Application notes

  1. Pipeline for acquisition and analysis of 3D MALDI imaging mass spectrometry data. MIL application note #1, 15/05/2012


  1. T. Alexandrov (2011) Determination of Tissue States by Imaging Mass Spectrometry. U.S. Patent Application 13/028,676
  2. D. Trede, P. Maass und T. Alexandrov (2011) Method for computational processing of a digital image (Verfahren zur rechnergestützten Verarbeitung eines digitalisierten Bildes). Patent application Nr. 10 2011 003 242.8 to the German Patent and Trade Mark Office
  3. T. Alexandrov (2010) Bestimmung von Gewebezuständen mittels bildgebender Massenspektrometrie. Patent application Nr. 20100225\267 to the German Patent and Trade Mark Office


  1. J.  Nüße, U. Mirastschijski, M. Waespy,  J. Oetjen,  N. Brandes,  O. Rebello, et al. (2016) Two new isoforms of the human hepatoma-derived growth factor interact with components of the cytoskeleton. Biological chemistry 397: 417–436.
  2. J. Oetjen, K. Veselkov,  J. Watrous,  J.S. McKenzie, M.  Becker, L. Hauberg-Lotte, L., et al. (2015) Benchmark datasets for 3D MALDI-and DESI-imaging mass spectrometry. GigaScience 4: 1–8.
  3. L. Krasny, F. Hoffmann, G. Ernst, D. Trede, T. Alexandrov, V. Havlicek, O. Guntinas-Lichius, F. von Eggeling, A.C. Crecelius (2015) Spatial Segmentation of MALDI FT-ICR MSI Data: A Powerful Tool to Explore the Head and Neck Tumor In Situ Lipidome. Journal of The American Society for Mass Spectrometry, 26(1), 36-43.
  4. T. Alexandrov, J. Decker, B. Mertens, A. M. Deelder, R. A. E. M. Tollenaar, P. Maass, H. Thiele (2009) Biomarker discovery in MALDI-TOF serum protein profiles using discrete wavelet transformation. Bioinformatics, 25(5):643–649
  5. R.M. Abed, L. Polerecky, A. Al-Habsi, J. Oetjen, M. Strous, D. de Beer, D. (2014) Rapid Recovery of Cyanobacterial Pigments in Desiccated Biological Soil Crusts following Addition of Water. PloS one, 9(11), e112372.
  6. O. Klein, K. Strohschein, G. Nebrich, J. Oetjen, D. Trede, H. Thiele, H., T. Alexandrov, P. Giavalisco, G.N. Duda, P. von Roth, S. Geissler, J. Klose, T. Winkler (2014) MALDI imaging mass spectrometry: Discrimination of pathophysiological regions in traumatized skeletal muscle by characteristic peptide signatures. Proteomics, 14(20), 2249-2260.
  7. S. Laouirem, J. Le Faouder, T. Alexandrov, D. Mestivier, T. Léger, X. Baudin, M. Mebarki, V. Paradis, J.M. Camadro, P. Bedossa (2014) Progression from cirrhosis to cancer is associated with early ubiquitin post-translational modifications: identification of new biomarkers of cirrhosis at risk of malignancy. J Pathol, doi: 10.1002/path.4398
  8. G. Ernst, O. Guntinas-Lichius, L. Hauberg-Lotte, D. Trede, M. Becker, T. Alexandrov T, F. von Eggeling F (2014) Histomolecular interpretation of pleomorphic adenomas of the salivary gland by MALDI imaging and spatial segmentation. Head Neck, doi: 10.1002/hed.23713
  9. J. Le Faouder J, S. Laouirem S, T. Alexandrov T, S. Ben-Harzallah S, T. Léger T, M. Albuquerque M, P. Bedossa P, V. Paradis V (2014) Tumoral heterogeneity of hepatic cholangiocarcinomas revealed by MALDI imaging mass spectrometry. Proteomics, 14(7-8):965-72
