Home PUBLICATIONS

2024

1. Torta F, Hoffmann N, Burla B, Alecu I, Arita M, Bamba T, Bennett SAL, Bertrand-Michel J, Brügger B, Cala MP, Camacho-Muñoz D, Checa A, Chen M, Chocholoušková M, Cinel M, Chu-Van E, Colsch B, Coman C, Connell L, Sousa BC, Dickens AM, Fedorova M, Eiríksson FF, Gallart-Ayala H, Ghorasaini M, Giera M, Guan XL, Haid M, Hankemeier T, Harms A, Höring M, Holčapek M, Hornemann T, Hu C, Hülsmeier AJ, Huynh K, Jones CM, Ivanisevic J, Izumi Y, Köfeler HC, Lam SM, Lange M, Lee JC, Liebisch G, Lippa K, Lopez-Clavijo AF, Manzi M, Martinefski MR, Math RGH, Mayor S, Meikle PJ, Monge ME, Moon MH, Muralidharan S, Nicolaou A, Nguyen-Tran T, O’Donnell VB, Orešič M, Ramanathan A, Riols F, Saigusa D, Schock TB, Schwartz-Zimmermann H, Shui G, Singh M, Takahashi M, Thorsteinsdóttir M, Tomiyasu N, Tournadre A, Tsugawa H, Tyrrell VJ, van der Gugten G, Wakelam MO, Wheelock CE, Wolrab D, Xu G, Xu T, Bowden JA, Ekroos K, Ahrends R, Wenk MR. Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards. Nat Commun. 2024 Oct 

2. Kopczynski D, Ejsing CS, McDonald JG, Bamba T, Baker ES, Bertrand-Michel J, Brügger B, Coman C, Ellis SR, Garrett TJ, Griffiths WJ, Guan XL, Han X, Höring M, Holčapek M, Hoffmann N, Huynh K, Lehmann R, Jones JW, Kaddurah-Daouk R, Köfeler HC, Meikle PJ, Metz TO, O’Donnell VB, Saigusa D,  Schwudke D, Shevchenko A, Torta F, Vizcaíno JA, Welti R, Wenk MR, Wolrab D, Xia Y, Ekroos K, Ahrends R, Gerhard Liebisch G. The Lipidomics Reporting Checklist A framework for transparency of lipidomic experiments and repurposing resource data. J Lipid Research. 2024 Aug

3. Skotland T, Ekroos K, McDonald J, Ahrends R, Liebisch G, Sandvig K. Pitfalls in lipid mass spectrometry of mammalian samples – a brief guide for biologists. Nat Rev Mol Cell Biol. 2024 Jul

4. Rubenzucker S, Manke MC, Lehmann R, Assinger A, Borst O, Ahrends R. A Targeted, Bioinert LC-MS/MS Method for Sensitive, Comprehensive Analysis of Signaling Lipids. Anal Chem. 2024 Jun

5. Kumar M, Has C, Lam-Kamath K, Ayciriex S, Dewett D, Bashir M, Poupault C, Schuhmann K, Thomas H, Knittelfelder O, Raghuraman BK, Ahrends R, Rister J, Shevchenko A. Eye proteome of Drosophila melanogaster. Proteomics. 2024 May

6. Kumar M, Has C, Lam-Kamath K, Ayciriex S, Dewett D, Bashir M, Poupault C, Schuhmann K, Thomas H, Knittelfelder O, Raghuraman BK, Ahrends R, Rister J, Shevchenko A. Lipidome Unsaturation Affects the Morphology and Proteome of the Drosophila Eye. J Proteome Res. 2024 Apr. Epub 2024 Mar

2023

1. Kumar M, Has C, Lam-Kamath K, Ayciriex S, Dewett D, Bashir M, Poupault C, Schuhmann K, Thomas H, Knittelfelder O, Raghuraman BK, Ahrends R, Rister J, Shevchenko A. Eye proteome of Drosophila melanogaster. Proteomics. 2023 Nov

2. Troppmair N, Kopczynski D, Assinger A, Lehmann R, Coman C, Ahrends R. Accurate Sphingolipid Quantification Reducing Fragmentation Bias by Nonlinear Models. Anal Chem. 2023 Oct

3. Kopczynski D, Hoffmann N, Troppmair N, Coman C, Ekroos K, Kreutz MR, Liebisch G, Schwudke D, Ahrends R. Simple Exploration, Reanalysis, and Quality Control of Large-Scalre Lipidomics Studies. Anal Chem. 2023 Oct

