Andrej Shevchenko

Summary

Affiliation: Max Planck Institute of Molecular Cell Biology and Genetics
Country: Germany

Publications

  1. ncbi request reprint In-gel digestion for mass spectrometric characterization of proteins and proteomes
    Andrej Shevchenko
    Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
    Nat Protoc 1:2856-60. 2006
  2. pmc LipidXplorer: a software for consensual cross-platform lipidomics
    Ronny Herzog
    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    PLoS ONE 7:e29851. 2012
  3. pmc Top-down lipidomics reveals ether lipid deficiency in blood plasma of hypertensive patients
    Juergen Graessler
    Department of Internal Medicine III, Carl Gustav Carus Medical School, Technical University Dresden, Dresden, Germany
    PLoS ONE 4:e6261. 2009
  4. ncbi request reprint Cryptic B-cell epitope identification through informational analysis of protein sequences
    Ludmila Alekseeva
    Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho Maklaya St, 16 10, Moscow 117997, Russian Federation
    Vaccine 25:2688-97. 2007
  5. ncbi request reprint "De novo" sequencing of peptides recovered from in-gel digested proteins by nanoelectrospray tandem mass spectrometry
    Andrej Shevchenko
    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    Mol Biotechnol 20:107-18. 2002
  6. pmc Tools for exploring the proteomosphere
    Andrej Shevchenko
    Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
    J Proteomics 72:137-44. 2009
  7. ncbi request reprint The yeast APC/C subunit Mnd2 prevents premature sister chromatid separation triggered by the meiosis-specific APC/C-Ama1
    Tobias Oelschlaegel
    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    Cell 120:773-88. 2005
  8. ncbi request reprint A comparative analysis of an orthologous proteomic environment in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe
    Assen Roguev
    Genomics, Technische Universitat Dresden, c o Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
    Mol Cell Proteomics 3:125-32. 2004
  9. pmc Swm1/Apc13 is an evolutionarily conserved subunit of the anaphase-promoting complex stabilizing the association of Cdc16 and Cdc27
    Martin Schwickart
    Max Planck Institute of Molecular Cell Biology and Genetics Scionics Computer Innovation GmbH, Dresden, Germany
    Mol Cell Biol 24:3562-76. 2004
  10. pmc Protein identification pipeline for the homology-driven proteomics
    Magno Junqueira
    Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
    J Proteomics 71:346-56. 2008

Detail Information

Publications78

  1. ncbi request reprint In-gel digestion for mass spectrometric characterization of proteins and proteomes
    Andrej Shevchenko
    Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
    Nat Protoc 1:2856-60. 2006
    ....
  2. pmc LipidXplorer: a software for consensual cross-platform lipidomics
    Ronny Herzog
    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    PLoS ONE 7:e29851. 2012
    ..mpi-cbg.de/wiki/lipidx/index.php/Main_Page...
  3. pmc Top-down lipidomics reveals ether lipid deficiency in blood plasma of hypertensive patients
    Juergen Graessler
    Department of Internal Medicine III, Carl Gustav Carus Medical School, Technical University Dresden, Dresden, Germany
    PLoS ONE 4:e6261. 2009
    ..The objective of this study was to determine whether hypertension specifically affects the plasma lipidome independently and differently from the effects induced by obesity and insulin resistance...
  4. ncbi request reprint Cryptic B-cell epitope identification through informational analysis of protein sequences
    Ludmila Alekseeva
    Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho Maklaya St, 16 10, Moscow 117997, Russian Federation
    Vaccine 25:2688-97. 2007
    ..This result suggests that the analysis of IS of proteins can be useful in the selection of peptides possessing cryptic B-cell epitope activity...
  5. ncbi request reprint "De novo" sequencing of peptides recovered from in-gel digested proteins by nanoelectrospray tandem mass spectrometry
    Andrej Shevchenko
    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    Mol Biotechnol 20:107-18. 2002
    ..The peptide sequences determined provide useful information for identification of proteins by homology searching for cloning of the cognate genes by PCR based approaches...
  6. pmc Tools for exploring the proteomosphere
    Andrej Shevchenko
    Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
    J Proteomics 72:137-44. 2009
    ....
