Matthias Mann

Summary

Affiliation: University of Southern Denmark
Country: Denmark

Publications

  1. ncbi request reprint Use of mass spectrometry-derived data to annotate nucleotide and protein sequence databases
    M Mann
    Protein Interaction Laboratory PIL, Center for Experimental Bioinformatics, University of Southern Denmark, Campusvej 55, DK 5230, and MDS Protana, Staermosegaardsvej 6, DK 5230, Odense M, Denmark
    Trends Biochem Sci 26:54-61. 2001
  2. 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
  3. 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
  4. ncbi request reprint Proteomic mapping of brain plasma membrane proteins
    Peter Aa Nielsen
    MDS Inc Denmark, 5230 Odense M, Denmark
    Mol Cell Proteomics 4:402-8. 2005
  5. ncbi request reprint Nucleolar proteome dynamics
    Jens S Andersen
    Department of Biochemistry and Molecular Biology, Campusvej 55, DK 5230 Odense M, Denmark
    Nature 433:77-83. 2005
  6. pmc Cloning of a novel signaling molecule, AMSH-2, that potentiates transforming growth factor beta signaling
    Nieves Ibarrola
    McKusick Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
    BMC Cell Biol 5:2. 2004
  7. ncbi request reprint Analysis of proteins and proteomes by mass spectrometry
    M Mann
    Protein Interaction Laboratory and Center for Experimental BioInformatics CEBI, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
    Annu Rev Biochem 70:437-73. 2001
  8. ncbi request reprint Proteomic analysis of post-translational modifications
    Matthias Mann
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M, DK 5230 Denmark
    Nat Biotechnol 21:255-61. 2003
  9. pmc Is mass spectrometry ready for proteome-wide protein expression analysis?
    Juri Rappsilber
    Protein Interaction Laboratory in the Center of Experimental Bioinformatics, Department of Biochemistry, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
    Genome Biol 3:COMMENT2008. 2002
  10. ncbi request reprint Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome
    Matthias Mann
    Center for Experimental Bioinformatics, University of Southern Denmark, M, DK 5230, Odense, Denmark
    Trends Biotechnol 20:261-8. 2002

Collaborators

Detail Information

Publications94

  1. ncbi request reprint Use of mass spectrometry-derived data to annotate nucleotide and protein sequence databases
    M Mann
    Protein Interaction Laboratory PIL, Center for Experimental Bioinformatics, University of Southern Denmark, Campusvej 55, DK 5230, and MDS Protana, Staermosegaardsvej 6, DK 5230, Odense M, Denmark
    Trends Biochem Sci 26:54-61. 2001
    ....
  2. 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...
  3. 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...
  4. ncbi request reprint Proteomic mapping of brain plasma membrane proteins
    Peter Aa Nielsen
    MDS Inc Denmark, 5230 Odense M, Denmark
    Mol Cell Proteomics 4:402-8. 2005
    ..Our work now allows in-depth study of brain membrane proteomes, such as of mouse models of neurological disease...
  5. ncbi request reprint Nucleolar proteome dynamics
    Jens S Andersen
    Department of Biochemistry and Molecular Biology, Campusvej 55, DK 5230 Odense M, Denmark
    Nature 433:77-83. 2005
    ....
  6. pmc Cloning of a novel signaling molecule, AMSH-2, that potentiates transforming growth factor beta signaling
    Nieves Ibarrola
    McKusick Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
    BMC Cell Biol 5:2. 2004
    ..Signaling by these factors is mediated chiefly by the Smad family of latent transcription factors...
  7. ncbi request reprint Analysis of proteins and proteomes by mass spectrometry
    M Mann
    Protein Interaction Laboratory and Center for Experimental BioInformatics CEBI, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
    Annu Rev Biochem 70:437-73. 2001
    ..By these and similar strategies, entire protein complexes, signaling pathways, and whole organelles are being characterized. Posttranslational modifications remain difficult to analyze but are starting to yield to generic strategies...