4. de Jonckheere B, Kollotzek F, Münzer P, Göb V, Fischer M, Mott K, Coman C, Troppmair NN, Manke MC, Zdanyte M, Harm T, Sigle M, Kopczynski D, Bileck A, Gerner C, Hoffmann N, Heinzmann D, Assinger A, Gawaz M, Stegner D, Schulze H, Borst O, Ahrends R. Critical shifts in lipid metabolism promote megakaryocyte differentiation and proplatelet formation. Nat Cardiovasc Res. 2023 Sep

5. Cheung HYF, Zou J, Tantiwong C, Fernandez DI, Huang J, Ahrends R, Roest M, Cavill R, Gibbins J, Heemskerk JWM. High-throughput assessment identifying major platelet Ca2+ entry pathways via tyrosinekinase-linked and G protein-coupled receptors. Cell Calcium. 2023 Jun

6. Foest D, Knodel A, Ahrends R, Coman C, Franzke J, Brandt S. Fliexible Microtube Plasma for the Consecutive-Ionization of Chlesterol in nano-Electrospray Mass Spectrometry. Anal Chem. 2023 Jun

7. Kumar M, Has C, Lam-Kamath K, Ayciriex S, Dewett D, Bashir M, Poupault C, Schuhmann K, Knittelfelder O, Raghuraman BK, Ahrends R, Rister J, Shevchenko A. Lipidome unsaturation affects the morphology and proteome of the Drosophila eye. bioRxiv [Preprint]. 2023 May

8. Wang Q, Hoene M, Hu C, Fritsche L, Ahrends R, Liebisch G, Ekroos K, Fritsche A, Birkenfeld AL, Liu X, Zhao X, Li Q, Su B, Peter A, Xu G, Lehmann R. Ex vivo instability of lipids in whole blood – preanalytical recommendations for clinical lipidomics studies. J Lipid Res. 2023 Apr

9. Heimerl S, Höring M, Kopczynski D, Sigruener A, Hart C, Burkhardt R, Black A, Ahrends R, Liebisch G. Quantification of bulk lipid species in human platelets and their thrombin-induced release. Sci Rep. 2023 Apr

10. Manke MC, Roslan A, Walker B, Münzer P, Kollotzek F, Peng B, Mencl S, Coman C, Szepanowski RD, Schulze H, Lieberman AP, Lang F, Gawaz M, Kleinschnitz C, Lukowski R, Ahrends R, Bobe R, Borst O. Niemann-Pick C1 protein regulates platelet membrane-associated calcium ion signaling in thrombo-occlusive diseases in mice. J Thromb Haemost. 2023 Apr

11. Kumar M, Has C, Lam-Kamath K, Ayciriex S, Dewett D, Bashir M, Poupault C, Schuhmann K, Knittelfelder O, Raghuraman BK, Ahrends R, Rister J, Shevchenko A. Eye proteome of Drosophila melanogaster. bioRxiv 2023 Mar

12. Ni Z, Wölk M, Jukes G, Mendivelso Espinosa K, Ahrends R, Aimo L, Alvarez-Jarreta J, Andrews S, Andrews R, Bridge A, Clair GC, Conroy MJ, Fahy E, Gaud C, Goracci L, Hartler J, Hoffmann N, Kopczyinki D, Korf A, Lopez-Clavijo AF, Malik A, Ackerman JM, Molenaar MR, O’Donovan C, Pluskal T, Shevchenko A, Slenter D, Siuzdak G, Kutmon M, Tsugawa H, Willighagen EL, Xia J, O’Donnell VB, Fedorova M. Guiding the choice of informatics software and tools for lipidomics research applications. Nat Methods. 2023 Feb

2022

1. Ni Z, Wölk M, Jukes G, Mendivelso Espinosa K, Ahrends R, Aimo L, Alvarez-Jarreta J, Andrews S, Andrews R, Bridge A, Clair GC, Conroy MJ, Fahy E, Gaud C, Goracci L, Hartler J, Hoffmann N, Kopczynski D, Korf A, Lopez-Clavijo AF, Malik A, Ackerman JM, Molenaar MR, O’Donovan C, Pluskal T, Shevchenko A, Slenter D, Siuzdak G, Kutmon M, Tsugawa H, Willighagen EL, Xia J, O’Donnell VB, Fedorova M. Guiding the choice of informatics software and tools for lipidomics research applications. Nat Methods. Epub 2022 Dec

