PUBLICATIONS

1: Nguyen CDL, Malchow S, Reich S, Steltgens S, Shuvaev KV, Loroch S, Lorenz C, Sickmann A, Knobbe-Thomsen CB, Tews B, Medenbach J, Ahrends R. A sensitive and simple targeted proteomics approach to quantify transcription factor and membrane proteins of the unfolded protein response pathway in glioblastoma cells. Sci Rep. 2019 Jun 20;9(1):8836. doi: 10.1038/s41598-019-45237-5.

2: Lütjohann D, Björkhem I, Friedrichs S, Kerksiek A, Lövgren-Sandblom A, Geilenkeuser WJ, Ahrends R, Andrade I, Ansorena D, Astiasarán I, Baila-Rueda L, Barriuso B, Becker S, Bretillon L, Browne RW, Caccia C, Ceglarek U, Cenarro A, Crick PJ, Fauler G, Garcia-Llatas G, Gray R, Griffiths WJ, Gylling H, Harding S,  Helmschrodt C, Iuliano L, Janssen HG, Jones P, Kaipiainen L, Kannenberg F, Lagarda MJ, Leoni V, Lottenberg AM, MacKay DS, Matysik S, McDonald J, Menendez-Carreño M, Myrie SB, Sutti Nunes V, Ostlund RE, Polisecki E, Ramos F, Rideout TC, Schaefer EJ, Schmitz G, Wang Y, Zerbinati C, Diczfalusy U, Schött HF. First international descriptive and interventional survey for cholesterol and non-cholesterol sterol determination by gas- and liquid-chromatography-Urgent need for harmonisation of analytical methods. J Steroid Biochem Mol Biol. 2019 Jun;190:115-125. doi: 10.1016/j.jsbmb.2019.03.025.

3: Wirthschaft P, Bode J, Soni H, Dietrich F, Krüwel T, Fischer B, Knobbe-Thomsen CB, Rossetti G, Hentschel A, Mack N, Schönig K, Breckwoldt MO, Schmandke A, Pusch S, Medenbach J, Bendszus M, Schwab ME, von Deimling A, Kool M, Herold-Mende C, Reifenberger G, Ahrends R, Tews B. RhoA regulates translation of the Nogo-A decoy SPARC in white matter-invading glioblastomas. Acta Neuropathol. 2019 May 6. doi:
10.1007/s00401-019-02021-z.

4: Viplav A, Saha T, Huertas J, Selenschik P, Ebrahimkutty MP, Grill D, Lehrich J, Hentschel A, Biasizzo M, Mengoni S, Ahrends R, Gerke V, Cojocaru V, Klingauf J, Galic M. ArhGEF37 assists dynamin 2 during clathrin-mediated endocytosis. J Cell Sci. 2019 May 8;132(9). pii: jcs226530. doi: 10.1242/jcs.226530.

5: 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.

6: Wegner MS, Schömel N, Gruber L, Örtel SB, Kjellberg MA, Mattjus P, Kurz J, Trautmann S, Peng B, Wegner M, Kaulich M, Ahrends R, Geisslinger G, Grösch S. UDP-glucose ceramide glucosyltransferase activates AKT, promoted proliferation, and doxorubicin resistance in breast cancer cells. Cell Mol Life Sci. 2018 Sep;75(18):3393-3410. doi:10.1007/s00018-018-2799-7.

7: Peng B, Geue S, Coman C, Münzer P, Kopczynski D, Has C, Hoffmann N, Manke MC, Lang F, Sickmann A, Gawaz M, Borst O, Ahrends R. Identification of key lipids critical for platelet activation by comprehensive analysis of the platelet lipidome. Blood. 2018 Aug 2;132(5):e1-e12. doi: 10.1182/blood-2017-12-822890.

8:Danne-Rasche N, Coman C, Ahrends R. Nano-LC/NSI MS Refines Lipidomics by Enhancing Lipid Coverage, Measurement Sensitivity, and Linear Dynamic Range. Anal Chem. 2018 Jul 3;90(13):8093-8101. doi: 10.1021/acs.analchem.8b01275.

9: Pauling JK, Hermansson M, Hartler J, Christiansen K, Gallego SF, Peng B, Ahrends R, Ejsing CS. Proposal for a common nomenclature for fragment ions in mass spectra of lipids. PLoS One. 2017 Nov 21;12(11):e0188394. doi: 10.1371/journal.pone.0188394.

10: Peng B, Weintraub ST, Coman C, Ponnaiyan S, Sharma R, Tews B, Winter D, Ahrends R. A Comprehensive High-Resolution Targeted Workflow for the Deep Profiling of Sphingolipids. Anal Chem. 2017 Nov 21;89(22):12480-12487. doi: 10.1021/acs.analchem.7b03576.

11: Schwudke D, Shevchenko A, Hoffmann N, Ahrends R. Lipidomics informatics for life-science. J Biotechnol. 2017 Nov 10;261:131-136. doi: 10.1016/j.jbiotec.2017.08.010.