  7. ncbi request reprint The yeast APC/C subunit Mnd2 prevents premature sister chromatid separation triggered by the meiosis-specific APC/C-Ama1
    Tobias Oelschlaegel
    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    Cell 120:773-88. 2005
    ..In vitro, Mnd2 inhibits ubiquitination of Pds1 by APC/C-Ama1 but not by other APC/C holo-enzymes. We conclude that chromosome segregation in meiosis depends on the selective inhibition of a meiosis-specific form of the APC/C...
  8. ncbi request reprint A comparative analysis of an orthologous proteomic environment in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe
    Assen Roguev
    Genomics, Technische Universitat Dresden, c o Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
    Mol Cell Proteomics 3:125-32. 2004
    ..We speculate that conservation of the core components of protein assemblies and variability of hyperlinks represents a general principle in the molecular organization of eukaryotic proteomes...
  9. pmc Swm1/Apc13 is an evolutionarily conserved subunit of the anaphase-promoting complex stabilizing the association of Cdc16 and Cdc27
    Martin Schwickart
    Max Planck Institute of Molecular Cell Biology and Genetics Scionics Computer Innovation GmbH, Dresden, Germany
    Mol Cell Biol 24:3562-76. 2004
    ..Accordingly, Swm1/Apc13 is required for ubiquitin ligase activity in vitro and for the timely execution of APC/C-dependent cell cycle events in vivo...
  10. pmc Protein identification pipeline for the homology-driven proteomics
    Magno Junqueira
    Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
    J Proteomics 71:346-56. 2008
    ..All essential software elements supporting the presented pipeline are either hosted at the publicly accessible web server, or are available for free download...
  11. pmc The Schizosaccharomyces pombe JmjC-protein, Msc1, prevents H2A.Z localization in centromeric and subtelomeric chromatin domains
    Luke Buchanan
    Genomics, BioInnovationsZentrum, Technische Universitat Dresden, Dresden, Germany
    PLoS Genet 5:e1000726. 2009
    ..Z from chromatin. These data describe H2A.Z action in S. pombe and identify a new mode of chromatin surveillance and maintenance based on negative regulation of histone variant misincorporation...
  12. ncbi request reprint Sequence similarity-driven proteomics in organisms with unknown genomes by LC-MS/MS and automated de novo sequencing
    Patrice Waridel
    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    Proteomics 7:2318-29. 2007
    ..This approach enabled a completely automated identification of novel proteins that were, otherwise, missed by conventional database searches...
  13. ncbi request reprint LET-767 is required for the production of branched chain and long chain fatty acids in Caenorhabditis elegans
    Eugeni V Entchev
    Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
    J Biol Chem 283:17550-60. 2008
    ..elegans required for the bulk production of monomethyl branched and long chain fatty acids, and the developmental arrest in let-767 (RNAi) worms is caused by the deficiency of the former...
  14. pmc Global analysis of the yeast lipidome by quantitative shotgun mass spectrometry
    Christer S Ejsing
    Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
    Proc Natl Acad Sci U S A 106:2136-41. 2009
    ..This work serves as a resource for molecular characterization of eukaryotic lipidomes, and establishes shotgun lipidomics as a powerful platform for complementing biochemical studies and other systems-level approaches...
  15. pmc Effects of diet and development on the Drosophila lipidome
    Maria Carvalho
    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    Mol Syst Biol 8:600. 2012
    ..This study provides a comprehensive, quantitative and expandable resource for further pharmacological and genetic studies of metabolic disorders and molecular mechanisms underlying dietary response...
  16. pmc Separating the wheat from the chaff: unbiased filtering of background tandem mass spectra improves protein identification
    Magno Junqueira
    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    J Proteome Res 7:3382-95. 2008
    ....
  17. pmc Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment
    Anna Shevchenko
    MPI of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
    Genome Biol 9:R167. 2008
    ..Because uncertainties remain regarding the accuracy of proteomic data, several issues need to be resolved before comparative proteomics can be fruitful...
  18. doi request reprint Dbf4-dependent CDC7 kinase links DNA replication to the segregation of homologous chromosomes in meiosis I
    Joao Matos
    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    Cell 135:662-78. 2008
    ..Thus, activation of DDK both initiates DNA replication and commits meiotic cells to reductional chromosome segregation in the first division of meiosis...