  8. ncbi request reprint Proteomic analysis of post-translational modifications
    Matthias Mann
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M, DK 5230 Denmark
    Nat Biotechnol 21:255-61. 2003
    ..Finally, stable isotope labeling strategies in combination with mass spectrometry have been applied successfully to study the dynamics of modifications...
  9. pmc Is mass spectrometry ready for proteome-wide protein expression analysis?
    Juri Rappsilber
    Protein Interaction Laboratory in the Center of Experimental Bioinformatics, Department of Biochemistry, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
    Genome Biol 3:COMMENT2008. 2002
    ..Recent advances in mass spectrometry will soon allow routine analysis of protein expression levels. How close are we to true quantitative proteomics?..
  10. ncbi request reprint Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome
    Matthias Mann
    Center for Experimental Bioinformatics, University of Southern Denmark, M, DK 5230, Odense, Denmark
    Trends Biotechnol 20:261-8. 2002
    ..In this article, we outline several methods for enrichment of phosphorylated proteins and peptides and discuss various options for their identification and quantitation with special emphasis on mass spectrometry-based techniques...
  11. 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...
  12. 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...
  13. 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...
  14. 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
    ....
  15. 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
    ....
  16. 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
    ....
  17. 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...
  18. 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
    ....
  19. 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 ...
  20. ncbi request reprint Mechanism of divergent growth factor effects in mesenchymal stem cell differentiation
    Irina Kratchmarova
    Center for Experimental Bioinformatics CEBI, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
    Science 308:1472-7. 2005
    ..Thus, quantitative proteomics can directly compare entire signaling networks and discover critical differences capable of changing cell fate...
  21. ncbi request reprint A mass spectrometry-based proteomic approach for identification of serine/threonine-phosphorylated proteins by enrichment with phospho-specific antibodies: identification of a novel protein, Frigg, as a protein kinase A substrate
    Mads Grønborg
    Department of Biochemistry and Molecular Biology, Center for Experimental Bioinformatics, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
    Mol Cell Proteomics 1:517-27. 2002
    ..Our method should be applicable as a generic strategy for enrichment and identification of serine/threonine-phosphorylated substrates in signal transduction pathways...
  22. ncbi request reprint Tyrosine phosphorylation mapping of the epidermal growth factor receptor signaling pathway
    Hanno Steen
    Protein Interaction Laboratory, Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
    J Biol Chem 277:1031-9. 2002
    ..Because of its sensitivity and selectivity, this approach will be useful in proteomic approaches to study tyrosine phosphorylation in a number of signal transduction pathways...
  23. 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
    ....
  24. ncbi request reprint Properties of 13C-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC)
    Shao En Ong
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
    J Proteome Res 2:173-81. 2003
    ....
  25. ncbi request reprint Trypsin cleaves exclusively C-terminal to arginine and lysine residues
    Jesper V Olsen
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
    Mol Cell Proteomics 3:608-14. 2004
    ..Our results indicate that such peptide hits in previous studies should be re-examined and that peptide identification should be based on strict trypsin specificity...
  26. ncbi request reprint Insulin-dependent interactions of proteins with GLUT4 revealed through stable isotope labeling by amino acids in cell culture (SILAC)
    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
    J Proteome Res 5:64-75. 2006
    ....
  27. ncbi request reprint Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
    Shao En Ong
    Protein Interaction Laboratory, University of Southern Denmark, Odense, Denmark
    Mol Cell Proteomics 1:376-86. 2002
    ..SILAC is a simple, inexpensive, and accurate procedure that can be used as a quantitative proteomic approach in any cell culture system...
  28. ncbi request reprint Signaling initiated by overexpression of the fibroblast growth factor receptor-1 investigated by mass spectrometry
    Anders M Hinsby
    MDS Proteomics A S, Staermosegaardsvej 6, Odense DK 5230, Denmark
    Mol Cell Proteomics 2:29-36. 2003
    ....
  29. 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...
