Matthias Mann

Summary

Country: Germany

Publications

  1. ncbi request reprint Functional and quantitative proteomics using SILAC
    Matthias Mann
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Nat Rev Mol Cell Biol 7:952-8. 2006
  2. pmc Expert system for computer-assisted annotation of MS/MS spectra
    Nadin Neuhauser
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Mol Cell Proteomics 11:1500-9. 2012
  3. pmc Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer
    Annette Michalski
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Mol Cell Proteomics 10:M111.011015. 2011
  4. pmc Super-SILAC allows classification of diffuse large B-cell lymphoma subtypes by their protein expression profiles
    Sally J Deeb
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, D 82152 Martinsried, Germany
    Mol Cell Proteomics 11:77-89. 2012
  5. pmc A framework for intelligent data acquisition and real-time database searching for shotgun proteomics
    Johannes Graumann
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Mol Cell Proteomics 11:M111.013185. 2012
  6. pmc MAPU 2.0: high-accuracy proteomes mapped to genomes
    Florian Gnad
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Nucleic Acids Res 37:D902-6. 2009
  7. pmc System-wide perturbation analysis with nearly complete coverage of the yeast proteome by single-shot ultra HPLC runs on a bench top Orbitrap
    Nagarjuna Nagaraj
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Mol Cell Proteomics 11:M111.013722. 2012
  8. pmc Quantitative proteomics reveals that Hsp90 inhibition preferentially targets kinases and the DNA damage response
    Kirti Sharma
    Departments of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    Mol Cell Proteomics 11:M111.014654. 2012
  9. pmc Initial quantitative proteomic map of 28 mouse tissues using the SILAC mouse
    Tamar Geiger
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Mol Cell Proteomics 12:1709-22. 2013
  10. pmc MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes
    Yanling Zhang
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    Nucleic Acids Res 35:D771-9. 2007

Collaborators

Detail Information

Publications178 found, 100 shown here

  1. ncbi request reprint Functional and quantitative proteomics using SILAC
    Matthias Mann
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Nat Rev Mol Cell Biol 7:952-8. 2006
    ....
  2. pmc Expert system for computer-assisted annotation of MS/MS spectra
    Nadin Neuhauser
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Mol Cell Proteomics 11:1500-9. 2012
    ..biochem.mpg.de/mann/tools/). It provides expert knowledge to beginners in the field of MS-based proteomics and helps advanced users to focus on unusual and possibly novel types of fragment ions...
  3. pmc Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer
    Annette Michalski
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Mol Cell Proteomics 10:M111.011015. 2011
    ..High performance in a robust benchtop format together with the ability to perform complex multiplexed scan modes make the Q Exactive an exciting new instrument for the proteomics and general analytical communities...
  4. pmc Super-SILAC allows classification of diffuse large B-cell lymphoma subtypes by their protein expression profiles
    Sally J Deeb
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, D 82152 Martinsried, Germany
    Mol Cell Proteomics 11:77-89. 2012
    ..These results show that high resolution shotgun proteomics combined with super-SILAC-based quantification is a promising new technology for tumor characterization and classification...
  5. pmc A framework for intelligent data acquisition and real-time database searching for shotgun proteomics
    Johannes Graumann
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Mol Cell Proteomics 11:M111.013185. 2012
    ..Our framework should be especially useful for new instrument types, such as the quadrupole-Orbitrap, that are currently becoming available...
  6. pmc MAPU 2.0: high-accuracy proteomes mapped to genomes
    Florian Gnad
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Nucleic Acids Res 37:D902-6. 2009
    ..MAPU 2.0 is a model for a database specifically designed for high-accuracy proteomics and a member of the ProteomExchange Consortium. It is available on line at http://www.mapuproteome.com...
  7. pmc System-wide perturbation analysis with nearly complete coverage of the yeast proteome by single-shot ultra HPLC runs on a bench top Orbitrap
    Nagarjuna Nagaraj
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Mol Cell Proteomics 11:M111.013722. 2012
    ..Conversely, stress-related pathways were up-regulated. The proteomic technology described here is straightforward, rapid, and robust, potentially enabling widespread use in the yeast and other biological research communities...
  8. pmc Quantitative proteomics reveals that Hsp90 inhibition preferentially targets kinases and the DNA damage response
    Kirti Sharma
    Departments of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    Mol Cell Proteomics 11:M111.014654. 2012
    ..This study defines the cellular response to Hsp90 inhibition at the proteome level and sheds light on the mechanisms by which it can be used to target cancer cells...