  19. pmc A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language
    Ronny Herzog
    Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
    Genome Biol 12:R8. 2011
    ....
  20. pmc Yeast lipids can phase-separate into micrometer-scale membrane domains
    Christian Klose
    Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
    J Biol Chem 285:30224-32. 2010
    ..Taken together, these results provide a mechanistic explanation for lipid raft-dependent lipid and protein sorting in yeast...
  21. pmc Membrane lipidome of an epithelial cell line
    Julio L Sampaio
    Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
    Proc Natl Acad Sci U S A 108:1903-7. 2011
    ..Moreover, during polarization, the sphingolipids became longer, more saturated, and more hydroxylated as required to generate an apical membrane domain that serves as a protective barrier for the epithelial sheet...
  22. pmc Quantitative analysis of the lipidomes of the influenza virus envelope and MDCK cell apical membrane
    Mathias J Gerl
    Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
    J Cell Biol 196:213-21. 2012
    ..Our data are consistent with and extend existing models of membrane raft-based biogenesis of the apical membrane and IFV envelope...
  23. pmc Identification of glycosylated marker proteins of epithelial polarity in MDCK cells by homology driven proteomics
    Joachim Fullekrug
    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    BMC Biochem 7:8. 2006
    ..Monoclonal antibodies against apical gp114 and basolateral p58 have served as important tools in these studies. However, the molecular identity of these membrane glycoproteins has not been known...
  24. ncbi request reprint Homology-based functional proteomics by mass spectrometry: application to the Xenopus microtubule-associated proteome
    Adam J Liska
    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    Proteomics 4:2707-21. 2004
    ..These findings were made possible due to the application of sequence-similarity methods, which extended mass spectrometric protein identification capabilities by 2-fold compared to conventional methods...
  25. pmc The histone 3 lysine 36 methyltransferase, SET2, is involved in transcriptional elongation
    Daniel Schaft
    BIOTEC, Technische Universitaet Dresden, MPI CBG, Pfotenhauerstrasse 108, D 01307, Germany
    Nucleic Acids Res 31:2475-82. 2003
    ..Since SET2 is also a histone methyltransferase, these results suggest a role for histone 3 lysine 36 methylation in transcriptional elongation...
  26. pmc Segregation of sphingolipids and sterols during formation of secretory vesicles at the trans-Golgi network
    Robin W Klemm
    Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
    J Cell Biol 185:601-12. 2009
    ....
  27. ncbi request reprint Top-down lipidomic screens by multivariate analysis of high-resolution survey mass spectra
    Dominik Schwudke
    MPI of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
    Anal Chem 79:4083-93. 2007
    ..The top-down lipidomics strategy lends itself for high-throughput screens complementing ongoing functional genomics efforts...
  28. pmc Flexibility of a eukaryotic lipidome--insights from yeast lipidomics
    Christian Klose
    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    PLoS ONE 7:e35063. 2012
    ..In addition, we established a baseline for future lipidomic experiments in yeast. Finally, flexibility of lipidomic features is proposed as a new parameter for the description of the physiological state of an organism...
  29. doi request reprint Bottom-up shotgun lipidomics by higher energy collisional dissociation on LTQ Orbitrap mass spectrometers
    Kai Schuhmann
    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    Anal Chem 83:5480-7. 2011
    ..We argue that now both bottom-up and top-down shotgun lipidomics could be performed on the same instrumentation platform...
  30. pmc Survival strategies of a sterol auxotroph
    Maria Carvalho
    Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
    Development 137:3675-85. 2010
    ..These changes allow survival, but not growth, when membrane sterol levels are low. This relationship between sterols and sphingolipids could be an ancient and conserved principle of membrane homeostasis...
  31. doi request reprint A genome-scale RNAi screen for Oct4 modulators defines a role of the Paf1 complex for embryonic stem cell identity
    Li Ding
    Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
    Cell Stem Cell 4:403-15. 2009
    ..We propose that the Paf1C plays an important role in maintaining ESC identity...