  30. ncbi request reprint Quantitative proteomics to study mitogen-activated protein kinases
    Blagoy Blagoev
    Center for Experimental Bioinformatics CEBI, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
    Methods 40:243-50. 2006
    ..In this chapter, we describe in detail the SILAC labeling procedure and explain how to design SILAC experiments to examine the level and duration of phosphorylation of endogenous MAP kinases and their substrates in cell culture systems...
  31. ncbi request reprint HysTag--a novel proteomic quantification tool applied to differential display analysis of membrane proteins from distinct areas of mouse brain
    Jesper V Olsen
    MDS Proteomics A S, Staermosegårdsvej 6, DK 5230 Odense M, Denmark
    Mol Cell Proteomics 3:82-92. 2004
    ....
  32. pmc Organellar proteomics: turning inventories into insights
    Jens S Andersen
    Centre for Experimental Bioinformatics, CEBI, University of Southern Denmark, Campusvej 55, DK 5230 Odense, Denmark
    EMBO Rep 7:874-9. 2006
    ..Here, we review the emerging trends in this rapidly expanding area and discuss the role of organellar proteomics in the context of functional genomics and systems biology...
  33. pmc Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation
    Jesper V Olsen
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
    Proc Natl Acad Sci U S A 101:13417-22. 2004
    ..When MS(3) is performed on the linear ion trap-Fourier transform mass spectrometer combination, accurate peptide masses further increase confidence in peptide identification...
  34. ncbi request reprint Phosphotyrosine mapping in Bcr/Abl oncoprotein using phosphotyrosine-specific immonium ion scanning
    Hanno Steen
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
    Mol Cell Proteomics 2:138-45. 2003
    ..This study shows the power of phosphotyrosine-specific immonium ion scanning for sensitive phosphotyrosine mapping when limited amounts of samples are available...
  35. ncbi request reprint Modular stop and go extraction tips with stacked disks for parallel and multidimensional Peptide fractionation in proteomics
    Yasushi Ishihama
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
    J Proteome Res 5:988-94. 2006
    ..This approach is suitable for high throughput protein identification for moderately complex, low abundance samples using automated nanoelectrospray-MS/MS or MALDI-MS...
  36. ncbi request reprint Quantitative proteomic assessment of very early cellular signaling events
    Joern Dengjel
    Center of Experimental BioInformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Campusvej 55, DK 5230, Odense, Denmark
    Nat Biotechnol 25:566-8. 2007
    ....
  37. ncbi request reprint Cloning and characterization of PAK5, a novel member of mammalian p21-activated kinase-II subfamily that is predominantly expressed in brain
    Akhilesh Pandey
    Center for Experimental Bioinformatics, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
    Oncogene 21:3939-48. 2002
    ..The expression pattern of PAK5 is distinct from that of PAK4 and PAK6, suggesting a functional division among PAK-II subfamily kinases based on differential tissue distribution...
  38. ncbi request reprint RNA and RNA binding proteins participate in early stages of cell spreading through spreading initiation centers
    Carmen L de Hoog
    Center for Experimental Bioinformatics CEBI, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
    Cell 117:649-62. 2004
    ..Spreading initiation centers are ribonucleoprotein complexes distinct from focal adhesions and demonstrate a role for RNA and RNA binding proteins in the initiation of cell spreading...
  39. ncbi request reprint Mass spectrometric-based approaches in quantitative proteomics
    Shao En Ong
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, M 5230 Odense, Denmark
    Methods 29:124-30. 2003
    ..The emerging nature of these techniques and the rapid pace of technological development make forecasting the directions of the field difficult but we speculate that SILAC will soon be a key tool of quantitative proteomics...
  40. ncbi request reprint Computational and experimental analysis reveals a novel Src family kinase in the C. elegans genome
    Akhilesh Pandey
    Center for Experimental Bioinformatics, University of Southern Denmark, Odense M, DK 5230, Denmark
    Bioinformatics 19:169-72. 2003
    ..However, the vast majority of annotated genes are derived by gene prediction methods. It is important to not only validate the predicted coding regions but also to identify genes that may have been missed by these programs...
