Differential changes in titin domain phosphorylation increase myofilament stiffness in failing human hearts. Cardiovasc Res. 2013 Sep 1;99(4):648-56. doi: 10.1093/cvr/cvt144. Epub 2013 Jun 13.
EL Magraoui FE, Brinkmeier R, Schrötter A, Girzalsky W, Müller T, Marcus K, Meyer HE, Erdmann R, Platta HW. Distinct ubiquitination cascades act on the peroxisomal targeting signal type 2 co-receptor Pex18p. Traffic. 2013 Dec;14(12):1290-301. doi: 10.1111/tra.12120. Epub 2013 Oct 7.
Venne AS, Vögtle FN, Meisinger C, Sickmann A, Zahedi RP. Novel highly sensitive, specific, and straightforward strategy for comprehensive N-terminal proteomics reveals unknown substrates of the mitochondrial peptidase icp55. J Proteome Res. 2013 Sep 6;12(9):3823-30. doi: 10.1021/pr400435d. Epub 2013 Aug.
Waldera-Lupa DM, Stefanksi A, Meyer HE, Stühler K. The fate of b-ions in the two worlds of collision-induced dissociation. Biochim Biophys Acta. 2013 Aug 27. doi:pii: S1570-9639(13)00298-7. 10.1016/j.bbapap.2013.08.007.
Wessel L, Balakrishnan-Renuka A, Henkel C, Meyer HE, Meller K, Brand-Saberi B, Theiss C. Long-term incubation with mifepristone (MLTI) increases the spine density in developing Purkinje cells: new insights into progesterone receptor mechanisms. Cell Mol Life Sci. 2013 Aug 28.
Matkovic T, Siebert M, Knoche E, Depner H, Mertel S, Owald D, Schmidt M, Thomas U, Sickmann A, Kamin D, Hell SW, Bürger J, Hollmann C, Mielke T, Wichmann C, Sigrist SJ. The Bruchpilot cytomatrix determines the size of the readily releasable pool of synaptic vesicles. J Cell Biol. 2013 Aug 19;202(4):667-83. doi: 10.1083/jcb.201301072.
Stahl S, Burkhart JM, Hinte F, Tirosh B, Mohr H, Zahedi RP, Sickmann A, Ruzsics Z, Budt M, Brune W. Cytomegalovirus Downregulates IRE1 to Repress the Unfolded Protein Response. PLoS Pathog. 2013 Aug;9(8):e1003544. doi: 10.1371/journal.ppat.1003544. Epub 2013 Aug 8.
Percy AJ, Chambers AG, Yang J, Jackson AM, Domanski D, Burkhart J, Sickmann A, Borchers CH. Method and platform standardization in MRM-based quantitative plasma proteomics. J Proteomics. 2013 Aug 7. doi:pii: S1874-3919(13)00431-4. 10.1016/j.jprot.2013.07.026. Epub 2013 Aug 7.
Wölfler MM, Meinhold-Heerlein IM, Henkel C, Rath W, Neulen J, Maass N, Bräutigam K. Reduced hemopexin levels in peritoneal fluid of patients with endometriosis. Fertil Steril. 2013 Jun 8. pii: S0015-0282(13)00608-0. doi: 10.1016/j.fertnstert.2013.05.010. Epub 2013 Jun 10.
Plum S, Helling S, Theiss C, Leite RE, May C, Jacob-Filho W, Eisenacher M, Kuhlmann K, Meyer HE, Riederer P, Grinberg LT, Gerlach M, Marcus K. Combined enrichment of neuromelanin granules and synaptosomes from human substantia nigra pars compacta tissue for proteomic analysis. J Proteomics. 2013 Dec 6;94:202-6. doi: 10.1016/j.jprot.2013.07.015. Epub 2013 Aug 3.