  9. pmc Initial quantitative proteomic map of 28 mouse tissues using the SILAC mouse
    Tamar Geiger
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Mol Cell Proteomics 12:1709-22. 2013
    ..Our data will be useful to the broad scientific community as an initial atlas of protein expression of a mammalian species...
  10. pmc MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes
    Yanling Zhang
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    Nucleic Acids Res 35:D771-9. 2007
    ..More than 4500 mouse and 2500 human proteins have already been identified in at least one proteome. Basic annotation information and links to other public databases are provided in MAPU and we plan to add further analysis tools...
  11. pmc Proteomic changes resulting from gene copy number variations in cancer cells
    Tamar Geiger
    Department for Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    PLoS Genet 6:e1001090. 2010
    ..By connecting the primary genome alteration to their proteomic consequences, this approach helps to interpret the data from large-scale cancer genomics efforts...
  12. pmc Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples
    Paul J Boersema
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Mol Cell Proteomics 12:158-71. 2013
    ..The combination of quantifying the secretome of cancer cell lines and of human plasma with a super-SILAC approach appears to be a promising new approach for finding markers of disease...
  13. pmc Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics
    Cuiping Pan
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried near Munich, Germany
    Mol Cell Proteomics 8:2796-808. 2009
    ..Our assay is streamlined and generic and could become a useful tool in kinase drug development...
  14. pmc Systems-wide analysis of a phosphatase knock-down by quantitative proteomics and phosphoproteomics
    Maximiliane Hilger
    Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Mol Cell Proteomics 8:1908-20. 2009
    ..Our analysis highlights a connection of Ptp61F to cytoskeletal regulation through GTPase regulating proteins and focal adhesion components...
  15. pmc Deep and highly sensitive proteome coverage by LC-MS/MS without prefractionation
    Suman S Thakur
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    Mol Cell Proteomics 10:M110.003699. 2011
    ..With further development, single-run analysis has the potential to radically simplify many proteomic studies while maintaining a systems-wide view of the proteome...
  16. pmc Deep proteome and transcriptome mapping of a human cancer cell line
    Nagarjuna Nagaraj
    Department for Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
    Mol Syst Biol 7:548. 2011
    ..Comparisons of the proteome and the transcriptome, and analysis of protein complex databases and GO categories, suggest that we achieved deep coverage of the functional transcriptome and the proteome of a single cell type...
  17. pmc PHOSIDA 2011: the posttranslational modification database
    Florian Gnad
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Nucleic Acids Res 39:D253-60. 2011
    ..The toolkit section contains methods that search for sequence motif matches or identify de novo consensus, sequences from large scale data sets...
  18. pmc Triple SILAC to determine stimulus specific interactions in the Wnt pathway
    Maximiliane Hilger
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    J Proteome Res 11:982-94. 2012
    ..The core destruction complex itself, which regulates beta-catenin stability as the key step in canonical Wnt signaling, remained essentially unchanged...
  19. pmc Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins
    Tamar Geiger
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Mol Cell Proteomics 11:M111.014050. 2012
    ..Together with the accompanying paper (Schaab, C. MCP 2012, PMID: 22301388) (17) these data can be used to obtain reference expression profiles for proteins of interest both within and across cell line proteomes...
  20. pmc A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed
    Jesper V Olsen
    Thermo Fisher Scientific Bremen GmbH, Hanna Kunath Strasse 11, 28199 Bremen, Germany
    Mol Cell Proteomics 8:2759-69. 2009
    ..Higher-collision energy dissociation with high mass accuracy Orbitrap readout is as sensitive as ion trap MS/MS scans in the previous generation of the instrument...
  21. pmc Ultra high resolution linear ion trap Orbitrap mass spectrometer (Orbitrap Elite) facilitates top down LC MS/MS and versatile peptide fragmentation modes
    Annette Michalski
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Mol Cell Proteomics 11:O111.013698. 2012
    ..5 s-increasing protein identifications in complex mixtures by about 30%. The speed of the Orbitrap Elite furthermore allows scan modes in which complementary dissociation mechanisms are routinely obtained of all fragmented peptides...
  22. pmc HOT1 is a mammalian direct telomere repeat-binding protein contributing to telomerase recruitment
    Dennis Kappei
    Medical Systems Biology, Faculty of Medicine Carl Gustav Carus, University Cancer Center, Dresden University of Technology, 01307 Dresden, Germany
    EMBO J 32:1681-701. 2013
    ..Collectively, these findings suggest that HOT1 supports telomerase-dependent telomere elongation...