12: Vögtle FN, Burkhart JM, Gonczarowska-Jorge H, Kücükköse C, Taskin AA, Kopczynski D, Ahrends R, Mossmann D, Sickmann A, Zahedi RP, Meisinger C. Landscape of submitochondrial protein distribution. Nat Commun. 2017 Aug 18;8(1):290. doi: 10.1038/s41467-017-00359-0.

13: Kopczynski D, Sickmann A, Ahrends R. Computational proteomics tools for identification and quality control. J Biotechnol. 2017 Nov 10;261:126-130. doi:10.1016/j.jbiotec.2017.06.1199.

14: Rampler E, Coman C, Hermann G, Sickmann A, Ahrends R, Koellensperger G. LILY-lipidome isotope labeling of yeast: in vivo synthesis of (13)C labeled reference lipids for quantification by mass spectrometry. Analyst. 2017 Jun 7;142(11):1891-1899. doi: 10.1039/c7an00107j.

15: Kopczynski D, Barsnes H, Njølstad PR, Sickmann A, Vaudel M, Ahrends R. PeptideMapper: efficient and versatile amino acid sequence and tag mapping. Bioinformatics. 2017 Jul 1;33(13):2042-2044. doi: 10.1093/bioinformatics/btx122.

16: Hendgen-Cotta UB, Esfeld S, Coman C, Ahrends R, Klein-Hitpass L, Flögel U, Rassaf T, Totzeck M. A novel physiological role for cardiac myoglobin in lipid metabolism. Sci Rep. 2017 Feb 23;7:43219. doi: 10.1038/srep43219.

17: Kopczynski D, Coman C, Zahedi RP, Lorenz K, Sickmann A, Ahrends R. Multi-OMICS: a critical technical perspective on integrative lipidomics approaches. Biochim Biophys Acta. 2017 Aug;1862(8):808-811. doi: 10.1016/j.bbalip.2017.02.003.

18: Coman C, Solari FA, Hentschel A, Sickmann A, Zahedi RP, Ahrends R. Simultaneous Metabolite, Protein, Lipid Extraction (SIMPLEX): A Combinatorial Multimolecular Omics Approach for Systems Biology. Mol Cell Proteomics. 2016 Apr;15(4):1453-66. doi: 10.1074/mcp.M115.053702.

19: Hentschel A, Ahrends R. Monitoring PPARG-Induced Changes in Glycolysis by Selected Reaction Monitoring Mass Spectrometry. Methods Mol Biol. 2016;1394:57-74. doi: 10.1007/978-1-4939-3341-9_5.

20: Hentschel A, Zahedi RP, Ahrends R. Protein lipid modifications–More than just a greasy ballast. Proteomics. 2016 Mar;16(5):759-82. doi: 10.1002/pmic.201500353.

21: Peng B, Ahrends R. Adaptation of Skyline for Targeted Lipidomics. J Proteome  Res. 2016 Jan 4;15(1):291-301. doi:10.1021/acs.jproteome.5b00841.

22: Ahrends R, Niewiadomski P, Teruel MN, Rohatgi R. Measuring Gli2 Phosphorylation by Selected Reaction Monitoring Mass Spectrometry. Methods Mol Biol. 2015;1322:105-23. doi: 10.1007/978-1-4939-2772-2_10. PubMed PMID: 26179043; PubMed Central PMCID: PMC4699800.

23: Ota A, Kovary KM, Wu OH, Ahrends R, Shen WJ, Costa MJ, Feldman BJ, Kraemer FB, Teruel MN. Using SRM-MS to quantify nuclear protein abundance differences between adipose tissue depots of insulin-resistant mice. J Lipid Res. 2015 May;56(5):1068-78. doi: 10.1194/jlr.D056317.

24: Khor VK, Ahrends R, Lin Y, Shen WJ, Adams CM, Roseman AN, Cortez Y, Teruel MN, Azhar S, Kraemer FB. The proteome of cholesteryl-ester-enriched versus triacylglycerol-enriched lipid droplets. PLoS One. 2014 Aug 11;9(8):e105047. doi: 10.1371/journal.pone.0105047.

25: Ahrends R, Ota A, Kovary KM, Kudo T, Park BO, Teruel MN. Controlling low rates of cell differentiation through noise and ultrahigh feedback. Science. 2014 Jun 20;344(6190):1384-9. doi: 10.1126/science.1252079.

26: Tinnefeld V, Sickmann A, Ahrends R. Catch me if you can: challenges and applications of cross-linking approaches. Eur J Mass Spectrom (Chichester). 2014;20(1):99-116. PubMed PMID: 24881459.

27: Niewiadomski P, Kong JH, Ahrends R, Ma Y, Humke EW, Khan S, Teruel MN, Novitch BG, Rohatgi R. Gli protein activity is controlled by multisite phosphorylation in vertebrate Hedgehog signaling. Cell Rep. 2014 Jan 16;6(1):168-181. doi: 10.1016/j.celrep.2013.12.003.