  32. doi request reprint Proteome and phosphoproteome of Africanized and European honeybee venoms
    Virginia Maria Ferreira Resende
    Division of Clinical Immunology and Allergy, Department of Medicine, University of Sao Paulo, Sao Paulo, SP, Brazil Institute for Investigation in Immunology iii INCT, Sao Paulo, SP, Brazil MPI of Molecular Cell Biology and Genetics, Dresden, Germany
    Proteomics 13:2638-48. 2013
    ..18) Ser phosphorylated melittin-the major of its two phosphorylated forms-was less toxic compared to the native peptide. ..
  33. ncbi request reprint Identification of regulators of germ layer morphogenesis using proteomics in zebrafish
    Vinzenz Link
    Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr 108, 01307 Dresden, Germany
    J Cell Sci 119:2073-83. 2006
    ..We demonstrate the feasibility of proteomics in zebrafish, concluding that proteomics is a valuable tool for analysis of early development...
  34. doi request reprint Shotgun lipidomics on a LTQ Orbitrap mass spectrometer by successive switching between acquisition polarity modes
    Kai Schuhmann
    Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
    J Mass Spectrom 47:96-104. 2012
    ..In this way, shotgun analysis of total lipid extracts of human blood plasma enabled to quantify 222 species from 15 major lipid classes within 7 min acquisition cycle...
  35. doi request reprint Discrimination between peptide O-sulfo- and O-phosphotyrosine residues by negative ion mode electrospray tandem mass spectrometry
    Marina Edelson-Averbukh
    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    J Am Soc Mass Spectrom 22:2256-68. 2011
    ....
  36. ncbi request reprint Automated identification and quantification of glycerophospholipid molecular species by multiple precursor ion scanning
    Christer S Ejsing
    Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
    Anal Chem 78:6202-14. 2006
    ..The automated analysis of total lipid extracts was powered by a robotic nanoflow ion source and produced currently the most detailed description of the glycerophospholipidome...
  37. ncbi request reprint High conservation of the Set1/Rad6 axis of histone 3 lysine 4 methylation in budding and fission yeasts
    Assen Roguev
    BIOTEC, Technische Universitaet Dresden, c o Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, Germany
    J Biol Chem 278:8487-93. 2003
    ..Thus, we infer that Set1C is highly conserved in eukaryotes but observe that its links to the proteome are not...
  38. pmc Comparative profiling identifies C13orf3 as a component of the Ska complex required for mammalian cell division
    Mirko Theis
    Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
    EMBO J 28:1453-65. 2009
    ..All together, these data identify C13orf3 as an important factor for metaphase to anaphase progression and highlight the potential of combined RNAi screening and protein localisation analyses...
  39. ncbi request reprint The power and the limitations of cross-species protein identification by mass spectrometry-driven sequence similarity searches
    Bianca Habermann
    Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
    Mol Cell Proteomics 3:238-49. 2004
    ..We also estimated phylogenetic distances between organisms under study and related reference organisms with completely sequenced genomes that allow substantial coverage of unknown proteomes...
  40. pmc Shotgun lipidomics on high resolution mass spectrometers
    Dominik Schwudke
    MPI of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
    Cold Spring Harb Perspect Biol 3:a004614. 2011
    ..By streamlining and simplifying the molecular characterization of lipidomes, high resolution mass spectrometry has developed into a generic tool for cell biology and molecular medicine...
  41. ncbi request reprint Lipid profiling by multiple precursor and neutral loss scanning driven by the data-dependent acquisition
    Dominik Schwudke
    MPI of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
    Anal Chem 78:585-95. 2006
    ..No separation of lipids is required, and the accuracy of identification and quantification is not compromised, compared to conventional precursor and neutral loss scanning...
  42. pmc Lipoproteins in Drosophila melanogaster--assembly, function, and influence on tissue lipid composition
    Wilhelm Palm
    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    PLoS Genet 8:e1002828. 2012
    ..These studies define major routes of interorgan lipid transport in Drosophila and uncover surprising tissue-specific differences in lipoprotein lipid utilization...
  43. ncbi request reprint Fast-response proteomics by accelerated in-gel digestion of proteins
    Jan Havlis
    Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, D 01307 Dresden, Germany
    Anal Chem 75:1300-6. 2003
    ..The accelerated digestion protocol was tested in identification of more than 120 proteins from budding and fission yeasts at the subpicomole level...