  23. pmc A Protein Epitope Signature Tag (PrEST) library allows SILAC-based absolute quantification and multiplexed determination of protein copy numbers in cell lines
    Marlis Zeiler
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, D 82152 Martinsried, Germany
    Mol Cell Proteomics 11:O111.009613. 2012
    ..The SILAC-PrEST combination allows accurate and streamlined quantification of the absolute or relative amount of proteins of interest in a wide variety of applications...
  24. pmc Analysis of high accuracy, quantitative proteomics data in the MaxQB database
    Christoph Schaab
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, D 82152 Martinsried, Germany
    Mol Cell Proteomics 11:M111.014068. 2012
    ..The information contained in MaxQB, including high resolution fragment spectra, is accessible to the community via a user-friendly web interface at http://www.biochem.mpg.de/maxqb...
  25. pmc Accurate quantification of more than 4000 mouse tissue proteins reveals minimal proteome changes during aging
    Dirk M Walther
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
    Mol Cell Proteomics 10:M110.004523. 2011
    ..Thus, unexpectedly, our results indicate that aging-related effects on the tissue proteome composition at the bulk level are only minor and that protein homeostasis remains functional up to a relatively high age...
  26. pmc A SILAC-based approach identifies substrates of caspase-dependent cleavage upon TRAIL-induced apoptosis
    Gabriele Stoehr
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Mol Cell Proteomics 12:1436-50. 2013
    ..The technology described here is extensible to a wide range of other proteolytic cleavage events...
  27. pmc Proteomics on an Orbitrap benchtop mass spectrometer using all-ion fragmentation
    Tamar Geiger
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Mol Cell Proteomics 9:2252-61. 2010
    ..AIF on a benchtop orbitrap instrument is therefore an attractive technology for a wide range of proteomics analyses...
  28. pmc Advancing cell biology through proteomics in space and time (PROSPECTS)
    Angus I Lamond
    Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH United Kingdom
    Mol Cell Proteomics 11:O112.017731. 2012
    ....
  29. pmc Proteome-wide analysis of disease-associated SNPs that show allele-specific transcription factor binding
    Falk Butter
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
    PLoS Genet 8:e1002982. 2012
    ..Thus, PWAS may be able to contribute to our understanding of the molecular consequences of human genetic variability underpinning susceptibility to multi-factorial disease...
  30. pmc In-vivo quantitative proteomics reveals a key contribution of post-transcriptional mechanisms to the circadian regulation of liver metabolism
    Maria S Robles
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
    PLoS Genet 10:e1004047. 2014
    ..Our large-scale proteomic analysis reveals thus that circadian post-transcriptional and post-translational mechanisms play a key role in the temporal orchestration of liver metabolism and physiology. ..
  31. pmc Quantitative mass spectrometry and PAR-CLIP to identify RNA-protein interactions
    Marion Scheibe
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    Nucleic Acids Res 40:9897-902. 2012
    ..We report near perfect agreement between the two approaches. Nevertheless, they are non-redundant, and ideally complement each other to map the RNA-protein interaction network...
  32. pmc The human proteome - a scientific opportunity for transforming diagnostics, therapeutics, and healthcare
    Marc Vidal
    University of Michigan, Ann Arbor, MI, USA
    Clin Proteomics 9:6. 2012
    ..This executive summary and the following full report describe the main discussions and outcomes of the workshop...
  33. pmc 1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data
    Juergen Cox
    Department for Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    BMC Bioinformatics 13:S12. 2012
    ..We also describe one-dimensional annotation enrichment, which can be applied to single omics data. The 1D and 2D annotation enrichment algorithms are freely available as part of the Perseus software...
  34. ncbi request reprint The coming age of complete, accurate, and ubiquitous proteomes
    Matthias Mann
    Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
    Mol Cell 49:583-90. 2013
    ..Developments discussed in this Perspective will soon enable complete proteome analysis of mammalian cells, as well, with profound impact on biology and biomedicine...
  35. pmc In-depth proteomic analysis of a mollusc shell: acid-soluble and acid-insoluble matrix of the limpet Lottia gigantea
    Karlheinz Mann
    Abteilung Proteomics und Signaltransduktion, Max Planck Institut fur Biochemie, Am Klopferspitz 18, D 82152, Martinsried, Munich, Germany
    Proteome Sci 10:28. 2012
    ..abstract:..
