Selected Publications (from 2005)

More: see: Researcher-ID: B-3407-2010; ORCID: 0000-0002-8687-6817  



Winkels K, Koudelka T, Tholey A (2021). Quantitative top-down proteomics by isobaric labeling with thiol-directed tandem mass tags. J Proteome Res, accepted, doi:10.1021/acs.jproteome.1c00460.

Cassidy L, Kaulich PT, Maaß S, Bartel J, Becher D, Tholey A (2021). Bottom-up and top-down proteomic approaches for the identification, characterization, and quantification of the low molecular weight proteome with focus on short open reading frame-encoded peptides. Proteomics, in press, 19:e2100008. doi: 10.1002/pmic.202100008.

Leipert J, Steinbach MK, Tholey A (2021). Isobaric Peptide Labeling on Digital Microfluidics for Quantitative Low Cell Number Proteomics. Anal Chem, in press; doi: 10.1021/acs.analchem.1c01205.

Kaulich PT, Cassidy L, Bartel J, Schmitz RA, Tholey A (2021). Multi-protease Approach for the Improved Identification and Molecular Characterization of Small Proteins and Short Open Reading Frame-Encoded Peptides. J Proteome Res, 20: 2895-2903, doi: 10.1021/acs.jproteome.1c00115.

Koudelka T, Boger J, Henkel A, Schönherr R, Krantz S, Fuchs S, Rodríguez E, Redecke L, Tholey A (2021). N-terminomics for the identification of in vitro substrates and cleavage site specificity of the SARS-CoV-2 main protease. Proteomics, 21: e2000246. Doi: 10.1002/pmic.202000246.

Cassidy L, Helbig AO, Kaulich PT, Weidenbach K, Schmitz RA, Tholey A (2021). Multidimensional separation schemes enhance the identification and molecular characterization of low molecular weight proteomes and short open reading frame-encoded peptides in top-down proteomics. J Proteomics, 230:103988. doi: 10.1016/ j.jprot.2020.103988.

Susat J, Lübke H, Immel A, Brinker U, Macāne A, Meadows J, Steer B, Tholey A, Zagorska I, Gerhards G, Schmölcke U, Kalniņš M, Franke A, Pētersone-Gordina E, Teßman B, Tõrv M, Schreiber S, Andree C, Bērziņš V, Nebel A, Krause-Kyora B (2021). A 5,000-year-old hunter-gatherer already plagued by Yersinia pestis. Cell Rep, 35:109278. doi: 10.1016/j.celrep.2021.109278.

Armbrust F, Bickenbach K, Koudelka T, Tholey A, Pietrzik C, Becker-Pauly C (2021). Phosphorylation of meprin β controls its cell surface abundance and subsequently diminishes ectodomain shedding. FASEB J, 35:e21677. doi: 10.1096/fj.202100271R.

Schürmann J, Gottwald J, Rottenaicher G, Tholey A, Röcken C (2021). MALDI mass spectrometry imaging unravels organ and amyloid-type specific peptide signatures in pulmonary and gastrointestinal amyloidosis.  Proteomics Clin Appl, in press; e2000079. doi: 10.1002/prca.202000079.

Zahn S, Kubatova N, Pyper DJ, Cassidy L, Saxena K, Tholey A, Schwalbe H, Soppa J (2021). Biological functions, genetic and biochemical characterization, and NMR structure determination of the small zinc finger protein HVO_2753 from Haloferax volcanii. FEBS J, 288: 2042-2062. doi: 10.1111/febs.15559.

Menzel S, Koudelka T, Rissiek B, Haag F, Meyer-Schwesinger C, Tholey A, Koch-Nolte F (2021). ADP-Ribosylation Regulates the Signaling Function of IFN-γ. Front Immunol, 12: 642545. doi: 10.3389/fimmu.2021.642545.

Gutt M, Jordan B, Weidenbach K, Gudzuhn M, Kiessling C, Cassidy L, Helbig A, Tholey A, Pyper DJ, Kubatova N, Schwalbe H, Schmitz RA (2021). High complexity of Glutamine synthetase regulation in Methanosarcina mazei: Small protein 26 interacts and enhances glutamine synthetase activity. FEBS J, in press, doi: 10.1111/febs.15799.



Kaulich PT, Cassidy L, Weidenbach K, Schmitz RA, Tholey A (2020). Complementarity of different SDS-PAGE gel staining methods for the identification of short open reading frame-encoded peptides. Proteomics, 19-20: e2000084. doi: 10.1002/pmic.202000084.

Helbig A, Tholey A (2020). Exopeptidase assisted N- and C-terminal proteome sequencing. Anal Chem, 92: 5023-5032. doi: 10.1021/acs.analchem.9b05288.

Kaleja P, Emmert H, Gerstel U, Weidinger S, Tholey A (2020). Evaluation and improvement of protein extraction methods for analysis of skin proteome by noninvasive tape stripping. J Proteomics, 217:103678. doi: 10.1016/j.jprot.2020.103678.