  41. ncbi request reprint Proteomic characterization of the human centrosome by protein correlation profiling
    Jens S Andersen
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
    Nature 426:570-4. 2003
    ..Protein correlation profiling permits the analysis of any multiprotein complex that can be enriched by fractionation but not purified to homogeneity...
  42. pmc Large-scale proteomic analysis of the human spliceosome
    Juri Rappsilber
    Protein Interaction Laboratory in the Center of Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK 5230 Odense M, Denmark
    Genome Res 12:1231-45. 2002
    ..This investigation provides the most detailed inventory of human spliceosome-associated factors to date, and the data indicate a number of interesting links coordinating splicing with other steps in the gene expression pathway...
  43. ncbi request reprint Microcolumns with self-assembled particle frits for proteomics
    Yasushi Ishihama
    Protein Interaction Laboratory in the Center of Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
    J Chromatogr A 979:233-9. 2002
    ..We also describe application of the SAP principle to make disposable pipette tip columns with short pieces of fused-silica capillary as the outlet...
  44. ncbi request reprint Proteomics
    Carmen L de Hoog
    Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK 5230 Odense M, Denmark
    Annu Rev Genomics Hum Genet 5:267-93. 2004
    ..Researchers are also beginning to integrate large-scale data sets from various "omics" disciplines in targeted investigations of specific biomedical areas and in pursuit of a general framework for systems biology...
  45. ncbi request reprint Peptide end sequencing by orthogonal MALDI tandem mass spectrometry
    Michael L Nielsen
    MDS Proteomics A S, Staermosegaardsvej 6, DK 5230 Odense M, Denmark
    J Proteome Res 1:63-71. 2002
    ..Given mass accuracy in the low ppm range, peptide end sequencing on one or two tryptic peptides is sufficient to uniquely identify a protein from gel samples in the low silver-stained range...
  46. pmc Unbiased quantitative proteomics of lipid rafts reveals high specificity for signaling factors
    Leonard J Foster
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
    Proc Natl Acad Sci U S A 100:5813-8. 2003
    ..Our results provide the first large-scale and unbiased evidence, to our knowledge, for the connection of rafts with signaling and place limits on the fraction of plasma membrane composed by rafts...
  47. ncbi request reprint Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics
    Juri Rappsilber
    Center of Experimental BioInformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
    Anal Chem 75:663-70. 2003
    ..Five femtomole of tryptic BSA digest could be recovered quantitatively. We have found that the Stage system is well-suited as a universal sample preparation system for proteomics...
  48. ncbi request reprint Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap
    Jesper V Olsen
    Center for Experimental Bioinformatics CEBI, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
    Mol Cell Proteomics 4:2010-21. 2005
    ..High and routine mass accuracy in a compact instrument will dramatically improve certainty of peptide and small molecule identification...
  49. ncbi request reprint Detection of arginine dimethylated peptides by parallel precursor ion scanning mass spectrometry in positive ion mode
    Juri Rappsilber
    Center for Experimental Bioinformatics and Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK 5230 Odense M, Denmark
    Anal Chem 75:3107-14. 2003
    ..The parallel monitoring of fragments in precursor ion scans is a versatile tool to specify the nature of protein modifications in cases where a single fragment is not conclusive...
  50. ncbi request reprint Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
    Yuen Ho
    MDS Proteomics, 251 Attwell Drive, Toronto, Canada M9W 7H4, and Staermosegaardsvej 6, DK 5230 Odense M, Denmark
    Nature 415:180-3. 2002
    ..Given the high degree of connectivity observed in this study, even partial HMS-PCI coverage of complex proteomes, including that of humans, should allow comprehensive identification of cellular networks...
  51. ncbi request reprint A proteomic approach for identification of secreted proteins during the differentiation of 3T3-L1 preadipocytes to adipocytes
    Irina Kratchmarova
    Center for Experimental Bioinformatics, University of Southern Denmark, Odense M, DK 5230 Denmark
    Mol Cell Proteomics 1:213-22. 2002
    ..To our knowledge, this is the first study to identify several novel secreted proteins by adipocytes by a proteomic approach using mass spectrometry...