  36. pmc In-depth analysis of the chicken egg white proteome using an LTQ Orbitrap Velos
    Karlheinz Mann
    Max Planck Institut fur Biochemie, Abteilung Proteomics und Signaltransduktion, Martinsried, Germany
    Proteome Sci 9:7. 2011
    ..abstract:..
  37. pmc Phosphoproteomes of Strongylocentrotus purpuratus shell and tooth matrix: identification of a major acidic sea urchin tooth phosphoprotein, phosphodontin
    Karlheinz Mann
    , Abteilung Proteomics und Signaltransduktion, D 82152 Martinsried, Am Klopferspitz 18, Germany
    Proteome Sci 8:6. 2010
    ..More than half of the detected proteins were not previously identified at the protein level, thus confirming the existence of proteins only known as genomic sequences previously...
  38. pmc PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites
    Florian Gnad
    Department for Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz, D 82152 Martinsried, Germany
    Genome Biol 8:R250. 2007
    ..For each phosphosite, PHOSIDA lists matching kinase motifs, predicted secondary structures, conservation patterns, and its dynamic regulation upon stimulus. Using support vector machines, PHOSIDA also predicts phosphosites...
  39. pmc Identification of 491 proteins in the tear fluid proteome reveals a large number of proteases and protease inhibitors
    Gustavo A De Souza
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej, Odense M, Denmark
    Genome Biol 7:R72. 2006
    ..Little is known about the protein composition of tear fluid but its deregulation is associated with disease states, such as diabetic dry eyes. This makes this body fluid an interesting candidate for in-depth proteomic analysis...
  40. pmc Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system
    Lyris M F de Godoy
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz, 82152 Martinsried, Germany
    Genome Biol 7:R50. 2006
    ..O'Shea, Weissman and co-workers have recently determined the copy number of yeast proteins, making this proteome an excellent model system to study factors affecting coverage...
  41. pmc Large-scale and high-confidence proteomic analysis of human seminal plasma
    Bartosz Pilch
    Center for Experimental Bioinformatics CEBI, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
    Genome Biol 7:R40. 2006
    ..The fluid is essential for the survival of spermatozoa and their successful journey through the female reproductive tract...
  42. pmc The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins
    Jun Adachi
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz, D 82152 Martinsried, Germany
    Genome Biol 7:R80. 2006
    ..Here we applied these methods to the analysis of the human urinary proteome...
  43. pmc Protein abundance profiling of the Escherichia coli cytosol
    Yasushi Ishihama
    Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997 0017, Japan
    BMC Genomics 9:102. 2008
    ..Thus far, protein concentrations have been difficult to measure on a large scale, but proteomic technologies have now advanced to a stage where this information becomes readily accessible...
  44. pmc Precision proteomics: the case for high resolution and high mass accuracy
    Matthias Mann
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Proc Natl Acad Sci U S A 105:18132-8. 2008
    ..Huge challenges and opportunities remain in technology development for proteomics; thus, this is not "the beginning of the end" but surely "the end of the beginning."..
  45. doi request reprint Lysine acetylation targets protein complexes and co-regulates major cellular functions
    Chunaram Choudhary
    Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Science 325:834-40. 2009
    ..Our data demonstrate that the regulatory scope of lysine acetylation is broad and comparable with that of other major posttranslational modifications...
  46. pmc Phosphotyrosine interactome of the ErbB-receptor kinase family
    Waltraud X Schulze
    Department of Biochemistry and Molecular Biology, Center for Experimental Bioinformatics, University of Southern Denmark, Odense, Denmark
    Mol Syst Biol 1:2005.0008. 2005
    ..Our results demonstrate that system-wide mapping of peptide-protein interactions sites is possible, and suggest shared and unique roles of ErbB-receptor family members in downstream signaling...
  47. doi request reprint Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis
    Jesper V Olsen
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried near Munich, Germany
    Sci Signal 3:ra3. 2010
    ..In particular, nuclear proteins and proteins involved in regulating metabolic processes have high phosphorylation site occupancy in mitosis. This suggests that these proteins may be inactivated by phosphorylation in mitotic cells...
  48. doi request reprint Constitutive and dynamic phosphorylation and acetylation sites on NUCKS, a hypermodified nuclear protein, studied by quantitative proteomics
    Jacek R Wisniewski
    Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Proteins 73:710-8. 2008
    ..Of the 243 amino acids, at least 36 can be modified with a total of 57 posttranslational modifications. Thus, NUCKS appears to have the highest ratio of modified to unmodified residues of any protein so far described...