Rangrez AY, Borlepawar A, Schmiedel N, Deshpande A, Remes A, Kumari M, Bernt A, Christen L, Helbig A, Jungmann A, Sossalla S, Tholey A, Müller OJ, Frank D, Frey N (2020). The E3 ubiquitin ligase HectD3 attenuates cardiac hypertrophy and inflammation in mice. Commun Biol, 3:562. doi: 10.1038/s42003-020-01289-2.

Düsterhöft S, Bartels AK, Koudelka T, Lilienthal E, Schäfer M, Garbers C, Tholey A, Grötzinger, J, Lorenzen I (2020). Distance dependent shedding of IL-6R.  Biochem Biophys Res Commun, 526: 355-360.

Berner D, Wessolowski L, Armbrust F, Schneppenheim J, Schlepckow K, Koudelka T, Scharfenberg F, Lucius R, Tholey A, Kleinberger G, Haass C, Arnold P, Becker-Pauly C (2020). Meprin β cleaves TREM2 and controls its phagocytic activity on macrophages. FASEB J, 34: 6675-6687.

Scharfenberg F, Helbig A, Sammel M, Benzel J, Schlomann U, Peters F, Wichert R, Bettendorff M, Schmidt-Arras D, Rose-John S, Moali C, Lichtenthaler SF, Pietrzik CU, Bartsch JW, Tholey A, Becker-Pauly C (2020). Degradome of soluble ADAM10 and ADAM17 metalloproteases. Cell Mol Life Sci, 77: 331-350.



Leipert J, Tholey A (2019). Miniaturized sample preparation on a digital microfluidics device for sensitive bottom-up microproteomics of mammalian cells using magnetic beads and mass spectrometry-compatible surfactants. Lab Chip, 19: 3490-3498. doi: 10.1039/c9lc00715f.

Lipinski S, Pfeuffer S, Arnold P, Treitz C, Aden K, Ebsen H, Falk-Paulsen M, Gisch N, Fazio A, Kuiper J, Luzius A, Billmann-Born S, Schreiber S, Nuñez G, Beer HD, Strowig T, Lamkanfi M, Tholey A, Rosenstiel P (2019). Prdx4 limits caspase-1 activation and restricts inflammasome-mediated signaling by extracellular vesicles. EMBO J, 38: e101266. doi: 10.15252/embj.2018101266.

Carini A, Koudelka T, Tholey A, Appel E, Gorb SN, Melzner F, Ramesh K (2019). Proteomic investigation of the blue mussel larval shell organic matrix. J Struct Biol, 208: 107385. doi: 10.1016/j.jsb.2019.09.002.

Kaleja P, Helbig AO, Tholey A (2019). Combination of SCX fractionation and charge-reversal derivatization facilitates the identification of non-tryptic peptides in C-terminomics. J Proteome Res, 18: 2954-2964.

Cassidy L, Kaulich PT, Tholey A (2019). Depletion of high molecular mass proteins for the identification of small proteins and short open reading frame encoded peptides in cellular proteomes. J Proteome Res, 18: 1725-1734.

Yang W, Petersen C, Pees B, Zimmermann J, Waschina S, Dirksen P, Rosenstiel P, Tholey A, Leippe M, Dierking K, Kaleta C, Schulenburg H (2019). The Inducible Response of the Nematode Caenorhabditis elegans to Members of Its Natural Microbiota Across Development and Adult Life. Front Microbiol, 10:1793. doi:10.3389/fmicb.2019.01793.

Wichert R, Scharfenberg F, Colmorgen C, Koudelka T, Schwarz J, Wetzel S, Potempa B, Potempa J, Bartsch JW, Sagi I, Tholey A, Saftig P, Rose-John S, Becker-Pauly C (2019). Meprin β induces activities of A disintegrin and metalloproteinases 9, 10, and 17 by specific prodomain cleavage. FASEB J, 33: 11925-11940.

Rabeharindranto H, Castaño-Cerezo S, Lautier T, Garcia-Alles LF, Treitz C, Tholey A, Truan G (2019). Enzyme-fusion strategies for redirecting and improving carotenoid synthesis in S. cerevisiae. Metab Eng Commun, 8: e00086. DOI: 10.1016/j.mec.2019.e00086.

Latendorf T, Gerstel U, Wu Z, Bartels J, Becker A, Tholey A, Schröder JM (2019). Cationic intrinsically disordered proteins and peptides are effector molecules of a barrier organ adaptive innate defense system. Sci Rep, 9: 3331. doi: 10.1038/s41598-019-39219-w.

Li  B, Habermann D, Kliche T, Klempt M, Wutkowski A, Calwin-Rädecker I, Koberg S, Brinks, Koudelka T, Tholey A, Bockelmann W, Franz CMAP, Heller KJ (2019). Soluble Lactobacillus delbrueckii subsp. bulgaricus 92059 PrtB proteinase derivatives for production of bioactive peptide hydrolysates from casein. Appl Microbiol Biotechnol, 103: 2731-2743.