Nel I, Baba HA, Ertle J, Weber F, Sitek B, Eisenacher M, Meyer HE, Schlaak JF, Hoffmann AC. Individual profiling of circulating tumor cell composition and therapeutic outcome in patients with hepatocellular carcinoma. Transl Oncol. 2013 Aug 1;6(4):420-8. Print 2013 Aug.
Walzer M, Qi D, Mayer G, Uszkoreit J, Eisenacher M, Sachsenberg T, Gonzalez-Galarza FF, Fan J, Bessant C, Deutsch EW, Reisinger F, Vizcaíno JA, Medina-Aunon JA, Albar JP, Kohlbacher O, Jones AR. The mzQuantML Data Standard for Mass Spectrometry-based Quantitative Studies in Proteomics. Mol Cell Proteomics. 2013 Aug;12(8):2332-40.
Poschmann G, Lendzian A, Uszkoreit J, Eisenacher M, Borght AV, Ramaekers FC, Meyer HE, Stühler K. A combination of two electrophoretical approaches for detailed proteome-based characterization of SCLC subtypes. Arch Physiol Biochem. 2013 Jul;119(3):114-25.
Geiger J, Burkhart JM, Gambaryan S, Walter U, Sickmann A, Zahedi RP. Response: platelet transcriptome and proteome--relation rather than correlation Response. Blood. 2013 Jun 27;121(26):5257-8. Doi: 10.1182/blood-2013-04-493493
Lindemann C, Lupilova N, Müller A, Warscheid B, Meyer HE, Kuhlmann K, Eisenacher M, Leichert LI. Redox Proteomics Uncovers Peroxynitrite-sensitive Proteins That Help Escherichia coli to Overcome Nitrosative Stress. J Biol Chem. 2013 Jul 5;288(27):19698-714.
Casjens S, Eckert A, Woitalla D, Ellrichmann G, Turewicz M, Stephan C, Eisenacher M, May C, Meyer HE, Brüning T, Pesch B. Diagnostic value of the impairment of olfaction in Parkinson's disease. PLoS One. 2013 May 16;8(5):e64735. doi: 10.1371/journal.pone.0064735. Print 2013.
Seikrit C, Henkel C, van Roeyen CR, Bokemeyer D, Eitner F, Martin IV, Boor P, Knüchel R, Meyer HE, Müller-Newen G, Eriksson U, Floege J, Ostendorf T. Biological responses to PDGF-AA versus PDGF-CC in renal fibroblasts. Nephrol Dial Transplant. 2013 Apr;28(4):889-900.
Maerkens A, Kley RA, Olivé M, Theis V, van der Ven PF, Reimann J, Milting H, Schreiner A, Uszkoreit J, Eisenacher M, Barkovits K, Güttsches AK, Tonillo J, Kuhlmann K, Meyer HE, Schröder R, Tegenthoff M, Fürst DO, Müller T, Goldfarb LG, Vorgerd M, Marcus K. Differential proteomic analysis of abnormal intramyoplasmic aggregates in desminopathy. J Proteomics. 2013 Sep 2;90:14-27. doi: 10.1016/j.jprot.2013.04.026. Epub 2013 Apr 30.
Subramanian H, Zahedi R, Sickmann A, Walter U, Gambaryan S. Phosphorylation of CalDAG-GEFI by Protein Kinase A prevents Rap1b activation in human platelets. J Thromb Haemost. 2013 Apr 24. doi: 10.1111/jth.12271.
Turewicz M, May C, Ahrens M, Woitalla D, Gold R, Casjens S, Pesch B, Brüning T, Meyer HE, Nordhoff E, Böckmann M, Stephan C, Eisenacher M. Improving the default data analysis workflow for large autoimmune biomarker discovery studies with protoarrays. Proteomics. 2013 Apr 25. doi: 10.1002/pmic.201200518. Epub 2013 Jun 20.