  49. doi request reprint Stable isotope labeling by amino acids in cell culture (SILAC) applied to quantitative proteomics of Bacillus subtilis
    Boumediene Soufi
    Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    J Proteome Res 9:3638-46. 2010
    ....
  50. ncbi request reprint Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser/Thr/Tyr phosphorylation
    Boris Macek
    Max Planck Institut for Biochemistry, Department of Proteomics and Signal Transduction, Am Klopferspitz 18, 82152 Martinsried, Germany
    Mol Cell Proteomics 7:299-307. 2008
    ..Our results establish Ser/Thr/Tyr phosphorylation as a common posttranslational modification in Eubacteria, present since the onset of cellular life...
  51. ncbi request reprint Global, in vivo, and site-specific phosphorylation dynamics in signaling networks
    Jesper V Olsen
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK 5230 Odense, Denmark
    Cell 127:635-48. 2006
    ..The dynamic phosphoproteome provides a missing link in a global, integrative view of cellular regulation...
  52. doi request reprint Quantitative phosphoproteome analysis of a mouse liver cell line reveals specificity of phosphatase inhibitors
    Cuiping Pan
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Proteomics 8:4534-46. 2008
    ..Finally, we devised a triple labeling strategy comprising control cells, stimulated cells, and phosphatase treated cells to derive an upper bound on phosphorylation occupancy...
  53. pmc Large-scale proteomics analysis of the human kinome
    Felix S Oppermann
    Department of Molecular Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
    Mol Cell Proteomics 8:1751-64. 2009
    ..In conclusion, the straightforward experimental procedures described here enable different implementations of kinase-selective proteomics with considerable potential for future signal transduction and kinase drug target analysis...
  54. pmc Unbiased RNA-protein interaction screen by quantitative proteomics
    Falk Butter
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    Proc Natl Acad Sci U S A 106:10626-31. 2009
    ..The 5' region of the mRNA of DGCR-8/Pasha, a component of the microprocessor complex, specifically interacts with components of the translational machinery, suggesting that it contains an internal ribosome entry site...
  55. doi request reprint Site-specific identification of SUMO-2 targets in cells reveals an inverted SUMOylation motif and a hydrophobic cluster SUMOylation motif
    Ivan Matic
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried D 82152, Germany
    Mol Cell 39:641-52. 2010
    ..In 16 proteins we identified a hydrophobic cluster SUMOylation motif (HCSM). SUMO conjugation of RanGAP1 and ZBTB1 via HCSMs is remarkably efficient...
  56. doi request reprint System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation
    Kristoffer T G Rigbolt
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
    Sci Signal 4:rs3. 2011
    ....
  57. ncbi request reprint A novel proteomic screen for peptide-protein interactions
    Waltraud X Schulze
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense
    J Biol Chem 279:10756-64. 2004
    ..Our data are consistent with a change in the role of Sos from Ras-dependent signaling to actin remodeling/endocytic signaling events by a proline-SH3 domain switch...
  58. doi request reprint High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast
    Florian Gnad
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Proteomics 9:4642-52. 2009
    ..We constructed a yeast-specific phosphorylation sites predictor on the basis of a support vector machine, which - together with the yeast phosphorylation data - is integrated into the PHOSIDA database (www.phosida.com)...
  59. ncbi request reprint Solid tumor proteome and phosphoproteome analysis by high resolution mass spectrometry
    Sara Zanivan
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    J Proteome Res 7:5314-26. 2008
    ..Thus, solid tumor can be analyzed by MS-based proteomics with similar efficiency as cell culture models and in amounts compatible with biopsies...
  60. doi request reprint Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast
    Lyris M F de Godoy
    Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Nature 455:1251-4. 2008
    ..Systems-wide, precise quantification directly at the protein level opens up new perspectives in post-genomics and systems biology...
  61. doi request reprint Systems-wide proteomic analysis in mammalian cells reveals conserved, functional protein turnover
    Sidney B Cambridge
    Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Munich Martinsried, Germany
    J Proteome Res 10:5275-84. 2011
    ..Likewise, the members of some protein complexes, such as the proteasome, have highly similar turnover rates. The high species conservation and the low complex variances thus imply great regulatory fine-tuning of protein turnover...