Mentrup T, Theodorou K, Cabrera F, Helbig A, Happ K, Gijbels M Gradtke AC, Rabe B, Fukumori A, Steiner H, Tholey A, Fluhrer R, Donners M, Schröder B (2019). Atherogenic LOX-1 signaling is controlled by SPPL2-mediated intramembrane proteolysis. J Exp Med, 216: 807-830.



Gerstel U, Latendorf T, Bartels J, Becker A, Tholey, A, Schröder JM (2018). Hornerin contains a linked series of ribosome-targeting antibiotics. Sci Rep, 8: 16158. doi: 10.1038/s41598-018-34467.

Leipert J, Bobis I, Schubert S, Fickenscher H, Leippe M, Tholey A (2018). Miniaturized dispersive liquid-liquid microextraction and MALDI MS using ionic liquid matrices for the detection of bacterial communication molecules and virulence factors. Anal Bioanal Chem, 410: 4237-4748. DOI: 10.1007/s00216-018-0937-6.

Beiroth F, Koudelka T, Overath T, Knight SD, Tholey A, Lindhorst TK (2018). Diazirine functionalized mannosides for photoaffinity labelling: Trouble with FimH. Beilstein J Org Chem, 14: 1890-1900.

Krause-Kyora B, Susat J, Key FM, Kühnert D, Bosse E, Immel A, Rinne C, Kornell SC, Yepes D, Franzenburg S, Heyne HO, Meier T, Lösch S, Meller H, Friederich S, Nicklisch N, Alt KW, Schreiber S, Tholey A, Herbig A, Nebel A, Krause J (2018). Neolithic and Medieval virus genomes reveal complex evolution of Hepatitis B. eLife, 7:e36666. doi: 10.7554/eLife.36666 .

Cassidy L, Petersen C, Treitz C, Dierking K, Schulenburg H, Leippe M, Tholey A (2018). The C. elegans proteome response to naturally associated microbiome members of the genus Ochrobactrum. Proteomics, 18: e1700426. doi: 10.1002/pmic.201700426.

Seipold L, Altmeppen H, Koudelka T, Tholey A, Kasparek P, Sedlacek R, Schweizer M, Bär J, Mikhaylova M, Glatzel M, Saftig P (2018). In vivo regulation of the A disintegrin and metalloproteinase 10 (ADAM10) by the tetraspanin 15. Cell Mol Life Sci, 75: 3251-3267. doi: 10.1007/s00018-018-2791-2.

Janga H, Cassidy L, Wang F, Spengler D, Oestern-Fitschen S, Krause MF, Seekamp A, Tholey A, Fuchs S (2018). Site-specific and endothelial mediated dysfunction of the alveolar- capillary barrier in response to LPS. J Cell Mol Med, 22: 982-998.



Tholey A, Taylor NL, Heazlewood JL, Bendixen E (2017). We are not alone: The iMOP initiative and its roles in a Biology and Disease driven Human Proteome Project. J Proteome Res, 16: 4273-4280.

Tholey A, Becker A (2017). Top-down proteomics for the analysis of proteolytic events - methods, applications and perspectives.  BBA Mol Cell Res, 1864: 2191-2199.

Krohn-Molt I, Alawi M, Förstner KU, Wiegandt A, Burkhardt L, Indenbirken D, Thieß M, Grundhoff A, Kehr J, Tholey A, Streit WR (2017). Insights into microalga and bacteria interactions of selected phycosphere biofilms using metagenomic, transcriptomic and proteomic approaches. Front Microbiol, 8: 1941. doi: 10.3389/fmicb.2017.01941.

Winter M, Tholey A, Kirsten A, Röcken C (2017). MALDI Mass Spectrometry Imaging: a novel Tool for the Identification and Classification of Amyloidosis. Proteomics, 17: 1700236,. doi: 10.1002/pmic.201700236.

Schäfer M, Granato DC, Krossa S, Bartels AK, Yokoo S, Düsterhoft S, Koudelka T, Scheidig AJ, Tholey A, Leme AFP, Grötzinger J, Lorenzen I (2017). GRP78 protects A Disintegrin and Metalloprotease 17 against Protein Disulfide Isomerase A6 catalyzed inactivation. FEBS Lett, 591: 3567-3587.

Leipert J, Treitz C, Leippe M, Tholey A (2017). Identification and quantification of N-acyl homoserine lactones involved in bacterial communication by small-scale synthesis of internal standards and matrix-assisted laser desorption/ionization mass spectrometry. J Am Soc Mass Spectrom, 28: 2538-2547.

Weidenbach K, Nickel L, Neve H, Alkhnbashi O, Künzel S, Kupczok A, Bauersachs T, Cassidy L, Tholey A, Backofen R, Schmitz RA (2017). MetSV, a novel archaeal lytic virus targeting Methanosarcina strains. J Virol, 91: pii: e00955-17. doi: 10.1128/JVI.00955-17.