  52. ncbi request reprint A new derivatization strategy for the analysis of phosphopeptides by precursor ion scanning in positive ion mode
    Hanno Steen
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense
    J Am Soc Mass Spectrom 13:996-1003. 2002
    ....
  53. 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...
  54. ncbi request reprint What does it mean to identify a protein in proteomics?
    Juri Rappsilber
    Protein Interaction Laboratory, Center of Experimental BioInformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 M Odense, Denmark
    Trends Biochem Sci 27:74-8. 2002
    ..As the common denominator of all the isoforms is a gene, in our opinion, it would be more accurate to state that a product of this particular gene rather than a certain protein has been identified by mass spectrometry...
  55. pmc Actin homolog MreB and RNA polymerase interact and are both required for chromosome segregation in Escherichia coli
    Thomas Kruse
    Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, DK 5230 Odense M, Denmark
    Genes Dev 20:113-24. 2006
    ..Thus, our results raise the possibility that the MreB-RNAP interaction is functionally important for chromosome segregation...
  56. ncbi request reprint Directed proteomic analysis of the human nucleolus
    Jens S Andersen
    Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230, Odense M, Denmark
    Curr Biol 12:1-11. 2002
    ..Recent studies suggest it may also have roles in RNA transport, RNA modification, and cell cycle regulation. Despite over 150 years of research into nucleoli, many aspects of their structure and function remain uncharacterized...
  57. doi request reprint PhosphoSiteAnalyzer: a bioinformatic platform for deciphering phospho proteomes using kinase predictions retrieved from NetworKIN
    Martin V Bennetzen
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Campusvej 55, DK 5230 Odense M, Denmark
    J Proteome Res 11:3480-6. 2012
    ..The interface of the software provides a high degree of analytical flexibility and is designed to be intuitive for most users. PhosphoSiteAnalyzer is a freeware program available at http://phosphosite.sourceforge.net . ..
  58. 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...
  59. ncbi request reprint A proteomic fingerprint of dissolved organic carbon and of soil particles
    Waltraud X Schulze
    Center for Experimental Bioinformatics CEBI, Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
    Oecologia 142:335-43. 2005
    ..These results demonstrate a novel application of proteomics to obtain a "proteomic fingerprint" of presence and activity of organisms in an ecosystem...
  60. ncbi request reprint Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry
    Edwin Lasonder
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
    Nature 419:537-42. 2002
    ..We also report a set of peptides with significant matches in the parasite genome but not in the protein set predicted by computational methods...
  61. ncbi request reprint Analysis of bromotryptophan and hydroxyproline modifications by high-resolution, high-accuracy precursor ion scanning utilizing fragment ions with mass-deficient mass tags
    Hanno Steen
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
    Anal Chem 74:6230-6. 2002
    ..This lead to the characterization of one novel C. textile conotoxin containing a bromotryptophan residue and one novel C. textile conotoxin carrying two hydroxyproline residues...
  62. ncbi request reprint Identifying proteins and post-translational modifications by mass spectrometry
    B Kuster
    Center for Experimental Bioinformatics, Odense University, Denmark
    Curr Opin Struct Biol 8:393-400. 1998
    ..Mass spectrometry vastly outperforms traditional sequencing technologies and thereby greatly facilitates the elucidation of the functions of individual proteins as well as multiprotein complexes and larger protein assemblages...
  63. ncbi request reprint Mass spectrometry allows direct identification of proteins in large genomes
    B Kuster
    Protein Interaction Laboratory PIL, University of Southern Denmark, Odense M, Denmark MDS Proteomics, Odense M, Denmark
    Proteomics 1:641-50. 2001
    ..Several novel proteins from Arabidopsis thaliana and human have been discovered in this way...