2. McDonald JG, Ejsing CS, Kopczynski D, Holčapek M, Aoki J, Arita M, Arita M, Baker ES, Bertrand-Michel J, Bowden JA, Brügger B, Ellis SR, Fedorova M, Griffiths WJ, Han X, Hartler J, Hoffmann N, Koelmel JP, Köfeler HC, Mitchell TW, O’Donnell VB, Saigusa D, Schwudke D, Shevchenko A, Ulmer CZ, Wenk MR, Witting M, Wolrab D, Xia Y, Ahrends R, Liebisch G, Ekroos K. Introducing the Lipidomics Minimal Reporting Checklist. Nat Metab. 2022 Sep

3. Manke MC, Ahrends R, Borst O. Platelet lipid metabolism in vascular thrombo-inflammation. Pharmacol Ther. 2022 Sep

4. Kumar M, Has C, Lam-Kamath K, Ayciriex S, Dewett D, Bashir M, Poupault C, Schuhmann K, Knittelfelder O, Raghuraman BK, Ahrends R, Rister J, Shevchenko A. Vitamin A Deficiency Alters the Phototransduction Machinery and Distinct Non-Vision-Specific Pathways in the Drosophila Eye Proteome. Biomolecules. 2022 Aug

5. Ariëns RA, Hunt BJ, Agbani EO, Ahnström J, Ahrends R, Alikhan R, Assinger A, Bagoly Z, Balduini A, Barbon E, Barrett CD, Batty P, Carneiro JDA, Chan WS, de Maat M, de Wit K, Denis C, Ellis MH, Eslick R, Fu H, Hayward CPM, Ho-Tin-Noé B, Klok FA, Kumar R, Leiderman K, Litvinov RI, Mackman N, McQuilten Z, Neal MD, Parker WAE, Preston RJS, Rayes J, Rezaie AR, Roberts LN, Rocca B, Shapiro S, Siegal DM, Sousa LP, Suzuki-Inoue K, Zafar T, Zhou J. Illustrated State-of-the-Art Capsules of the ISTH 2022 Congress. Res Pract Thromb Haemost. 2022 Jul

6. Hoffmann N, Mayer G, Has C, Kopczynski D, Al Machot F, Schwudke D, Ahrends R, Marcus K, Eisenacher M, Turewicz M. A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics. Metabolites. 2022 Jun

7. Kopczynski D, Hoffmann N, Peng B, Liebisch G, Spener F, Ahrends R. Goslin 2.0 Implements the Recent Lipid Shorthand Nomenclature for MS-Derived Lipid Structures. Anal Chem. 2022 Apr

8. Li T, Hentschel A, Ahrends R. Analytical comparison of absolute quantification strategies to investigate the insulin signaling pathway in fat
cells. Proteomics. 2022 Apr

9. Michel L, Helfrich I, Hendgen-Cotta UB, Mincu RI, Korste S, Mrotzek SM, Spomer A, Odersky A, Rischpler C, Herrmann K, Umutlu L, Coman C, Ahrends R, Sickmann A, Löffek S, Livingstone E, Ugurel S, Zimmer L, Gunzer M, Schadendorf D, Totzeck M, Rassaf T. Targeting early stages of cardiotoxicity from anti-PD1 immune checkpoint inhibitor therapy. Eur Heart J. 2022 Jan

10. Wolrab D, Jirásko R, Cífková E, Höring M, Mei D, Chocholoušková M, Peterka O, Idkowiak J, Hrnčiarová T, Kuchař L, Ahrends R, Brumarová R, Friedecký D, Vivo-Truyols G, Škrha P, Škrha J, Kučera R, Melichar B, Liebisch G, Burkhardt R, Wenk MR, Cazenave-Gassiot A, Karásek P, Novotný I, Greplová K, Hrstka R, Holčapek M. Lipidomic profiling of human serum enables detection of pancreatic cancer. Nat Commun. 2022 Jan

11. Confettura AD, Cuboni E, Ammar MR, Jia S, Gomes GM, Yuanxiang P, Raman R, Li T, Grochowska KM, Ahrends R, Karpova A, Dityatev A, Kreutz MR. Neddylation-dependent protein degradation is a nexus between synaptic insulin resistance, neuroinflammation and Alzheimer’s disease. Transl Neurodegener. 2022 Jan