Pietschke C, Treitz C, Forêt S, Schultze A, Künzel S, Tholey A, Bosch T, Fraune S (2017). Host modification of a bacterial quorum sensing signal induces a phenotypic switch in bacterial symbionts. Proc Natl Acad Sci, 114: E8488-E8497, doi: 10.1073/pnas.1706879114.

Sommer F, Rühlemann MC, Bang C, Höppner M, Rehman A, Kaleta C, Schmitt-Kopplin P, Dempfle A, Weidinger S, Ellinghaus E, Krauss-Etschmann S, Schmidt-Arras D, Aden K, Schulte D, Ellinghaus D, Schreiber S, Tholey A, Rupp J, Laudes M, Baines JF, Rosenstiel P, Franke A (2017). Microbiomarkers in inflammatory bowel diseases: caveats come with caviar. Gut, 66:1734-1738.

Bedau T, Schumacher N, Peters F, Prox J, Arnold P, Koudelka T, Helm O, Schmidt F, Rabe B, Jentzsch M, Rosenstiel P, Sebens S, Tholey A, Rose-John S, Becker-Pauly C. (2017). Cancer-associated mutations in the canonical cleavage site do not influence CD99 shedding by the metalloprotease meprin β but alter cell migration in vitro.  Oncotarget, 8: 54873-54888.

Fernandez R, Koudelka T, Tholey A, Dreves A (2017). A novel tertiary prep-HPLC method for the isolation of single amino acids for AMS-radiocarbon measurement. J Chrom B, 1058: 85-92.

Arnold P, Boll I, Rothaug M, Schumacher N, Schmidt F, Wichert R, Schneppenhein J, Lokau J, Pickhinke U, Koudelka T, Tholey A, Rabe B, Scheller J, Lucius R, Garbers C, Rose-John S, Becker-Pauly C (2017). Meprin metalloproteases generate biologically acive soluble interleukin-6 receptor to induce trans-signalling. Sci Rep, Article No. 44053, doi:10.1038/srep44053.

Riethmüller S, Somasundaram P, Ehlers JC, Hung CW, Flynn CM, Lokau J, Agthe M, Düsterhöft S, Zhu Y, Grötzinger J, Lorenzen I, Koudelka T, Yamamoto K, Pickhinke U, Wichert R, Becker-Pauly C, Rädisch M, Albrecht A, Hessefort M, Stahnke D, Unverzagt C, Rose-John S, Tholey A, Garbers C (2017). Proteolytic origin of the soluble human IL-6R in vivo and a decisive role of N-glycosyation.  Plos Biol,

Bedau T, Peters F, Prox J, Arnold F, Schmidt F, Finkernagel M, Köllmann S, Wichert R, Otte A, Ohler A, Stirnberg M, Lucius R, Koudelka T, Tholey A, Biasin V, Pietrzik CU, Kwapiszewska G, Becker-Pauly C (2017). Ectodomain shedding of CD99 within highly conserved regions is mediated by the metalloprotease meprin β and promotes transendothelial cell migration. FASEB J, 31: 1226-1237.

Ott SJ, Waetzig GH, Rehman A, Moltzau-Anderson J, Bharti R, Grasis JA, Cassidy L, Tholey A, Fickenscher H, Seegert D, Rosenstiel P, Schreiber S (2017). Efficacy of sterile fecal filtrate transfer for treating patients with Clostridium diffcicile infection. Gastroenterology, 152: 799-811.

Klettner A, Tholey A, Wiegandt A, Richert E, Nölle B, Roider J, Schneider SA (2017). Reduction of GAPDH in lenses of Parkinson patients - a possible new biomarker. Mov Dis, 32: 459-462.



Treitz C, Enjalbert B, Portais JC, Letisse F, Tholey A (2016). Differential quantitative proteome analysis of Escherichia coli grown on acetate vs. glucose. Proteomics, 16: 2742-2746.

Cassidy L, Prasse D, Linke D, Schmitz RA, Tholey A (2016). Combination of bottom-up 2D-LC-MS and semi-top-down GelFree-LC-MS enhances coverage of proteome and low molecular weight short open reading frame encoded peptides of the archeon Methanosarcina mazei. J Proteome Res, 15: 3773-3783.

Hung CW, Klein T, Cassidy L, Linke D, Lange S, Anders U, Bureik M, Heinzle E, Schneider K, Tholey A (2016). Comparative Proteome Analysis in Schizosaccharomyces pombe Identifies Metabolic Targets to Improve Protein Production and Secretion. Mol Cell Proteomics, 15: 3090-3106.