  62. doi request reprint MSQuant, an open source platform for mass spectrometry-based quantitative proteomics
    Peter Mortensen
    Department of Biochemistry and Molecular Biology, University of Southern Denmark, Center for Experimental Bioinformatics, Odense, Campusvej 55, DK 5230 Odense M, Denmark
    J Proteome Res 9:393-403. 2010
    ..g., SILAC and ICAT), termini labels (e.g., (18)O), functional group labels (e.g., mTRAQ), and label-free ion intensity approaches. MSQuant is available, including an installer and supporting scripts, at http://msquant.sourceforge.net ...
  63. doi request reprint Feasibility of large-scale phosphoproteomics with higher energy collisional dissociation fragmentation
    Nagarjuna Nagaraj
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, 82152 Martinsried, Germany
    J Proteome Res 9:6786-94. 2010
    ..We conclude that HCD in the new configuration is now a viable method for large-scale phosphoproteome analysis alongside collisional induced dissociation, (CID) and electron capture/transfer dissociation (ECD/ETD)...
  64. doi request reprint Combined use of RNAi and quantitative proteomics to study gene function in Drosophila
    Tiziana Bonaldi
    Max Planck Institute of Biochemistry, Department of Proteomics and Signal Transduction, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Mol Cell 31:762-72. 2008
    ..We found little overall correlation between changes in the transcriptome and proteome with many protein changes unaccompanied by message changes. However, correlation was high for those mRNAs that changed significantly by microarray...
  65. doi request reprint Peptide separation with immobilized pI strips is an attractive alternative to in-gel protein digestion for proteome analysis
    Nina C Hubner
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Proteomics 8:4862-72. 2008
    ..Advantages of the in-gel format include better reliability and robustness. Considering its superior performance, diminished sample and work-up requirements, peptide IEF will become a method of choice for sample preparation in proteomics...
  66. pmc Beta1 integrin cytoplasmic tyrosines promote skin tumorigenesis independent of their phosphorylation
    Alexander Meves
    Department of Molecular Medicine, Max Planck Institute for Biochemistry, 82152 Martinsried, Germany
    Proc Natl Acad Sci U S A 108:15213-8. 2011
    ..We conclude that a Src/FAK signaling unit inhibits differentiation to promote tumorigenesis downstream of β1 integrin and independent of β1 integrin tyrosine phosphorylation...
  67. pmc Ser/Thr/Tyr protein phosphorylation in the archaeon Halobacterium salinarum--a representative of the third domain of life
    Michalis Aivaliotis
    Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
    PLoS ONE 4:e4777. 2009
    ....
  68. pmc Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
    Mol Syst Biol 8:611. 2012
    ..Our proteomic data set furthermore allows mapping quantitative changes of functional protein classes, enabling novel insights into the biology of colon cancer...
  69. pmc Proteomic investigations reveal a role for RNA processing factor THRAP3 in the DNA damage response
    Petra Beli
    The NNF Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, DK 2200 Copenhagen, Denmark
    Mol Cell 46:212-25. 2012
    ..Moreover, THRAP3 depletion causes cellular hypersensitivity to DNA-damaging agents. Collectively, these data broaden our knowledge of DNA damage signaling networks and highlight an important link between RNA metabolism and DNA repair...
  70. doi request reprint A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics
    Jürgen Cox
    Department for Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Nat Protoc 4:698-705. 2009
    ..The software is freely available at the MaxQuant home page...
  71. ncbi request reprint Tyrosine phosphoproteomics of fibroblast growth factor signaling: a role for insulin receptor substrate-4
    Anders M Hinsby
    Protein Laboratory, Panum Institute 6 1, Blegdamsvej 3C, University of Copenhagen, DK 2200, Denmark
    J Biol Chem 279:46438-47. 2004
    ..Finally, we present evidence for a complex containing insulin receptor substrate-4 and ShcA in signaling by the fibroblast growth factor receptor...
  72. ncbi request reprint A mammalian organelle map by protein correlation profiling
    Leonard J Foster
    Center for Experimental Bioinformatics CEBI, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
    Cell 125:187-99. 2006
    ..Our analysis ties biochemistry, cell biology, and genomics into a common framework for organelle analysis...
  73. pmc A genome-wide screen for genes affecting eisosomes reveals Nce102 function in sphingolipid signaling
    Florian Fröhlich
    Organelle Architecture and Dynamics, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
    J Cell Biol 185:1227-42. 2009
    ..Furthermore, Nce102 inhibits Pkh kinase signaling and is required for plasma membrane organization. Therefore, Nce102 might act as a sensor of sphingolipids that regulates plasma membrane function...