  10. D. Hölscher, S. Dhakshinamoorthy, T. Alexandrov, M. Becker, T. Bretschneider, A. Buerkert, A.C. Crecelius, D. De Waele, A. Elsen, D.G. Heckel, H. Heklau, C. Hertweck, M. Kai, D. Knop, C. Krafft, R.K. Maddula, C. Matthäus, J. Popp, B. Schneider, U.S. Schubert, R.A. Sikora, A. Svatoš, R.L. Swennen (2014) Phenalenone-type phytoalexins mediate resistance of banana plants (Musa spp.) to the burrowing nematode Radopholus similis. Proc Natl Acad Sci U S A, 7;111(1):105-10
  11. J. de Ridder, Y. Bromberg, M. Michaut, V.P. Satagopam, M. Corpas, G. MacIntyre, T. Alexandrov (2013) The young PI buzz: learning from the organizers of the Junior Principal Investigator Meeting at ISMB-ECCB 201. PLoS Comput Biol, (11):e1003350
  12. T. Alexandrov, P.E. Bourne (2013) Learning how to run a lab: interviews with principal investigators. PLoS Comput Biol, 9(11):e1003349
  13. T. Alexandrov, I. Chernyavsky, M. Becker, F. von Eggeling, S. Nikolenko (2013) Analysis and interpretation of imaging mass spectrometry data by clustering mass-to-charge images according to their spatial similarity. Anal Che, 3;85(23):11189-95
  14. J. Watrous, P. Roach, B. Heath, T. Alexandrov, J. Laskin, P.C. Dorrestein (2013) Metabolic profiling directly from the Petri dish using nanospray desorption electrospray ionization imaging mass spectrometry. Anal Chem, 5;85(21):10385-91
  15. M.F. Traxler, J.D. Watrous, T. Alexandrov, P.C. Dorrestein, R. Kolter (2013) Interspecies interactions stimulate diversification of the Streptomyces coelicolor secreted metabolome. MBio, 20;4(4)
  16. T. Alexandrov, A. Bartels (2013) Testing for presence of known and unknown molecules in imaging mass spectrometry. Bioinformatics, 15;29(18):2335-42
  17. T. Alexandrov, P. Lasch (2013) Segmentation of confocal Raman microspectroscopic imaging data using edge-preserving denoising and clustering. Anal Chem. 18;85(12):5676-83
  18. C.M. Rath, J.Y. Yang, T. Alexandrov, P.C. Dorrestein (2013) Data-independent microbial metabolomics with ambient ionization mass spectrometry. J Am Soc Mass Spectrom, 24(8):1167-76
  19. N. Poté, T. Alexandrov, J. Le Faouder, S. Laouirem, T. Léger, M. Mebarki, J. Belghiti, J.M. Camadro, P. Bedossa, V. Paradis (2013) Imaging mass spectrometry reveals modified forms of histone H4 as new biomarkers of microvascular invasion in hepatocellular carcinomas. Hepatology, 58(3):983-94
  20. J.D. Watrous, V.V. Phelan, C.C Hsu, W.J. Moree, B.M. Duggan, T. Alexandrov T, P.C. Dorrestein (2013) Microbial metabolic exchange in 3D. ISME J., 7(4):770-80
  21. J. Oetjen, M. Aichler, D. Trede, J. Strehlow, J. Berger, S. Heldmann, M. Becker, J. H. Kobarg, S. Wirtz, S. Schiffler, H. Thiele, A. K. Walch, P. Maass and T. Alexandrov (2013) MRI-compatible pipeline for three-dimensional MALDI imaging mass spectrometry using PAXgene fixation. J Proteomics, 90:52-60
  22. J.  Watrous, V. V. Phelan, C. Hsu, W. J. Moree, B. M. Duggan, T. Alexandrov and P. C. Dorrstein (2013) Microbial metabolic exchange in 3D. ISME Journal,
  23. T. Alexandrov, M. Becker, O. Guntinas-Lichius, G. Ernst, F. von Eggeling (2013) MALDI-imaging segmentation is a powerful tool for spatial functional proteomic analysis of human larynx carcinoma. Journal of Cancer Research and Clinical Oncology, 139(1):85-95
  24. J. Watrous, P. J. Roach, T. Alexandrov, B. S. Heath, J. Y. Yang, R. Kersten, M. vander Voort, K. Pogliano, H. Gross, J. M. Raaijmakers, B. S. Moore, J. Laskin, N. Bandeira, P. C. Dorrestein (2012) Mass spectral molecular networking of living microbial colonies. Proceedings of the National Academy of Sciences USA, 109(26): E1743-1752