2021

  1. Jennings MJ, Hathazi D, Nguyen CDL, Munro B, Münchberg U, Ahrends R, Schenck A, Eidhof I, Freier E, Synofzik M, Horvath R, Roos A. Intracellular Lipid Accumulation and Mitochondrial Dysfunction Accompanies Endoplasmic Reticulum Stress Caused by Loss of the Co-chaperone DNAJC3. Front Cell Dev Biol. 2021
  1. Li T, Hentschel A, Ahrends R. Analytical comparison of absolute quantification strategies to investigate the Insulin signaling pathway in fat cells. Proteomics. 2021
  1. Köfeler HC, Ahrends R, Baker ES, Ekroos K, Han X, Hoffmann N, Holčapek M, Wenk MR, Liebisch G. Recommendations for good practice in MS-based lipidomics. J Lipid Res. 2021
  1. Borgmeyer M, Coman C, Has C, Schött HF, Li T, Westhoff P, Cheung YFH, Hoffmann N, Yuanxiang P, Behnisch T, Gomes GM, Dumenieu M, Schweizer M, Chocholoušková M, Holčapek M, Mikhaylova M, Kreutz MR, Ahrends R. Multiomics of synaptic junctions reveals altered lipid metabolism and signaling following environmental enrichment. Cell Rep. 2021 Oct
  1. Michel L, Helfrich I, Hendgen-Cotta UB, Mincu RI, Korste S, Mrotzek SM, Spomer A, Odersky A, Rischpler C, Herrmann K, Umutlu L, Coman C, Ahrends R, Sickmann A, Löffek S, Livingstone E, Ugurel S, Zimmer L, Gunzer M, Schadendorf D, Totzeck M, Rassaf T. Targeting early stages of cardiotoxicity from anti-PD1 immune checkpoint inhibitor therapy. Eur Heart J. 2022 Jan
  1. Köfeler HC, Eichmann TO, Ahrends R, Bowden JA, Danne-Rasche N, Dennis EA, Fedorova M, Griffiths WJ, Han X, Hartler J, Holčapek M, Jirásko R, Koelmel JP, Ejsing CS, Liebisch G, Ni Z, O’Donnell VB, Quehenberger O, Schwudke D, Shevchenko A, Wakelam MJO, Wenk MR, Wolrab D, Ekroos K. Quality control requirements for the correct annotation of lipidomics data. Nat Commun. 2021 Aug
  1. Manke MC, Geue S, Coman C, Peng B, Kollotzek F, Münzer P, Walker B, Huber SM, Rath D, Sickmann A, Stegner D, Duerschmied D, Lang F, Nieswandt B, Gawaz M, Ahrends R, Borst O. ANXA7 Regulates Platelet Lipid Metabolism and Ca2+ Release in Arterial Thrombosis. Circ Res. 2021 Aug
  1. Cheung HYF, Coman C, Westhoff P, Manke M, Sickmann A, Borst O, Gawaz M, Watson SP, Heemskerk JWM, Ahrends R. Targeted Phosphoinositides Analysis Using High-Performance Ion Chromatography-Coupled Selected Reaction Monitoring Mass Spectrometry. J Proteome Res. 2021 Jun

