NACH OBEN

Publikationen


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2020

Schuld J, Orfanos Z, Chevessier F, Eggers B, Heil L, Uszkoreit J, Unger A, Kirfel G, van der Ven P, Marcus K, Linke WA, Clemen CS, Schröder R, Fürst DO. Homozygous expression of the myofibrillar myopathy-associated p.W2710X filamin C variant reveals major pathomechanisms of sarcomeric lesion formation. eingereicht bei Acta Neuropathol Commun.

PubMed

Kaziales A, Barkovits K, Marcus K, Richter K. Glucocorticoid receptor complexes form cooperatively with the Hsp90 co-chaperones PPH-5 and FKB 6. eingereicht bei Sci Rep.

PubMed

Dadras M, May C, Wagner J, Wallner C, Becerikli M, Dittfeld S, Serschnitzki B, Schilde L, Guntermann A, Köller M, Sengstock C, Köller, M, Seybold C, Geßmann J, Schildhauer TA, Lehnhardt M, Marcus K, Behr B. Comparative proteomic analysis of osteogenic differentiated human adipose tissue and bone marrow-derived stromal cells. eingereicht bei J Cell Mol Med.

PubMed

Schilde L, Steinbach S, Serschnitzki B, Bähr M, Lingor P, Marcus K, May C. Human cerebrospinal fluid data for use as spectral library for biomarker research. eingereicht bei Data in Brief

PubMed

Montesinos-Rongen M, Terrao M, May C, Marcus K, Blümcke I, Hellmich M, Küppers R, Brunn A, Deckert M. The process of somatic hypermutation increases polyreactivity for CNS antigens in primary CNS lymphoma. Haematologica, im Druck

PubMed

Kohl M, Stepath M, Bracht T, Megger DA, Sitek B, Marcus K, Eisenacher M. CalibraCurve: A Tool for Calibration of Targeted MS-Based Measurements. (2020) Proteomics, e1900143

PubMed

Meschede J, Šadić M, Furthmann N, Miedema T, Sehr DA, Nastase MV, Müller-Rischart AK, Bader V, Berlemann LA, Pilsl A, Schlierf A, Barkovits K, Kachholz B, Rittinger K, Ikeda F, Marcus K, Schaefer L, Tatzelt J, Winklhofer KF. The Parkin-coregulated gene PACRG promotes TNF signaling by stabilizing the linear ubiquitin chain assembly complex. (2020) Science Signalling, 13(617), pii: eaav1256

PubMed

Barkovits K, Kruse N, Uszkoreit J, Linden A, Tönges L, Pfeiffer K, Mollenhauer B, Marcus K. Quantification of artificial blood contamination in CSF and its impact on the quantitative analysis of alpha-synuclein. (2020) 5;9(2). pii: E370

PubMed

Güttsches AK, Jacobsen F, Schreiner A, Mertens-Rill J, Tegenthoff M, Marcus K, Vorgerd M, Kley RA. Chaperones in sporadic inclusion body myositis-Validation of proteomic data. (2020) Muscle & Nerve, 61(1), 116-121

PubMed

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. (2020) Mol Cell Proteomics, 19(1),181-197

PubMed

Ruggieri A, Naumenko S, Smith MA, Iannibelli E, Blasenvich F, Bragato C, Gibertini S, Barton K, Vorgerd M, Marcus K, Wang P, Maggi L, Mantegazza R, Dowling JJ, Kley RA, Mora M, Minassian BAR. Multiomic elucidation of a coding 99-mer repeat-expansion skletal muscle disease. Acta Neuropathol,. in press

PubMed

Glaesek K, May C, Marcus K, Matschke V, Theiss C, Theis V. microRNA-129 and mircroRNA-130 regulate VEGFR-2 expression in sensory and motor neurons during development. Int J Mol Sci

PubMed

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

PubMed

Kinast V, Plociennikowska  A, Anggakusuma , Bracht T, Todt D, Brown R, Boldanova T, Zhang Y, Brueggemann Y, Friesland M, Engelmann M, Vieyres G, Broering R, Vondran F, Heim M, Sitek B, Bartenschlager  R, Pietschmann T, Steinmann E.  C19orf66 Is an Interferon-Induced Inhibitor of HCV Replication That Restricts Formation of the Viral Replication Organelle. J Hepatol 2020 Apr 12;S0168-8278(20)30209-9. doi: 10.1016/j.jhep.2020.03.047 PMID 32294532

PubMed

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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. Molecular & Cellular Proteomics November 7, 2019. doi: 10.1074/mcp.RA119.001714

PubMed

Stepath M, Zülch B, Maghnouj A, Schork K, Turewicz M, Eisenacher M, Hahn S, Sitek B, Bracht T. A systematic comparison of label-free, SILAC and TMT techniques to study early adaption towards inhibition of EGFR signaling in the colorectal cancer cell line Difi. Proteome Res. 2019 Dec 8. doi: 10.1021/acs.jproteome.9b00701.