  44. ncbi request reprint Lipidomics: coming to grips with lipid diversity
    Andrej Shevchenko
    Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
    Nat Rev Mol Cell Biol 11:593-8. 2010
    ..Here, we argue that lipidomics will become an essential tool kit in cell and developmental biology, molecular medicine and nutrition...
  45. pmc A genome-scale DNA repair RNAi screen identifies SPG48 as a novel gene associated with hereditary spastic paraplegia
    Mikołaj Słabicki
    Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
    PLoS Biol 8:e1000408. 2010
    ..The discovery that proteins forming a novel protein complex are required for efficient HR-DSBR and are mutated in patients suffering from HSP suggests a link between HSP and DNA repair...
  46. pmc Human lysophosphatidylcholine acyltransferases 1 and 2 are located in lipid droplets where they catalyze the formation of phosphatidylcholine
    Christine Moessinger
    Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, D 01307 Dresden, Germany
    J Biol Chem 286:21330-9. 2011
    ..This suggests that LPCAT1 and -2 have, in addition to their known function in specialized cells, a ubiquitous role in LD-associated lipid metabolism...
  47. pmc Nucleocytoplasmic shuttling of the Golgi phosphatidylinositol 4-kinase Pik1 is regulated by 14-3-3 proteins and coordinates Golgi function with cell growth
    Lars Demmel
    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden D 01307, Germany
    Mol Biol Cell 19:1046-61. 2008
    ..These data suggest a role of Pik1p nucleocytoplasmic shuttling in coordination of biosynthetic transport from the Golgi with nutrient signaling...
  48. pmc Lipid extraction by methyl-tert-butyl ether for high-throughput lipidomics
    Vitali Matyash
    Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
    J Lipid Res 49:1137-46. 2008
    ..Rigorous testing demonstrated that the MTBE protocol delivers similar or better recoveries of species of most all major lipid classes compared with the "gold-standard" Folch or Bligh and Dyer recipes...
  49. ncbi request reprint Sequence similarity-based proteomics in insects: characterization of the larvae venom of the Brazilian moth Cerodirphia speciosa
    Anna Shevchenko
    Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
    J Proteome Res 4:862-9. 2005
    ..The protein composition of the venom suggested that envenoming by C. speciosa toxins might proceed through the contact with its hemolymph, similarly to another toxic Lepidoptera organism, Lonomia obliqua...
  50. pmc Simplified validation of borderline hits of database searches
    Henrik Thomas
    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    Proteomics 8:4173-7. 2008
    ..We demonstrate that comparing hit database sequences and independent de novo interpretations of the same MS/MS spectra assists in rapid examination of ambiguous matches...
  51. ncbi request reprint Shotgun lipidomics by tandem mass spectrometry under data-dependent acquisition control
    Dominik Schwudke
    MPI of Molecular Cell Biology and Genetics, Dresden, Germany
    Methods Enzymol 433:175-91. 2007
    ....
  52. ncbi request reprint Rapid validation of protein identifications with the borderline statistical confidence via de novo sequencing and MS BLAST searches
    Natalie Wielsch
    Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
    J Proteome Res 5:2448-56. 2006
    ....
  53. doi request reprint Tissue proteomics by one-dimensional gel electrophoresis combined with label-free protein quantification
    Andrej Vasilj
    Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
    J Proteome Res 11:3680-9. 2012
    ..Better proteome coverage and quantification accuracy revealed molecular details of the perturbed energy metabolism...
  54. pmc Ablation of cholesterol biosynthesis in neural stem cells increases their VEGF expression and angiogenesis but causes neuron apoptosis
    Kanako Saito
    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    Proc Natl Acad Sci U S A 106:8350-5. 2009
    ..Moreover, our data reveal a hitherto unknown compensatory process by which the neural stem and progenitor cells of the developing mammalian brain evade the detrimental consequences of impaired endogenous cholesterol biosynthesis...
  55. ncbi request reprint Error-tolerant EST database searches by tandem mass spectrometry and multiTag software
    Adam J Liska
    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    Proteomics 5:4118-22. 2005
    ..The MultiTag outperformed conventional database searching software that only utilizes stringent matching of tandem mass spectra to nucleotide sequences of ESTs...