  64. ncbi request reprint Top-down quantitation and characterization of SILAC-labeled proteins
    Leonie F Waanders
    Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    J Am Soc Mass Spectrom 18:2058-64. 2007
    ..The quantized mass offset between fragments provided information about the number of labeled residues in the fragments, thereby simplifying protein identification and characterization...
  65. ncbi request reprint Stable isotope labeling by amino acids in cell culture for quantitative proteomics
    Shao En Ong
    Proteomics and Biomarker Discovery, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
    Methods Mol Biol 359:37-52. 2007
    ..In this chapter, we provide detailed SILAC protocols and explain how to incorporate SILAC into any experiment...
  66. 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...
  67. 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...
  68. doi request reprint Human Proteinpedia enables sharing of human protein data
    Suresh Mathivanan
    Nat Biotechnol 26:164-7. 2008
  69. pmc Dissection of the insulin signaling pathway via quantitative phosphoproteomics
    Marcus Kruger
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
    Proc Natl Acad Sci U S A 105:2451-6. 2008
    ..The combination of quantitative phosphoproteomics with cell culture models provides a powerful strategy to dissect the insulin signaling pathways in intact cells...
  70. doi request reprint Identifying and quantifying sites of protein methylation by heavy methyl SILAC
    Shao En Ong
    The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Curr Protoc Protein Sci . 2006
    ..Cells incorporate this 'heavy' methyl group throughout their methylated substrates. This technique increases confidence in identifying and quantifying of sites of protein methylation...
  71. doi request reprint Phosphorylation of the human full-length protein kinase Ciota
    Boris Macek
    Abteilung Proteomics and Signaltransduktion, Max Planck Institut fur Biochemie, Am Klopferspitz 18, 82152 Martinsried, Germany
    J Proteome Res 7:2928-35. 2008
    ..The most interesting new phosphorylation site was detected in a well-accessible loop of the PB1 domain (pSer35/pSer37) and may be involved in the interactions of the PB1 domain with different partners in the relevant signaling pathways...
  72. doi request reprint High confidence determination of specific protein-protein interactions using quantitative mass spectrometry
    Michiel Vermeulen
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    Curr Opin Biotechnol 19:331-7. 2008
    ..This principle is revolutionizing the protein interaction field as demonstrated by recent applications in fields as diverse as tyrosine signaling pathways, cell adhesion, and chromatin biology...
  73. doi request reprint Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle
    Henrik Daub
    Cell Signaling Group, Department of Molecular Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    Mol Cell 31:438-48. 2008
    ..These results provide a vastly extended knowledge base for functional studies on kinases and their regulation through site-specific phosphorylation...
  74. 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...
  75. pmc Axin-mediated CKI phosphorylation of beta-catenin at Ser 45: a molecular switch for the Wnt pathway
    Sharon Amit
    The Lautenberg Center for Immunology, The Hebrew University Hadassah Medical School, Jerusalem 91120, Israel
    Genes Dev 16:1066-76. 2002
    ..Wnt3A signaling and Dvl overexpression suppress S45 phosphorylation, thereby precluding the initiation of the cascade. Thus, a single, CKI-dependent phosphorylation event serves as a molecular switch for the Wnt pathway...
  76. pmc Pseudosubstrate regulation of the SCF(beta-TrCP) ubiquitin ligase by hnRNP-U
    Matti Davis
    The Lautenberg Center for Immunology, The Hebrew University Hadassah Medical School, Jerusalem 91120, Israel
    Genes Dev 16:439-51. 2002
    ..Our study points to a novel regulatory mechanism, which secures the localization, stability, substrate binding threshold, and efficacy of a specific protein-ubiquitin ligase...
  77. ncbi request reprint Differential expression profiling of membrane proteins by quantitative proteomics in a human mesenchymal stem cell line undergoing osteoblast differentiation
    Leonard J Foster
    UBC Center for Proteomics, Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
    Stem Cells 23:1367-77. 2005
    ..In conclusion, MS-based proteomics can reveal novel markers for MSCs that can be used for their isolation and for monitoring OB differentiation...
  78. ncbi request reprint A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC)
    Shao En Ong
    The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Protoc 1:2650-60. 2006
    ..This procedure can be completed in 8 days...