28: Park BO, Ahrends R, Teruel MN. Consecutive positive feedback loops create a bistable switch that controls preadipocyte-to-adipocyte conversion. Cell Rep. 2012 Oct 25;2(4):976-90. doi: 10.1016/j.celrep.2012.08.038.

29: Ahrends R, Lichtner B, Buck F, Hildebrand D, Kotasinska M, Kohlbacher O, Kwiatkowski M, Wagner M, Trusch M, Schlüter H. Comparison of displacement versus  gradient mode for separation of a complex protein mixture by anion-exchange chromatography. J Chromatogr B Analyt Technol Biomed Life Sci. 2012 Jul 15;901:34-40. doi: 10.1016/j.jchromb.2012.05.037

30: Esteban-Fernández D, Ahrends R, Linscheid MW. MeCAT peptide labeling for the  absolute quantification of proteins by 2D-LC-ICP-MS. J Mass Spectrom. 2012 Jun;47(6):760-8. doi: 10.1002/jms.3013.

31: Bergmann U, Ahrends R, Neumann B, Scheler C, Linscheid MW. Application of metal-coded affinity tags (MeCAT): absolute protein quantification with top-down  and bottom-up workflows by metal-coded tagging. Anal Chem. 2012 Jun 19;84(12):5268-75. doi: 10.1021/ac203460b.

32: Lang C, Rastew E, Hermes B, Siegbrecht E, Ahrends R, Banerji S, Flieger A. Zinc metalloproteinase ProA directly activates Legionella pneumophila PlaC glycerophospholipid:cholesterol acyltransferase. J Biol Chem. 2012 Jul 6;287(28):23464-78. doi: 10.1074/jbc.M112.346387.

33: Trusch M, Tillack K, Kwiatkowski M, Bertsch A, Ahrends R, Kohlbacher O, Martin R, Sospedra M, Schlüter H. Displacement chromatography as first separating step in online two-dimensional liquid chromatography coupled to mass spectrometry analysis of a complex protein sample–the proteome of neutrophils. J Chromatogr A. 2012 Apr 6;1232:288-94. doi: 10.1016/j.chroma.2012.02.029.

34: Abell E, Ahrends R, Bandara S, Park BO, Teruel MN. Parallel adaptive feedback enhances reliability of the Ca2+ signaling system. Proc Natl Acad Sci U S A. 2011 Aug 30;108(35):14485-90. doi: 10.1073/pnas.1018266108.

35: Ahrends R, Lichtner B, Bertsch A, Kohlbacher O, Hildebrand D, Trusch M, Schlüter H. Application of displacement chromatography for the proteome analysis  of a human plasma protein fraction. J Chromatogr A. 2010 May 7;1217(19):3321-9. doi: 10.1016/j.chroma.2009.10.028.

36: Linscheid MW, Ahrends R, Pieper S, Kühn A. Liquid chromatography-mass spectrometry-based quantitative proteomics. Methods Mol Biol. 2009;564:189-205. doi: 10.1007/978-1-60761-157-8_11.

37: Pieper S, Beck S, Ahrends R, Scheler C, Linscheid MW. Fragmentation behavior  of metal-coded affinity tag (MeCAT)-labeled peptides. Rapid Commun Mass Spectrom. 2009 Jul;23(13):2045-52. doi: 10.1002/rcm.4118.

38: Ahrends R, Pieper S, Neumann B, Scheler C, Linscheid MW. Metal-coded affinity tag labeling: a demonstration of analytical robustness and suitability for biological applications. Anal Chem. 2009 Mar 15;81(6):2176-84. doi: 10.1021/ac802310c.

39: Ahrends R, Pieper S, Kühn A, Weisshoff H, Hamester M, Lindemann T, Scheler C, Lehmann K, Taubner K, Linscheid MW. A metal-coded affinity tag approach to quantitative proteomics. Mol Cell Proteomics. 2007 Nov;6(11):1907-16. Epub 2007 Jul 11.

40: Ahrends R, Kosinski J, Kirsch D, Manelyte L, Giron-Monzon L, Hummerich L, Schulz O, Spengler B, Friedhoff P. Identifying an interaction site between MutH and the C-terminal domain of MutL by crosslinking, affinity purification, chemical coding and mass spectrometry. Nucleic Acids Res. 2006 Jun 13;34(10):3169-80. Print 2006. PubMed PMID: 16772401; PubMed Central PMCID: PMC1483222.

41: Giron-Monzon L, Manelyte L, Ahrends R, Kirsch D, Spengler B, Friedhoff P. Mapping protein-protein interactions between MutL and MutH by cross-linking. J Biol Chem. 2004 Nov 19;279(47):49338-45. Epub 2004 Sep 14. PubMed PMID: 15371440.