PubMed

Güttsches AK, Jacobsen F, Schreiner A, Mertens-Rill J, Tegenthoff M, Marcus K, Vorgerd M, Kley RA. Chaperones in sporadic inclusion body myositis-Validation of proteomic data. Muscle Nerve. 2019 Oct 23. doi: 10.1002/mus.26742. PMID:31644823

Pubmed

Solga R, Behrens J, Ziemann A, Riou A, Berwanger C, Becker L, Garrett L, de Angelis MH, Fischer L, Coras R, Barkovits K, Marcus K, Mahabir E, Eichinger L, Schröder R, Noegel AA, Clemen CS. CRN2 binds to TIMP4 and MMP14 and promotes perivascular invasion of glioblastoma cells. German Mouse Clinic Consortium. Eur J Cell Biol. 2019 Oct 11:151046. doi: 10.1016/j.ejcb.2019.151046. PMID:31677819

Pubmed

Kopczynski D, Bittremieux W, Bouyssié D, Dorfer V, Locard-Paulet M, Van Puyvelde B, Schwämmle V, Soggiu A, Willems S, Uszkoreit J. Proceedings of the EuBIC Winter School 2019. EuPA open Proteomics. doi: 10.1016/j.euprot.2019.07.002

Pubmed

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. doi: 10.1016/j.euprot.2019.07.007

Pubmed

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

Pubmed

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

Pubmed

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

Pubmed

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

Pubmed

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

Pubmed

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

Pubmed

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

Pubmed

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

Pubmed

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 

Pubmed

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.

Pubmed

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. PMID: 31081335

Pubmed

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.

Pubmed

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

Pubmed

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

Pubmed

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

Pubmed

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

Pubmed

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

Pubmed

nach oben

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

Pubmed

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

Pubmed

 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

Pubmed

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.

Pubmed

Xie K, Bunse C, Marcus K, Leichert L. Quantifying changes in the bacterial thiol redox proteome during host-pathogen interaction. Redox Biol. 2019 Feb;21:101087. doi: 10.1016/j.redox.2018.101087. Epub 2018 Dec 19.

Pubmed

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. 2019 Jan 14;9:3285. doi: 10.3389/fmicb.2018.03285. eCollection 2018.

Pubmed

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.

Pubmed

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.

Pubmed

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.

Pubmed

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.

Pubmed

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.

Pubmed

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.

Pubmed

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.

Pubmed

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

Pubmed

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

Pubmed

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.

Pubmed

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.

Pubmed

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.

Pubmed

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.

Pubmed

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.

Pubmed

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.

Pubmed
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.

Pubmed

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.

Pubmed

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: 2880062

Pubmed

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.

Pubmed

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.

Pubmed

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.

Pubmed

Mora MI, Molina M, Odriozola L, Elortza F, Mato JM, Sitek B, Zhang P, He F, Latasa MU, Avila M, Corrales FJ. 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.

Pubmed

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.

Pubmed

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.

Pubmed

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.

Pubmed

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.

Pubmed

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.

Pubmed

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.

Pubmed

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.

Pubmed

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.

Pubmed

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.

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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.

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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.

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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.

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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.

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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.

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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.

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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

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Nöbauer K, Hummel K, Mayrhofer C, Ahrens M, Setyabudi FMC, Schmidt-Heydt M, Eisenacher M, Razzazi-Fazeli E. Comprehensive Proteomic Analysis of Penicillium Verrucosum. 2017 May;17(9). doi: 10.1002/pmic.201600467.

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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.

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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.

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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.

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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.

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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.

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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.

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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 Mol Biol. 2018;1841:189-206. doi: 10.1007/978-1-4939-8695-8_14.

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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.

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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.

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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.

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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.

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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.

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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

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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.

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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.

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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.

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