Janke K, Brockmeier U, Kuhlmann K, Eisenacher M, Nolde J, Meyer HE, Mairbäurl H, Metzen E. Factor Inhibiting HIF-1 (FIH-1) modulates protein interactions of Apoptosis-Stimulating p53 binding Protein 2 (ASPP2). J Cell Sci. 2013 Jun 15;126 Pt 12:2629-40.
Loroch S, Dickhut C, Zahedi RP, Sickmann A. Phosphoproteomics - More than meets the eye. Electrophoresis. 2013 Apr 10. doi: 10.1002/elps.201200710. Epub 2013 May 14.
Megger DA, Bracht T, Meyer HE, Sitek B. Label-Free Quantification in Clinical Proteomics. Biochim Biophys Acta. 2013 Apr 5. doi:pii: S1570-9639(13)00155-6. 10.1016/j.bbapap.2013.04.001. Epub 2013 Apr 6.
Müller A, Hoffmann JH, Meyer HE, Narberhaus F, Jakob U, Leichert LI. Non-native disulfide bond formation activates the σ32-dependent heat shock response in Escherichia coli. J Bacteriol. 2013 Jun;195(12):2807-16. doi: 10.1128/JB.00127-13. Epub 2013 Apr 12.
Schrötter A, Mastalski T, Nensa FM, Neumann M, Loosse C, Pfeiffer K, Magraoui FE, Platta HW, Erdmann R, Theiss C, Uszkoreit J, Eisenacher M, Meyer HE, Marcus K, Müller T. FE65 regulates and interacts with the Bloom syndrome protein in dynamic nuclear spheres - potential relevance to Alzheimer's disease. J Cell Sci. 2013 Jun 1;126(Pt 11):2480-92. doi: 10.1242/jcs.121004. Epub 2013 Apr 9.
Hagemann S, Wohlschlaeger J, Bertram S, Levkau B, Musacchio A, Conway EM, Moellmann D, Kneiseler G, Pless-Petig G, Lorenz K, Sitek B, Baba HA. Loss of Survivin influences liver regeneration and is associated with impaired Aurora B function. Cell Death Differ. 2013 Jun;20(6):834-44. doi: 10.1038/cdd.2013.20. Epub 2013 Mar 22.
Megger DA, Bracht T, Kohl M, Ahrens M, Naboulsi W, Weber F, Hoffmann AC, Stephan C, Kuhlmann K, Eisenacher M, Schlaak JF, Baba HA, Meyer HE, Sitek B. Proteomic differences between hepatocellular carcinoma and non-tumorous liver tissue investigated by a combined gel-based and label-free quantitative proteomics study. Mol Cell Proteomics. 2013 Jul;12(7):2006-20. doi: 10.1074/mcp.M113.028027. Epub 2013 Mar 5.
Mayer G, Montecchi-Palazzi L, Ovelleiro D, Jones AR, Binz PA, Deutsch EW, Chambers M, Kallhardt M, Levander F, Shofstahl J, Orchard S, Antonio Vizcaíno J, Hermjakob H, Stephan C, Meyer HE, Eisenacher M; on behalf of the HUPO-PSI Group. The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. Database (Oxford). 2013 Mar 12;2013:bat009. doi: 10.1093/database/bat009. Print 2013.
Zahedi R, Sickmann A. Analysis of Post-translational Modifications. Proteomics. 2013 Mar;13(6):901-3
Atemnkeng VA, Pink M, Schmitz-Spanke S, Wu XJ, Dong LL, Zhao KH, May C, Laufer S, Langer B, Kaiser A. Deoxyhypusine Hydroxylase from Plasmodium vivax, the Neglected Human Malaria Parasite: Molecular Cloning, Expression and Specific Inhibition by the 5-LOX Inhibitor Zileuton. PLoS One. 2013;8(3):e58318. doi: 10.1371/journal.pone.0058318. Epub 2013 Mar 7.