Sommer A, Kordowski F, Büch J, Maretzki T, Evers A, Andrä J, Düsterhoft S, Michalek M, Lorenzen I, Somasundaram P, Tholey A, Sönnichsen FD, Kunzelmann K, Nehls C, Heinbockel L, Gutsmann T, Grötzinger J, Bakhdi S, Reiss K (2016). Phosphatidylserine exposure is required for ADAM17 sheddase function. Nat Commun, 7: 11523. doi: 10.1038/NCOMMS11523.

Somasundaram P, Koudelka T, Linke D, Tholey A (2016). C-terminal charge-reversal modification and parallel use of multiple proteases facilitates identification of protein C-termini by C-terminomics. J Proteome Res, 15: 1369-1378.

Hung CW, Koudelka T, Anastasi C, Becker A, Moali C, Tholey A (2016). Characterization of post-translational modifications in full-length human BMP-1 confirms the presence of a rare vicinal disulfide linkage in the catalytic domain and highlights novel features of the EGF domain. J Proteomics, 138: 136-145.

Tucher J, Koudelka T, Schlenk J, Tholey A (2016). From top-down to bottom-up: Time-dependent monitoring of proteolytic protein degradation by LC-MS. J Chrom B, 1015-1016: 111-120.

Herbst FA, Lünsmann V, Kjeldal H, Jehmlich N, Tholey A, von Bergen M, Lund Nielsen J, Hettich RL, Seifert J, Nielsen PH (2016). Enhancing metaproteomics - the value of models and defined microbial systems. Proteomics, 16: 783-798.

Wilde SC, Treitz C, Keppler JK, Koudelka T, Kalpani K, Tholey A, Rawel HM, Schwarz K (2016). ß-Lactoglobulin as nanotransporter - part II: characterization of the covalent protein modification by allicin and diallyl disulfide. Food Chem, 197: 1022-1029.



Hartmann J, Linke D, Boenninger C, Tholey A, Sauter M (2015). Conserved phosphorylation sites in the activation loop of the Arabidopsis phytosulfokine receptor PSKR1 differentially affect kinase and receptor activity. Biochem J, 472: 379-391.

Brinkmann J, Koudelka T, Keppler JK, Tholey A, Schwarz K, Thaller G, Tetens J (2015). Characterization of an equine a-S2-casein variant due to a 1.3 kb deletion spanning two coding exons. Plos One, 10:e0139700. doi: 10.1371/journal.pone.0139700.

Heazlewood JL, Schrimpf SP, Becher D, Riedel K, Tholey A, Bendixen E (2015). Multi-organism proteomes (iMOP): advancing our understanding of human biology. Proteomics, 15: 2885-2894.

Menzel S, Rissiek B, Bannas P, Jakoby T, Miksiewicz M, Schwarz N, Nissen M, Haag F, Tholey A, Koch-Nolte F (2015). Nucleotide-induced membrane-proximal proteolysis controls the substrate specificity of T-cell ecto-ADP ribosyltransferase ARTC2.2. J Immunol, 195: 2057-2066.

Winter M, Tholey A, Krüger S, Schmidt H, Röcken C (2015). MALDI mass spectrometry imaging identifies vitronectin as common constituent of amyloid deposits. J Histochem Cytochem, 63: 772-779.

Jäckle F, Schmidt F, Wichert R, Arnold P, Prox J, Mangold M, Ohler A, Pietrzik CU, Koudelka T, Tholey A, Gütschow M, Stirnberg M, Becker-Pauly C (2015). Metalloprotease meprin ß is activated by transmembrane serine protease matriptase-2 at the cell surface thereby enhancing APP shedding. Biochem J, 470: 91-103.

Linke D, Koudelka T, Becker A & Tholey A (2015). Identification and relative quantification of phosphopeptides by a combination of multi-protease digestion and isobaric labeling. Rapid Commun Mass Spectrom, 29: 919-926.

Yang W, Dierking K, Esser D, Tholey A, Leippe M, Rosenstiel P & Schulenburg H (2015). Overlapping and unique signatures in the proteomic and transcriptomic responses of the nematode Caenorhabditis elegans towards pathogenic Bacillus thuringiensis. Dev Comp Immunol, 51: 1-9.

Treitz C, Cassidy L, Höckendorf A, Leippe M, Tholey A (2015). Quantitative proteome analysis of Caenorhabditis elegans upon exposure to nematicidal Bacillus thuringiensis. J Proteomics, 113: 336-350.

Tenorio-Daussat CL, Hauser-Davis RA, Saint’Pierre TD, Tholey A, Schaumlöffel D (2015). Peptide labeling with lanthanide-NHS-ester-DOTA investigated by nano-HPLC. Microchem J, 118: 238-241.



Krishna A, Biryukov M, Trefois C, Antony PM, Hussong R, Lin J, Heinäniemi M, Glusman G, Koeglsberger S, Boyd O, van den Berg BH, Linke D, Huang D, Wang K, Hood L, Tholey A, Schneider R, Galas DJ, Balling R, May P (2014). Systems genomics evaluation of the SH-SY5Y neuroblastoma cell line as a model for Parkinson's disease. BMC Genomics, 15:1154.