  56. ncbi request reprint The CCT chaperonin promotes activation of the anaphase-promoting complex through the generation of functional Cdc20
    Alain Camasses
    Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
    Mol Cell 12:87-100. 2003
    ..We propose that folding of the Cdc20 family of APC/C activators is an essential and evolutionary conserved function of the CCT chaperonin...
  57. pmc The lipidomes of vesicular stomatitis virus, semliki forest virus, and the host plasma membrane analyzed by quantitative shotgun mass spectrometry
    Lucie Kalvodova
    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    J Virol 83:7996-8003. 2009
    ....
  58. ncbi request reprint Expanding the organismal scope of proteomics: cross-species protein identification by mass spectrometry and its implications
    Adam J Liska
    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    Proteomics 3:19-28. 2003
    ..Both the integration of mass spectrometry with bioinformatics and genomic sequencing drive the expanding organismal scope of proteomics...
  59. doi request reprint Systematic screening for novel lipids by shotgun lipidomics
    Cyrus Papan
    Max Planck Institute for Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
    Anal Chem 86:2703-10. 2014
    ..The search, covering more than 1.5 million putative chemical compositions, identified a novel class of lyso-maradolipids specifically enriched in dauer larvae. ..
  60. pmc Molecular strategies of the Caenorhabditis elegans dauer larva to survive extreme desiccation
    Cihan Erkut
    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    PLoS ONE 8:e82473. 2013
    ..Remarkably, this response is specific and involves a small number of functional pathways, which represent the generic toolkit for anhydrobiosis in plants and animals. ..
  61. doi request reprint Horizontal carryover of proteins on one-dimensional polyacrylamide gels may jeopardize gel-enhanced liquid chromatography mass spectrometry proteomic interpretations
    Andrea Knaust
    MPI of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
    Anal Biochem 421:779-81. 2012
    ..Therefore, we suggest that experimental and control samples should always be loaded on separate gels...
  62. doi request reprint Gas-phase intramolecular phosphate shift in phosphotyrosine-containing peptide monoanions
    Marina Edelson-Averbukh
    Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
    Anal Chem 81:4369-81. 2009
    ..This work demonstrates that the established phosphate-specific neutral loss fragmentation rules of protonated pTyr-peptides cannot be applied to the CID spectra of their [M-H](-) ions...
  63. ncbi request reprint Absolute quantification of proteins in solutions and in polyacrylamide gels by mass spectrometry
    Jan Havlis
    Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, D 01307 Dresden, Germany
    Anal Chem 76:3029-36. 2004
    ..Under optimized experimental conditions, it was possible to provide a semiquantitative estimate of the absolute amount of gel separated proteins within better than 50% error margin...
  64. ncbi request reprint Dried-droplet probe preparation on AnchorChip targets for navigating the acquisition of matrix-assisted laser desorption/ionization time-of-flight spectra by fluorescence of matrix/analyte crystals
    Henrik Thomas
    Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
    Rapid Commun Mass Spectrom 18:923-30. 2004
    ..The sensitivity of the peptide mass mapping was at the low-femtomole level...
  65. pmc Proteomics of early zebrafish embryos
    Vinzenz Link
    Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauer Str 108, 01307 Dresden, Germany
    BMC Dev Biol 6:1. 2006
    ..While genetic methods are readily available in zebrafish, protocols for two dimensional (2D) gel electrophoresis and proteomics have yet to be developed...
  66. pmc Enhanced photosynthesis and redox energy production contribute to salinity tolerance in Dunaliella as revealed by homology-based proteomics
    Adam J Liska
    Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
    Plant Physiol 136:2806-17. 2004
    ..The results demonstrated the power of MS BLAST searches for the identification of proteins in organisms whose genomes are not known and paved the way for dissecting molecular mechanisms of salinity tolerance in algae and higher plants...
  67. ncbi request reprint Collision-induced dissociation pathways of yeast sphingolipids and their molecular profiling in total lipid extracts: a study by quadrupole TOF and linear ion trap-orbitrap mass spectrometry
    Christer S Ejsing
    Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
    J Mass Spectrom 41:372-89. 2006
    ....