2020

  1. an Geffen JP, Swieringa F, van Kuijk K, Tullemans BME, Solari FA, Peng  B, Clemetson KJ, Farndale RW, Dubois LJ, Sickmann A, Zahedi RP, Ahrends R, Biessen EAL, Sluimer JC, Heemskerk JWM, Kuijpers MJE. Mild hyperlipidemia in mice aggravates platelet responsiveness in thrombus formation and exploration of platelet proteome and lipidome. Sci Rep. 2020 Dec 8;10(1):21407. doi: 10.1038/s41598-020-78522-9. PMID: 33293576; PMCID: PMC7722935.
  2. Danne-Rasche N, Rubenzucker S, Ahrends R. Uncovering the complexity of the yeast lipidome by means of nLC/NSI-MS/MS. Analytica Chimica Acta. 2020 Dec 15;1140:199-209. doi: 10.1016/j.aca.2020.10.012. Epub 2020 Oct 14. PMID: 33218482.
  3. Kopczynski D, Hentschel A, Coman C, Schebb NH, Hornemann T, Mashek DG, Hartung NM, Shevchuk O, Schött HF, Lorenz K, Torta F, Burla B, Zahedi RP, Sickmann A, Kreutz MR, Ejsing CS, Medenbach J, Ahrends R. Simple targeted assays for metabolic pathways and signaling: a powerful tool for targeted proteomics. Anal Chem. 2020 Aug 31. doi: 10.1021/acs.analchem.0c02793.
  4. Kopczynski D, Hoffmann N, Peng B, Ahrends R. Goslin: A Grammar of Succinct Lipid Nomenclature. Anal Chem. 2020 Aug 18;92(16):10957-10960. doi: 10.1021/acs.analchem.0c01690.
  5. Reich S*, Nguyen CDL*, Has C, Steltgens S, Soni H, Coman C, Freyberg M, Bichler A, Seifert N, Conrad D, Knobbe-Thomsen CB, Tews B, Toedt G, Ahrends R*, Medenbach J*. A multi-omics analysis reveals the unfolded protein response regulon and stress-induced resistance to folate-based antimetabolites. Nat Commun. 2020 Jun 10;11(1):2936. doi: 10.1038/s41467-020-16747-y.
  6. Coman C, Ahrends R. Targeted Omics: Finding the Needle. Proteomics. 2020 Jun;20(11):e1900024. doi: 10.1002/pmic.201900024.
  7. Peng B, Kopczynski D, Pratt BS, Ejsing CS, Burla B, Hermansson M, Benke PI, Tan SH, Chan MY, Torta F, Schwudke D, Meckelmann SW, Coman C, Schmitz OJ,bMacLean B, Manke MC, Borst O, Wenk MR, Hoffmann N, Ahrends R. LipidCreator workbench to probe the lipidomic landscape. Nat Commun. 2020 Apr 28;11(1):2057.doi: 10.1038/s41467-020-15960-z.
  8. Hentschel A, Ahrends R. Developing a Robust Assay to Monitor and Quantify Key Players of Metabolic Pathways during Adipogenesis by Targeted Proteomics. 2020 Jun;20(11):e1900141. doi: 10.1002/pmic.201900141.
  9. Soni H, Bode J, Nguyen CDL, Puccio L, Neßling M, Piro RM, Bub J, Phillips E, Ahrends R, Eipper BA, Tews B, Goidts V. PERK-mediated expression of peptidylglycine α-amidating monooxygenase supports angiogenesis in glioblastoma. Oncogenesis. 2020 Feb 13;9(2):18. doi: 10.1038/s41389-020-0201-8.
  10. Scheller I, Stritt S, Beck S, Peng B, Pleines I, Heinze KG, Braun A, Otto O, Ahrends R, Sickmann A, Bender M, Nieswandt B. Coactosin-like 1 integrates signaling critical for shear-dependent thrombus formation in mouse platelets. Haematologica. 2020 Jun;105(6):1667-1676. doi: 10.3324/haematol.2019.225516.
  11. Széliová D, Schoeny H, Knez Š, Troyer C, Coman C, Rampler E, Koellensperger G, Ahrends R, Hann S, Borth N, Zanghellini J, Ruckerbauer DE. Robust Analytical Methods for the Accurate Quantification of the Total Biomass Composition of Mammalian Cells. Methods Mol Biol. 2020;2088:119-160. doi: 1007/978-1-0716-0159-4_7.

2019

  1. Scheller I, Stritt S, Beck S, Peng B, Pleines I, Heinze KG, Braun A, Otto O, Ahrends R, Sickmann A, Bender M, Nieswandt B. Coactosin-like 1 integrates signaling critical for shear-dependent thrombus formation in mouse platelets. 2019 Oct 3. pii: haematol.2019.225516. doi: 10.3324/haematol.2019.225516.
  2. Hoffmann N, Hartler J, Ahrends R. jmzTab-M: A Reference Parser, Writer, and Validator for the Proteomics Standards Initiative mzTab 2.0 Metabolomics Anal Chem. 2019 Oct 15;91(20):12615-12618. doi: 10.1021/acs.analchem.9b01987. Epub 2019 Sep 26. PubMed PMID: 31525911.
  3. 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.
  4. 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.
  5. 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:1007/s00401-019-02021-z.
  6. 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.
  7. 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.

2018

  1. 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.
  2. 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. 2018 Aug 2;132(5):e1-e12. doi: 10.1182/blood-2017-12-822890.
  3. 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.
  4. 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.
  5. 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.
  6. 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.

2017

  1. 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.
  2. 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.
  3. 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. 2017 Jun 7;142(11):1891-1899. doi: 10.1039/c7an00107j.
  4. Kopczynski D, Barsnes H, Njølstad PR, Sickmann A, Vaudel M, Ahrends R. PeptideMapper: efficient and versatile amino acid sequence and tag mapping. 2017 Jul 1;33(13):2042-2044. doi: 10.1093/bioinformatics/btx122.
  5. 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.
  6. 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.

2016

  1. 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.
  2. 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.
  3. 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.
  1. 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.

2015

  1. 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.
  2. 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.

2014

  1. 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.
  2. 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.
  3. 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.
  4. 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.

– 2012

  1. 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.
  1. 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
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.