Hung CW, Jung S, Grötzinger J, Gelhaus C, Leippe M, Tholey A (2014). Determination of disulfide linkages in antimicrobial peptides of the macin family by combination of top-down and bottom-up proteomics. J Proteomics, 103: 216-226.

Keppler JK, Koudelka T, Palani K, Tholey A, Schwarz K. (2014). Interaction of β-Lactoglobulin with Small Hydrophobic Ligands - Influence of Covalent AITC Modification on β-LG Tryptic Cleavage. Food Biophys, 9:349-358.

Tasiemski A, Jung S, Boidin-Wichlacz C, Jollivet D, Cuvillier-Hot V, Pradillon F, Vetriani C, Hecht O, Sönnichsen FD, Gelhaus C, Hung CW, Tholey A, Leippe M, Grötzinger J, Gaill F (2014). Characterization and function of the first antibiotic isolated from a vent organism: the extremophile metazoan Alvinella pompejana. PLoS One, 9:e95737. doi: 10.1371/journal.pone.0095737.

Tucher J, Linke D, Koudelka T, Cassidy L, Tredup C, Wichert R, Pietrzik C, Becker-Pauly C, Tholey A. (2014). LC-MS Based Cleavage Site Profiling of the Proteases ADAM10 and ADAM17 Using Proteome-Derived Peptide Libraries. J Proteome Res, 13: 2205-2214.

Cassidy L, Tholey A. (2014). Model organism proteomics as a tool for the study of host-microbiome interactions. Proteomics Clin Appl, 8:665-676.

Becker-Pauly C, Broder C, Prox J, Koudelka T, Tholey A. (2014). Mapping orphan proteases by proteomics: Meprin metalloproteases deciphered as potential therapeutic targets. Proteomics Clin Appl, 8: 382-388.

Schwarz J, Schmidt S, Will O, Koudelka T, Köhler K, Boss M, Rabe B, Tholey A, Scheller J, Schmidt-Arras D, Schwake M, Rose-John S, Chalaris A. (2014). Polo-like kinase 2, a novel ADAM17 signaling component, regulates tumor necrosis factor α ectodomain shedding. J Biol Chem, 289:3080-3093.

Keppler JK, Koudelka T, Palani K, Stuhldreier MC, Temps F, Tholey A, Schwarz K. (2014). Characterization of the covalent binding of allyl isothiocyanate to β-lactoglobulin by fluorescence quenching, equilibrium measurement, and mass spectrometry. J Biomol Struct Dyn, 32:1103-1117.



Tholey A, Treitz C, Kussmann M, Bendixen E, Schrimpf SP, Hengartner MO. (2013). Model organism proteomics - from holobionts to human nutrition. Proteomics, 13: 2537-2541.

Broder C, Vadon-Le Goff S, Arnold P, Konerding M, Bahr K, Fisher LW, Müller S, Overall CM, Bond JS, Koudelka T, Tholey A, Hulmes DJS, Moali C, Becker-Pauly C. (2013). Metalloproteases meprin α and meprin β are C- and N-procollagen proteinases important for collagen assembly and tensile strength. Proc Natl Acad Sci, 110: 14219-14224.

Linke D, Hung CW, Cassidy L, Tholey A. (2013). Optimized fragmentation conditions for iTRAQ labeled phosphopeptides. J Proteome Res, 12: 2755–2763.

Oldefest M, Nowinski J, Hung CW, Neelsen D, Trad A, Tholey A, Grötzinger J, Lorenzen I (2013). Upd3 - an ancestor of the four-helix bundle cytokines. Biochem Biophys Res Commun, 436: 66-72.

Maixner F, Overath T, Linke D, Jankoc M, Guerrierod G, van den Berg BJH, Stade B, Leidinger P, Backes C, Jaremek M, Kneissl B, Mederi B, Franke A, Egarter-Viglj E, Meese E, Schwarz A, Tholey A, Zink A & Keller A. (2013) Paleoproteomic study of the Iceman’s brain tissue. Cell Mol Life Sci, 70: 3709-3722.

Gregorius B, Jakoby T, Schaumlöffel D, Tholey A. (2013). Monitoring of protease catalyzed reactions by quantitative MALDI MS using metal labeling. Anal Chem, 85: 5184-5190.

Düsterhöft S, Jung S, Hung CW, Tholey A, Sönnichsen FD, Grötzinger J, Lorenzen I. (2013). The membrane-proximal domain of ADAM17 represents the putative molecular switch of its shedding activity operated by protein-disulfide isomerase. J Am Chem Soc, 135: 5776-5781.

Holste A, Tholey A, Hung CW, Schaumlöffel D. (2013). A NanoHPLC with online precleaning coupled to ICPMS for the analysis of lanthanide labeled peptides in tryptic protein digests. Anal Chem, 85: 3064-3070.