  79. ncbi request reprint Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein
    Yasushi Ishihama
    Laboratory of Seeds Finding Technology LSFT, Eisai Co, Ltd, 5 1 3 Tokodai, Tsukuba, Ibaraki 300 2635, Japan
    Mol Cell Proteomics 4:1265-72. 2005
    ..The values of emPAI are easily calculated and add important quantitation information to proteomic experiments; therefore we suggest that they should be reported in large scale proteomic identification projects...
  80. ncbi request reprint [From genome to proteome--aim of human proteomics]
    Kazuyuki Nakamura
    Department of Biochemistry and Biomolecular Recognition, Fatulty of Medicine, Yamaguchi University, 1 1 1 Minami kogushi, Ube, Yamaguchi 755 8505, Japan
    Seikagaku 76:1271-4. 2004
  81. ncbi request reprint Top-down protein sequencing and MS3 on a hybrid linear quadrupole ion trap-orbitrap mass spectrometer
    Boris Macek
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    Mol Cell Proteomics 5:949-58. 2006
    ..Given the ready availability and ease of operation of the LTQ-Orbitrap, it may have significant impact on top-down proteomics...
  82. 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...
  83. ncbi request reprint In-depth analysis of the membrane and cytosolic proteome of red blood cells
    Erica M Pasini
    Department of Proteomics and Signal Transduction, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Blood 108:791-801. 2006
    ..Our data reveal unexpected complexity of the RBC proteome, provide a wealth of data on its composition, shed light on several open issues in RBC biology, and form a departure point for comprehensive understanding of RBC functions...
  84. ncbi request reprint Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics
    Blagoy Blagoev
    Nat Biotechnol 22:1139-45. 2004
    ..Global activation profiles provide an informative perspective on cell signaling and will be crucial to modeling signaling networks in a systems biology approach...
  85. 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...
  86. ncbi request reprint Mass spectrometry-based proteomics
    Ruedi Aebersold
    Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103 8904, USA
    Nature 422:198-207. 2003
    ..The ability of mass spectrometry to identify and, increasingly, to precisely quantify thousands of proteins from complex samples can be expected to impact broadly on biology and medicine...
  87. ncbi request reprint Distinct and overlapping sets of SUMO-1 and SUMO-2 target proteins revealed by quantitative proteomics
    Alfred C O Vertegaal
    Department of Molecular Cell Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
    Mol Cell Proteomics 5:2298-310. 2006
    ....
  88. 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...
  89. ncbi request reprint From genomics to proteomics
    Mike Tyers
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, and Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Canada M5G 1X5
    Nature 422:193-7. 2003
    ..But further technological improvements, organization of international proteomics projects and open access to results are needed for proteomics to fulfil its potential...
  90. 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...
  91. 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
    ....
  92. ncbi request reprint Analysis of tyrosine phosphorylation sites in signaling molecules by a phosphotyrosine-specific immonium ion scanning method
    Hanno Steen
    Harvard Medical School, Department of Cell Biology, 240 Longwood Avenue, Boston, MA 02115, USA
    Sci STKE 2002:pl16. 2002
    ..Because of its simplicity and specificity, PSI scanning is likely to become an important tool in proteomic studies of pathways involving tyrosine phosphorylation...
  93. ncbi request reprint The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis
    Boris Macek
    Max Planck Institute for Biochemistry, Proteomics, and Signal Transduction, Am Klopferspitz 18a, D 82152 Martinsried, Germany
    Mol Cell Proteomics 6:697-707. 2007
    ....
  94. ncbi request reprint Stable isotope labeling by amino acids in cell culture (SILAC) and proteome quantitation of mouse embryonic stem cells to a depth of 5,111 proteins
    Johannes Graumann
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    Mol Cell Proteomics 7:672-83. 2008
    ..We compared the proteome with a recently published map of chromatin states of promoters in ES cells and found excellent correlation between protein expression and the presence of active and repressive chromatin marks...