  74. doi request reprint Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics
    Tamar Geiger
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
    Nat Protoc 6:147-57. 2011
    ..It includes the selection and preparation of the spike-in SILAC standard, the sample preparation procedure, and analysis and evaluation of the results...
  75. doi request reprint Caenorhabditis elegans has a phosphoproteome atypical for metazoans that is enriched in developmental and sex determination proteins
    Dorota F Zielinska
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    J Proteome Res 8:4039-49. 2009
    ..Availability of the C. elegans phosphoproteome should add a novel dimension to functional data obtained by genetic screens in this organism...
  76. doi request reprint β1- and αv-class integrins cooperate to regulate myosin II during rigidity sensing of fibronectin-based microenvironments
    Herbert B Schiller
    Department of Molecular Medicine, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
    Nat Cell Biol 15:625-36. 2013
    ....
  77. doi request reprint Proteome, phosphoproteome, and N-glycoproteome are quantitatively preserved in formalin-fixed paraffin-embedded tissue and analyzable by high-resolution mass spectrometry
    Paweł Ostasiewicz
    Department for Proteomics and Signal Transduction at Max Planck Institute for Biochemistry, 82152 Martinsried, Germany
    J Proteome Res 9:3688-700. 2010
    ..Thus, FFPE biobank material can be analyzed by quantitative proteomics at the level of proteins and post-translational modifications...
  78. doi request reprint Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers
    Michiel Vermeulen
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, D 82152 Martinsried, Germany
    Cell 142:967-80. 2010
    ..Our data reveal a highly adapted interplay between chromatin marks and their associated protein complexes. Reading specific trimethyl-lysine sites by specialized complexes appears to be a widespread mechanism to mediate gene expression...
  79. doi request reprint Andromeda: a peptide search engine integrated into the MaxQuant environment
    Jürgen Cox
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    J Proteome Res 10:1794-805. 2011
    ..We demonstrate the flexibility of the system by implementing the capability to identify cofragmented peptides, significantly improving the total number of identified peptides...
  80. doi request reprint Mapping N-glycosylation sites across seven evolutionarily distant species reveals a divergent substrate proteome despite a common core machinery
    Dorota F Zielinska
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
    Mol Cell 46:542-8. 2012
    ..Many N-glycosylated proteins coevolved with the rise of extracellular processes that are specific within corresponding phylogenetic groups and essential for organismal development, body growth, and organ formation...
  81. doi request reprint A map of general and specialized chromatin readers in mouse tissues generated by label-free interaction proteomics
    H Christian Eberl
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Mol Cell 49:368-78. 2013
    ..Apart from defining the chromatin interaction landscape in mouse tissues, our workflow can be used for peptides with different modifications and cell types of any organism...
  82. ncbi request reprint Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway
    Albrecht Gruhler
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Campusvej 55, DK 5230 Odense M, Denmark
    Mol Cell Proteomics 4:310-27. 2005
    ....
  83. doi request reprint Brain phosphoproteome obtained by a FASP-based method reveals plasma membrane protein topology
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, Martinsried near Munich, Germany
    J Proteome Res 9:3280-9. 2010
    ..Together with the glycosylation sites from a recent large-scale study, they can confirm or correct predicted membrane topologies of these proteins, as we show for the examples calcium channels and glutamate receptors...
  84. ncbi request reprint How much peptide sequence information is contained in ion trap tandem mass spectra?
    Jürgen Cox
    Department for Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    J Am Soc Mass Spectrom 19:1813-20. 2008
    ..Thus, optimal de novo sequencing algorithms should be able to obtain substantial sequence information in at least half of all cases...
  85. doi request reprint High performance computational analysis of large-scale proteome data sets to assess incremental contribution to coverage of the human genome
    Nadin Neuhauser
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    J Proteome Res 12:2858-68. 2013
    ..We apply our high performance platform to investigate incremental coverage of the human proteome by high resolution MS data originating from in-depth cell line and cancer tissue proteome measurements...
  86. ncbi request reprint Identifying and quantifying in vivo methylation sites by heavy methyl SILAC
    Shao En Ong
    Center for Experimental Bioinformatics, University of Southern Denmark, Odense M 5230, Denmark
    Nat Methods 1:119-26. 2004
    ....
  87. ncbi request reprint Mass spectrometric mapping of linker histone H1 variants reveals multiple acetylations, methylations, and phosphorylation as well as differences between cell culture and tissue
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, D 82152 Martinsried, Germany
    Mol Cell Proteomics 6:72-87. 2007
    ..For example, whereas methylation sites are frequent in tissues, this type of modification was much less abundant in cultured cells and escaped detection. Our study significantly extends the known spectrum of linker histone variability...