Gregorius B, Jakoby T, Schaumlöffel D, Tholey A. (2013). Metal labeling for accurate multiplexed peptide quantification via matrix-assisted laser desorption/ionization mass spectrometry. Anal Bioanal Chem, 405: 2735-2741.

Michalek M, Sönnichsen FD, Wechselberger R, Dingley AJ, Hung CW, Kopp A, Wienk H, Simanski M, Herbst R, Lorenzen I, Marciano-Cabral F, Gelhaus C, Gutsmann T, Tholey A, Grötzinger J, Leippe M. (2013). Structure and function of a unique pore-forming protein from a pathogenic acanthamoeba. Nat Chem Biol, 9: 37-42.



Slawski M, Hussong R, Tholey A, Jakoby T, Gregorius B, Hildebrandt A, Hein M (2012). Isotope pattern deconvolution for peptide mass spectrometry by non-negative least squares/least absolute deviation template matching. BMC Bioinformatics, 13: 291, doi:10.1186/1471-2105-13-291.

Jakoby T, Tholey A, van den Berg BHJ (2012). Improved reporter ion assignment of raw isobaric stable isotope labeled LC-MALDI-TOF/TOF MS/MS spectral data for quantitative proteomics. Rapid Commun Mass Spectrom, 26: 2777-2785.

Luehr I, Friedl A, Overath T, Tholey A, Kunze T, Hilpert F, Sebens S, Arnold N, Roesel F, Oberg H-H, Maass N, Mundhenke C, Jonat W, Bauer M (2012). Mammary fibroblasts regulate morphogenesis of normal and tumorigenic breast epithelial cells by mechanical and paracrine signals. Cancer Lett, 325: 175-188.

Jung S, Sönnichsen FD, Hung CW, Tholey A, Boidin-Wichlacz C, Haeusgen W, Gelhaus C, Desel C, Podschun R, Waetzig V, Tasiemski A, Leippe M, Grötzinger J (2012). The Macin Family of Antimicrobial Proteins Combines Antimicrobial and Nerve-Repair Activities. J Biol Chem, 287: 14246-14258.

Jakoby T, van den Berg BHJ, Tholey A (2012). Quantitative protease cleavage site profiling using tandem mass tag labeling and LC-MALDI-TOF/TOF MS/MS analysis. J Proteome Res, 11: 1812-1820.

Philipp S, Jakoby T, Tholey A, Janssen O, Leippe M, Gelhaus C (2012). Cationic detergents enable the separation of membrane proteins of Plasmodium falciparum-infected erythrocytes by 2-D gel electrophoresis. Electrophoresis, 33: 1120-1128.

Hung CW, Tholey A (2012). Tandem mass tag protein labeling for top-down identification and quantification. Anal Chem, 84: 161-170.

Jones AM, Aebersold R, Ahrens CH, Apweiler R, Baerenfaller K, Baker M, Bendixen E, Briggs S, Brownridge P, Brunner E, Daube M, Deutsch EW, Grossniklaus U, Heazlewood J, Hengartner MO, Hermjakob H, Jovanovic M, Lawless C, Lochnit G, Martens L, Ravnsborg C, Schrimpf SP, Shim YH, Subasic D, Tholey A, van Wijk K, von Mering C, Weiss M, Zheng X (2012). The HUPO initiative on Model Organism Proteomes, iMOP. Proteomics, 12: 340-345.

van den Berg B, Tholey A (2012). Mass spectrometry-based proteomics strategies for protease cleavage sites identification. Proteomics, 12: 516-529.

Krüger R, Tholey A, Jakoby T, Vogelsberger R, Mönnikes R., Rossmann H, Beck M, Lackner KJ (2012). Quantification of the Fabry Marker LysoGb3 in Human Plasma by Tandem Mass spectrometry. J Chrom B, 883-884: 128-135.



Schaumlöffel D, Tholey A (2011). Recent directions of electrospray mass spectrometry for elemental speciation analysis. Anal Bioanal Chem, 400: 1645-1652.

Krüger R, Tholey A, Jakoby T, Vogelsberger R, Lackner KJ (2011). Quantification of the Fabry marker LysoGB3 by tandem mass spectrometry. Clin Chem Lab Med, 49: S764-S764. Meeting Abstract



Gregorius B, Schaumlöffel D, Hildebrandt A & Tholey A (2010). Characterization of metal labelled peptides by MALDI MS and MS/MS. Rapid Commun Mass Spectrom, 24: 3279-3289.

Melchior K, Tholey A, Heisel S, Keller A, Lenhof HP, Meese E & Huber CG (2010). Protein- versus peptide fractionation in the first dimension of two-dimensional high-performance liquid chromatography - matrix-assisted laser desorption/ionization tandem mass spectrometry for qualitative proteome analysis of tissue samples. J Chrom A, 1217: 6159-6168.

Tholey A, Schaumlöffel D (2010). Metal labeling for quantitative protein and proteome analysis using inductively-coupled plasma mass spectrometry. Trends Anal Chem, 29: 399-408.