Martinez-Bartolome S, Deutsch EW, Binz PA, Jones AR, Eisenacher M, Mayer G, Campos A, Canals F, Bech-Serra JJ, Carrascal M, Gay M, Paradela A, Navajas R, Marcilla M, Hernaez ML, Gutierrez-Blazquez MD, Velarde LF, Aloria K, Beaskoetxea J, Medina-Aunon JA, Albar JP. Guidelines for reporting quantitative mass spectrometry based experiments in proteomics. J Proteomics. 2013 Dec 16;95:84-8. doi: 10.1016/j.jprot.2013.02.026. Epub 2013 Mar 14.
Korrodi-Gregório L, Ferreira M, Vintém AP, Wu W, Muller T, Marcus K, Vijayaraghavan S, Brautigan DL, da Cruz E Silva OA, Fardilha M, da Cruz E Silva EF. Identification and characterization of two distinct PPP1R2 isoforms in human spermatozoa. BMC Cell Biol. 2013 Mar 18;14(1):15.
Schweigel H, Geiger J, Beck F, Buhs S, Gerull H, Walter U, Sickmann A, Nollau P. Deciphering of ADP-induced, phosphotyrosine-dependent signaling networks in human platelets by SH2 profiling. Proteomics. 2013 Mar;13(6):1016-27. doi: 10.1002/pmic.201200353. Epub 2013 Feb 18.
Hansen T, Albers M, Hedberg C, Sickmann A. Adenylylation, mass spectrometry and proteomics - introducing a "new" modification to bottom up proteomics. Proteomics. 2013 Mar;13(6):955-963.
Kaltwaßer B, Schulenborg T, Beck F, Klotz M, Schäfer KH, Schmitt M, Sickmann A, Friauf E. Developmental changes of the protein repertoire in the rat auditory brainstem: A comparative proteomics approach in the superior olivary complex and the inferior colliculus with DIGE and iTRAQ. J Proteomics. 2013 Feb 21;79:43-59
Raatschen N, Wenzel M, Leichert LI, Düchting P, Krämer U, Bandow JE. Extracting iron and manganese from bacteria with ionophores - a mechanism against competitors characterized by increased potency in environments low in micronutrients. Proteomics. 2013 Apr;13(8):1358-70.
Rosenkranz K, Tenbusch M, May C, Marcus K, Meier C. Changes in Interleukin-1 alpha serum levels after transplantation of umbilical cord blood cells in a model of perinatal hypoxic-ischemic brain damage. Ann Anat. 2013 Mar;195(2):122-7. doi: 10.1016/j.aanat.2012.09.003. Epub 2012 Oct 6.
Patra AK, Avots A, Zahedi RP, Schüler T, Sickmann A, Bommhardt U, Serfling E. An alternative NFAT-activation pathway mediated by IL-7 is critical for early thymocyte development. Nat Immunol. 2013 Feb;14(2):127-35.
Dahl JU, Radon C, Buhning M, Nimtz M, Leichert LI, Denis Y, Jourlin-Castelli C, Iobbi-Nivol C, Mejean V, Leimkuhler S. The sulfur carrier protein TusA has a pleiotropic role in Escherichia coli which also affects molybdenum cofactor biosynthesis. J Biol Chem. 2013 Feb 22;288(8):5426-42.
Gronemeyer T, Wiese S, Grinhagens S, Schollenberger L, Satiagraha A, Huber LA, Meyer HE, Warscheid B, Just WW. Localization of Rab Proteins to Peroxisomes: a Proteomics and Immunofluorescence Study. FEBS Lett. 2013 Feb 14;587(4):328-38.
Gronemeyer T, Wiese S, Ofman R, Bunse C, Pawlas M, Hayen H, Eisenacher M, Stephan C, Meyer HE, Waterham HR, Erdmann R, Wanders RJ, Warscheid B. The Proteome of Human Liver Peroxisomes: Identification of Five New Peroxisomal Constituents by a Label-Free Quantitative Proteomics Survey. PLoS ONE 8(2): e57395. Febr. 2013.