  88. doi request reprint Proteome differences between brown and white fat mitochondria reveal specialized metabolic functions
    Francesca Forner
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, 82152 Martinsried, Germany
    Cell Metab 10:324-35. 2009
    ..In vivo comparison of organellar proteomes can thus directly address functional questions in metabolism...
  89. doi request reprint Mislocalized activation of oncogenic RTKs switches downstream signaling outcomes
    Chunaram Choudhary
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Mol Cell 36:326-39. 2009
    ..Thus, intracellular activation of RTKs by oncogenic mutations in the biosynthetic route may exploit cellular architecture to initiate aberrant signaling cascades, thus evading negative regulation...
  90. ncbi request reprint In vivo SILAC-based proteomics reveals phosphoproteome changes during mouse skin carcinogenesis
    Sara Zanivan
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    Cell Rep 3:552-66. 2013
    ..This detailed molecular picture, both at the proteome and phosphoproteome level, will prove useful for the study of mechanisms of tumor progression...
  91. pmc Comparative proteomics of two life cycle stages of stable isotope-labeled Trypanosoma brucei reveals novel components of the parasite's host adaptation machinery
    Falk Butter
    Department of Proteomics, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    Mol Cell Proteomics 12:172-9. 2013
    ..A DEAD-box RNA helicase, which is highly up-regulated in the bloodstream form of this parasite and which is essential for viability and proper cell cycle progression in this stage is described as an example...
  92. pmc Integrin-linked kinase controls microtubule dynamics required for plasma membrane targeting of caveolae
    Sara A Wickström
    Department of Molecular Medicine, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    Dev Cell 19:574-88. 2010
    ..Our results assign an important role to the integrin/ILK complex for caveolar trafficking to the cell surface...
  93. doi request reprint Differential substrate specificity of group I and group II chaperonins in the archaeon Methanosarcina mazei
    Angela M Hirtreiter
    Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Mol Microbiol 74:1152-68. 2009
    ..Thus, the group II chaperonins may have facilitated the evolution of the highly complex proteomes characteristic of eukaryotic cells...
  94. doi request reprint Comparison of ultrafiltration units for proteomic and N-glycoproteomic analysis by the filter-aided sample preparation method
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, D 82152 Martinsried, Germany
    Anal Biochem 410:307-9. 2011
    ..The use of filters with these relatively large cutoffs facilitates depletion of detergents...
  95. ncbi request reprint Stable isotope labeling of Arabidopsis thaliana cells and quantitative proteomics by mass spectrometry
    Albrecht Gruhler
    Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
    Mol Cell Proteomics 4:1697-709. 2005
    ....
  96. ncbi request reprint A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling
    Blagoy Blagoev
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
    Nat Biotechnol 21:315-8. 2003
    ..SILAC combined with modification-based affinity purification is a useful approach to detect specific and functional protein-protein interactions...
  97. ncbi request reprint Inhibition of adipocyte differentiation by resistin-like molecule alpha. Biochemical characterization of its oligomeric nature
    Blagoy Blagoev
    Center for Experimental Bioinformatics, University of Southern Denmark, Odense M DK 5230, Denmark
    J Biol Chem 277:42011-6. 2002
    ..Since RELMalpha is expressed by adipose tissue and it is a secreted factor, our findings suggest that RELMalpha may be involved in the control of the adipogenesis as well as in the process of muscle differentiation...
  98. pmc Investigation of protein-tyrosine phosphatase 1B function by quantitative proteomics
    Philipp Mertins
    Department of Molecular Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    Mol Cell Proteomics 7:1763-77. 2008
    ..Importantly the MS-based strategies described here are entirely generic and can be used to address the poorly understood aspects of cellular PTP function...
  99. pmc A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements
    Gerhard Mittler
    Center for Experimental Bioinformatics, University of Southern Denmark, DK 5230 Odense M, Denmark
    Genome Res 19:284-93. 2009
    ..The approach is robust, sensitive, and specific and offers the potential for high-throughput determination of TF binding profiles...
  100. ncbi request reprint Quantitative proteomic profiling of membrane proteins from the mouse brain cortex, hippocampus, and cerebellum using the HysTag reagent: mapping of neurotransmitter receptors and ion channels
    Jesper V Olsen
    Center for Experimental Bioinformatics CEBI, University of Southern Denmark, Denmark
    Brain Res 1134:95-106. 2007
    ....