Melchior K, Tholey A, Heisel S, Keller A, Lenhof HP, Meese E, Huber CG. (2009). Proteomic study of human glioblastoma multiforme tissue employing complementary two-dimensional liquid chromatography- and mass spectrometry-based approaches. J Proteome Res, 8: 4604–4614.

Lasaosa M, Jakoby T, Delmotte N, Huber CG, Heinzle E, Tholey A (2009). Rapid selection of peptide containing fractions in off-line two-dimensional HPLC in shotgun proteome analysis by screening with MALDI TOF MS. Proteomics, 9: 4577-4581.

Hussong R, Gregorius B, Tholey A, Hildebrandt A (2009). Highly accelerated feature detection in proteomics data sets using modern graphics processing units. Bioinformatics, 25: 1937-1943.

Delmotte N, Lasaosa M, Tholey A, Heinzle E, vanDorsselaer A, Huber CG (2009). Repeatability of peptide identifications in shotgun proteome analysis employing off-line 2Dchromatographic separations and ion-trap tandem mass spectrometry. J Sep Sci, 32: 1156-1164.

Lasaosa M, Delmotte N, Melchior K, Heinzle E, Huber CG, Tholey A (2009). A two-dimensional reversed-phase x ion-pair reversed-phase HPLC MALDI TOF/TOF MS approach to shotgun proteome analysis. Anal Bioanal Chem, 393: 1245-1256.

Kim YJ, Klotz M, Tholey A, Henn W, Schäfer KH, Feiden W (2009). Comparative proteome analyses of meningiomas of different grades in the identification of progression associated proteins. Acta Neuropathol, 118: 446-446. Meeting Abstract

Selevsek N, Rival S, Tholey A, Heinzle E, Heinz U, Hemmingsen L, Adolph HW (2009). Zinc ion-induced domain organization in metallo-beta-lactamases: A flexible “zinc arm” for rapid metal ion transfer? J Biol Chem, 284: 16419-16431.



Brüchert W, Krüger R, Tholey A, Montes-Bayón M, Bettmer J (2008). A novel approach for analysis of oligonucleotide-cisplatin interactions by continuous elution gel electrophoresis coupled to isotope dilution ICP-MS and MALDI-MS. Electrophoresis, 29: 1451-1459.



Delmotte N, Lasaosa M, Tholey A, Heinzle E, Huber CG (2007). Two-dimensional reversed phase x ion-pair reversed-phase HPLC: an alternative approach to high-resolution peptide separation for shotgun proteome analysis. J Proteome Res, 6: 4363-4373.

Hussong R, Tholey A, Hildebrandt A (2007). Efficient analysis of mass spectrometry data using the isotope wavelet. Proceedings of the 3rd international symposium on Computational Life Science (CompLife 2007). American Institute of Physics (AIP) Proceedings.



Tholey A, Heinzle E (2006). Ionic (liquid) matrices for matrix-assisted laser desorption/ionization mass spectrometry-applications and perspectives. Anal Bioanal Chem, 386: 34-37.

Zabet-Moghaddam M, Heinzle E, Lasaosa M, Tholey A (2006). Pyridinium based ionic liquid matrices can improve the identification of proteins by peptide mass fingerprint analysis with matrix assisted laser desorption/ionization mass spectrometry. Anal Bioanal Chem, 384: 215-224.

Tholey A, Zabet-Moghaddam M, Heinzle E (2006). Quantification of peptides for the monitoring of protease catalyzed reactions by MALDI mass spectrometry using ionic liquid matrixes. Anal Chem, 78: 291-297.

Selevsek N, Tholey A, Liénard BMR, Heinzle E, Heinz U, Adolph HW, Frère JM, Oldham NJ, Schofield CJ (2006). Studies on ternary metallo-ß-lactamase-inhibitor complexes using electrospray ionization mass spectrometry. J Am Soc Mass Spectrom, 17: 1000-1004.

Tholey A (2006). MALDI Mass Spectrometry for Quantitative Proteomics – Approaches, Scopes and Limitations. Dagstuhl Seminar Proceedings 05471 (2005): Computational Proteomics. CG. Huber, K. Reinhardt & O. Kohlbacher (Eds.). Published online: index.php?semnr=05471.

Tholey A (2006). Ionic liquid matrices with phosphoric acid as matrix additive for the facilitated analysis of phosphopeptides by matrix assisted laser desorption/ionization mass spectrometry. Rapid Commun Mass Spectrom, 20: 1761-1768.



Tholey A, Toll H, Huber CG (2005). Separation and detection of phosphorylated and nonphosphorylated peptides in liquid chromatography-mass spectrometry using monolithic columns and acidic or alkaline mobile phases. Anal Chem, 77: 4618-4625.

Adolph HW, Heinz U, Tholey A, Kiefer M (2005). On the competition for available Zinc. J Biol Chem, 280: 3197-3207.