Mayer G, Jones AR, Binz PA, Deutsch EW, Orchard S, Montecchi-Palazzi L, Vizcaíno JA, Hermjakob H, Oveillero D, Julian R, Stephan C, Meyer HE, Eisenacher M. Controlled Vocabularies and Ontologies in Proteomics: Overview, Principles and Practice. Biochim Biophys Acta. 2013 Feb 19. pii: S1570-9639(13).
Gröttrup B, May C, Meyer HE, Grinberg LT, Park YM. Progresses in Neuroproteomics of Neurodegenerative Diseases - 18(th) HUPO BPP Workshop: September 12, 2012, Boston, USA. Proteomics. 2013 Jan;13(2):217-8.
Gröttrup B, Esselmann H, May C, Schrötter A, Woitalla D, Heinsen H, Marcus K, Wiltfang J, Meyer HE, Grinberg LT, Park YM. Challenges in Modern Biomarker Discovery - 17(th) HUPO BPP Workshop: May 24-25, 2012, Sao Paulo, Brazil. Proteomics. 2013 Jan;13(2):210-6.
Labbus K, Henning M, Borkham-Kamphorst E, Geisler C, Berger T, Mak TW, Knüchel R, Meyer HE, Weiskirchen R, Henkel C. Proteomic profiling in Lipocalin 2 deficient mice under normal and inflammatory conditions. J Proteomics. 2013 Jan 14;78:188-96.
Müller T, Schrötter A, Loosse C, Pfeiffer K, Theiss C, Kauth M, Meyer HE, Marcus K. A ternary complex consisting of AICD, FE65, and TIP60 down-regulates Stathmin1. Biochim Biophys Acta. 2013, Jan;1834(1):387-94.
Pietsch J, Riwaldt S, Bauer J, Sickmann A, Weber G, Grosse J, Infanger M, Eilles C, Grimm D. Interaction of proteins identified in human thyroid cells. Int J Mol Sci. 2013 Jan 9;14(1):1164-78. Doi: 10.1002/pmic.201370054
Koutsonas A, Carstesen D, Henkel C, Walter P, Thumann G, Weinberger AW. Effects of Coagulation on the Autofluorescence Pattern of ARPE-19 Cells: An in vitro Study. Ophthalmic Res. 2013;49(1):11-9.
Kley RA, Maerkens A, Leber Y, Theis V, Schreiner A, van der Ven PF, Uszkoreit J, Stephan C, Eulitz S, Euler N, Kirschner J, Müller K, Meyer HE, Tegenthoff M, Fürst DO, Vorgerd M, Müller T, Marcus K. A combined laser microdissection and mass spectrometry approach reveals new disease relevant proteins accumulating in aggregates of filaminopathy patients. Mol Cell Proteomics. 2013 Jan;12(1):215-27.
Xiang W, Schlachetzki JC, Helling S, Bussmann JC, Berlinghof M, Schäffer TE, Marcus K, Winkler J, Klucken J, Becker CM. Oxidative stress-induced posttranslational modifications of alpha-synuclein: Specific modification of alpha-synuclein by 4-hydroxy-2-nonenal increases dopaminergic toxicity. Mol Cell Neurosci. 2013 Jan 28;54C:71-83.
Baraniskin A, Nöpel-Dünnebacke S, Ahrens M, Jensen SG, Zöllner H, Maghnouj A, Wos A, Mayerle J, Munding J, Kost D, Reinacher-Schick A, Liffers S, Schroers R, Chromik AM, Meyer HE, Uhl W, Klein-Scory S, Weiss FU, Stephan C, Schwarte-Waldhoff I, Lerch MM, Tannapfel A, Schmiegel W, Andersen CL, Hahn SA. Circulating U2 small nuclear RNA fragments as a novel diagnostic biomarker for pancreatic and colorectal adenocarcinoma. Int J Cancer. 2013 Jan 15;132(2):E48-57.