  68. ncbi request reprint Deciphering protein complexes and protein interaction networks by tandem affinity purification and mass spectrometry: analytical perspective
    Anna Shevchenko
    Max Planck Institute of Molecular Cell Biology and Genetics MPI CBG, Pfotenhauerstrasse 108, 01307 Dresden, Germany
    Mol Cell Proteomics 1:204-12. 2002
    ..Concordance with the results of genome-wide two-hybrid screening was poor (14% of identified interactors overlapped) suggesting that the two approaches may provide complementary views on physical interactions within the proteome...
  69. ncbi request reprint Polyene-lipids: a new tool to image lipids
    Lars Kuerschner
    Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr 108, 01307 Dresden, Germany
    Nat Methods 2:39-45. 2005
    ..Applying two-photon excitation microscopy, we imaged the distribution of polyene-lipids in living mammalian cells. For the first time, ether lipids, important for the function of the brain, were successfully visualized...
  70. ncbi request reprint Quantitative profiling of phospholipids by multiple precursor ion scanning on a hybrid quadrupole time-of-flight mass spectrometer
    Kim Ekroos
    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    Anal Chem 74:941-9. 2002
    ..Taken together, a combination of multiple precursor ion scans allowed quantitative monitoring of major perturbation in phospholipid composition and elucidating of molecular heterogeneity of individual lipid species...
  71. ncbi request reprint Charting molecular composition of phosphatidylcholines by fatty acid scanning and ion trap MS3 fragmentation
    Kim Ekroos
    Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
    J Lipid Res 44:2181-92. 2003
    ....
  72. ncbi request reprint Nanoelectrospray tandem mass spectrometry and sequence similarity searching for identification of proteins from organisms with unknown genomes
    Anna Shevchenko
    European Molecular Biology Laboratory, Heidelberg, Germany
    Methods Mol Biol 211:221-34. 2003
  73. ncbi request reprint MultiTag: multiple error-tolerant sequence tag search for the sequence-similarity identification of proteins by mass spectrometry
    Shamil Sunyaev
    European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Anal Chem 75:1307-15. 2003
    ..This feature facilitates the identification of low abundance proteins, since noisy and low-intensity tandem mass spectra can be utilized...
  74. ncbi request reprint Charting the protein complexome in yeast by mass spectrometry
    Raymond J Deshaies
    Divison of Biology, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California 91125, USA
    Mol Cell Proteomics 1:3-10. 2002
    ..In this article we review some of our recent efforts, and describe a promising new approach for using mass spectrometry to dissect protein interaction networks...
  75. ncbi request reprint Thermostable trypsin conjugates for high-throughput proteomics: synthesis and performance evaluation
    Marek Sebela
    Department of Biochemistry, Faculty of Science, Palacky University, Slechtitelu 11, 783 71 Olomouc, Czech Republic
    Proteomics 6:2959-63. 2006
    ..These conjugates accelerated the digestion of protein substrates both in solution and in gel, compared to commonly used unmodified and methylated trypsins...
  76. pmc Analysis of the adenovirus E1B-55K-anchored proteome reveals its link to ubiquitination machinery
    Josephine N Harada
    Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095 1570, USA
    J Virol 76:9194-206. 2002
    ..Lastly, we describe the identification and characterization of two novel E1B-55K interacting factors, importin-alpha 1 and pp32, that may also participate in the functions previously ascribed to E1B-55K and E4-orf6...
  77. ncbi request reprint Salt-induced changes in the plasma membrane proteome of the halotolerant alga Dunaliella salina as revealed by blue native gel electrophoresis and nano-LC-MS/MS analysis
    Adriana Katz
    Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
    Mol Cell Proteomics 6:1459-72. 2007
    ..The migration profiles of native protein complexes on blue native gels revealed oligomerization or co-migration of major surface-exposed proteins, which may indicate mechanisms of stabilization at high salinity...
  78. pmc KNL-1 directs assembly of the microtubule-binding interface of the kinetochore in C. elegans
    Arshad Desai
    Max Planck Institute for Molecular Cell Biology and Genetics MPI CBG, Dresden 01307, Germany
    Genes Dev 17:2421-35. 2003
    ..Thus, KNL-1 plays a central role in translating the initiation of kinetochore assembly by CeCENP-A and CeCENP-C into the formation of a functional microtubule-binding interface...