  25. T. Alexandrov (2012) MALDI imaging mass spectrometry: statistical data analysis and current computational challenges. BMC Bioinformatics 13:(Suppl. 16):S11
  26. A. Crecelius, R. Steinacker, A. Meier, T. Alexandrov, J. Vitz, U. Schubert (2012) Application of matrix-assisted laser desorption/ionization mass spectrometric imaging for photolithographic structuring. Analytical Chemistry, 84(16): 6921-6925
  27. M. Lagarrigue, T. Alexandrov, G. Dieuset, A. Perrin, R. Lavigne, S. Baulac, H. Thiele, B. Martin, C. Pineau (2012) A new analysis workflow for MALDI imaging mass spectrometry: application to the discovery and identification of potential markers of Childhood Absence Epilepsy. Journal of Proteome Research, 11(11):5453-5463
  28. C. Rath, T. Alexandrov, S. Higginbottom, J. Song, M. Milla, M. Fischbach, J. Sonnenburg, P. Dorrestein. (2012) Molecular analysis of model gut microbiotas by imaging mass spectrometry and nano-desorption electrospray ionization reveals dietary metabolite transformations. Analytical Chemistry, 84(21):9259-67
  29. D. Trede, T. Alexandrov, C. Sagiv, P. Maass (2012) Magnification of label maps with a topology-preserving level-set method. IEEE Transactions on Image Processing, 21(9): 4040-4053
  30. D. Trede, S. Schiffler, M. Becker, S. Wirtz, K. Steinhorst, J. Strehlow, M. Aichler, J. Kobarg, J. Oetjen, A. Dyatlov, S. Heldmann, A. Walch, H. Thiele, P. Maass, T. Alexandrov (2012) Exploring 3D MALDI imaging mass spectrometry data: 3D spatial segmentation of mouse kidney. Analytical Chemistry, 84(14): 6079-6087
  31. T. Alexandrov, S. Meding, D. Trede, J. H. Kobarg, B. Balluff, A. Walch, H. Thiele, P. Maass (2011) Super-resolution segmentation of imaging mass spectrometry data: solving the issue of low lateral resolution. Journal of Proteomics, 75(1):237-245
  32. J. Bruand, T. Alexandrov, S. Sistla, M. Wisztorski, C. Meriaux, M. Becker, M. Salzet, I. Fournier, E. Macagno, V. Bafna (2011) AMASS: algorithm for MSI (mass spectrometric imaging) analysis by semi-supervised segmentation. Journal of Proteome Research, 10(10):4734-4743
  33. A. C. Crecelius, T. Alexandrov, U. S. Schubert (2011) Application of MALDI-MSI to monitor surface changes of UV irradiated poly(styrene) films. Rapid Communications in Mass Spectrometry, 25(19):2809-2814
  34. T. Alexandrov, J. H. Kobarg (2011) Efficient spatial segmentation of large imaging mass spectrometry datasets with spatially aware clustering. Bioinformatics, 27: i230-i238
  35. J. Watrous, T. Alexandrov, P. C. Dorrestein (2011) The evolving field of imaging mass spectrometry and its impact on future biological research. Journal of Mass Spectrometry, 46(2):209-222
  36. T. Alexandrov, M. Becker, S.-O. Deininger, G. Ernst, L. Wehder, M. Grasmair, F. von Eggeling, H. Thiele, P. Maass (2010) Spatial segmentation of imaging mass spectrometry data with edge-preserving image denoising and clustering. Journal of Proteome Research, 9(12): 6535-6546
  37. C. I. Balog, T. Alexandrov, R.J. Derks, P.J. Hensbergen, G.J. van Dam, E.M. Tukahebwa, N.B. Kabatereine, H. Thiele, B.J. Vennervald, O.A. Mayboroda, A.M. Deelder (2010) The feasibility of mass spectrometry and advanced data processing for monitoring Schistosoma mansoni infection. Proteomics - Clinical Applications, 4(5):499-510