Research Topics
Genomes and Genes
| Matthias MannSummaryAffiliation: University of Southern Denmark Country: Denmark Publications
| Collaborators
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Detail Information
Publications
Use of mass spectrometry-derived data to annotate nucleotide and protein sequence databasesM 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....- Global, in vivo, and site-specific phosphorylation dynamics in signaling networksJesper 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... 
Phosphotyrosine interactome of the ErbB-receptor kinase familyWaltraud 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...- Proteomic mapping of brain plasma membrane proteinsPeter 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... - Nucleolar proteome dynamicsJens S Andersen
Department of Biochemistry and Molecular Biology, Campusvej 55, DK-5230 Odense M, Denmark
Nature 433:77-83. 2005.... - Cloning of a novel signaling molecule, AMSH-2, that potentiates transforming growth factor beta signalingNieves 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... - Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteomeMatthias 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... - Proteomic analysis of post-translational modificationsMatthias 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... - 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?.. - Analysis of proteins and proteomes by mass spectrometryM 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... - A novel proteomic screen for peptide-protein interactionsWaltraud 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... 
System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiationKristoffer 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....- Inhibition of adipocyte differentiation by resistin-like molecule alpha. Biochemical characterization of its oligomeric natureBlagoy 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... - A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signalingBlagoy 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... - A mammalian organelle map by protein correlation profilingLeonard 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... - Quantitative proteomic profiling of membrane proteins from the mouse brain cortex, hippocampus, and cerebellum using the HysTag reagent: mapping of neurotransmitter receptors and ion channelsJesper V Olsen
Center for Experimental Bioinformatics CEBI, University of Southern Denmark, Denmark
Brain Res 1134:95-106. 2007.... - Identifying and quantifying in vivo methylation sites by heavy methyl SILACShao-En Ong
Center for Experimental Bioinformatics, University of Southern Denmark, Odense M 5230, Denmark
Nat Methods 1:119-26. 2004.... - MSQuant, an open source platform for mass spectrometry-based quantitative proteomicsPeter 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 ... - Quantitative phosphoproteomics applied to the yeast pheromone signaling pathwayAlbrecht 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.... - 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.... - Trypsin cleaves exclusively C-terminal to arginine and lysine residuesJesper 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... - Stable isotope labeling of Arabidopsis thaliana cells and quantitative proteomics by mass spectrometryAlbrecht 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.... - Mechanism of divergent growth factor effects in mesenchymal stem cell differentiationIrina 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... - 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 substrateMads 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... - Signaling initiated by overexpression of the fibroblast growth factor receptor-1 investigated by mass spectrometryAnders M Hinsby
MDS Proteomics A S, Staermosegaardsvej 6, Odense DK 5230, Denmark
Mol Cell Proteomics 2:29-36. 2003.... - Quantitative proteomics to study mitogen-activated protein kinasesBlagoy 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... - A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elementsGerhard 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... - Organellar proteomics: turning inventories into insightsJens 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... - Quantitative proteomic assessment of very early cellular signaling eventsJoern 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.... - 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.... - Phosphotyrosine mapping in Bcr/Abl oncoprotein using phosphotyrosine-specific immonium ion scanningHanno 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... - Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomicsShao-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... - Modular stop and go extraction tips with stacked disks for parallel and multidimensional Peptide fractionation in proteomicsYasushi 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... - Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentationJesper 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... - RNA and RNA binding proteins participate in early stages of cell spreading through spreading initiation centersCarmen 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... - Mass spectrometric-based approaches in quantitative proteomicsShao-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... - Unbiased quantitative proteomics of lipid rafts reveals high specificity for signaling factorsLeonard 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... - Microcolumns with self-assembled particle frits for proteomicsYasushi 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... - Proteomic characterization of the human centrosome by protein correlation profilingJens 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... - A proteomic approach for identification of secreted proteins during the differentiation of 3T3-L1 preadipocytes to adipocytesIrina 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... - Peptide end sequencing by orthogonal MALDI tandem mass spectrometryMichael 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... - Large-scale proteomic analysis of the human spliceosomeJuri 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... - ProteomicsCarmen 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... - Detection of arginine dimethylated peptides by parallel precursor ion scanning mass spectrometry in positive ion modeJuri 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... - Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trapJesper 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... - Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomicsJuri 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... - Tyrosine phosphorylation mapping of the epidermal growth factor receptor signaling pathwayHanno 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... - Computational and experimental analysis reveals a novel Src family kinase in the C. elegans genomeAkhilesh 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... - A new derivatization strategy for the analysis of phosphopeptides by precursor ion scanning in positive ion modeHanno 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.... - Actin homolog MreB and RNA polymerase interact and are both required for chromosome segregation in Escherichia coliThomas 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... - Directed proteomic analysis of the human nucleolusJens 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..The data also show that the protein composition of nucleoli is not static and can alter significantly in response to the metabolic state of the cell... - Identification of 491 proteins in the tear fluid proteome reveals a large number of proteases and protease inhibitorsGustavo 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... - 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... - Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometryEdwin 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... - Large-scale and high-confidence proteomic analysis of human seminal plasmaBartosz 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..When combined with quantitative proteomics methodologies, it should be useful for studies of fertilization, male infertility, and prostatic and testicular cancers... - Cloning and characterization of PAK5, a novel member of mammalian p21-activated kinase-II subfamily that is predominantly expressed in brainAkhilesh 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... - A proteomic fingerprint of dissolved organic carbon and of soil particlesWaltraud 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... - Analysis of bromotryptophan and hydroxyproline modifications by high-resolution, high-accuracy precursor ion scanning utilizing fragment ions with mass-deficient mass tagsHanno 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... - Identifying proteins and post-translational modifications by mass spectrometryB 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... - Mass spectrometry allows direct identification of proteins in large genomesB 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... - Stable isotope labeling by amino acids in cell culture for quantitative proteomicsShao 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... - PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphositesFlorian 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... - Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser/Thr/Tyr phosphorylationBoris 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... - 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... - Top-down quantitation and characterization of SILAC-labeled proteinsLeonie 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... - Stable isotope labeling by amino acids in cell culture (SILAC) and proteome quantitation of mouse embryonic stem cells to a depth of 5,111 proteinsJohannes 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... - Phosphorylation of the human full-length protein kinase CiotaBoris 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... - Combined use of RNAi and quantitative proteomics to study gene function in DrosophilaTiziana 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... - Human Proteinpedia enables sharing of human protein dataSuresh Mathivanan
Nat Biotechnol 26:164-7. 2008 - Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycleHenrik 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... - Dissection of the insulin signaling pathway via quantitative phosphoproteomicsMarcus 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... - Identifying and quantifying sites of protein methylation by heavy methyl SILACShao-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... - High confidence determination of specific protein-protein interactions using quantitative mass spectrometryMichiel 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... - The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilisBoris Macek
Max Planck Institute for Biochemistry, Proteomics, and Signal Transduction, Am Klopferspitz 18a, D 82152 Martinsried, Germany
Mol Cell Proteomics 6:697-707. 2007.... - In-depth analysis of the membrane and cytosolic proteome of red blood cellsErica 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... - Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomicsBlagoy 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... - Mass spectrometry-based proteomicsRuedi 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... - From genomics to proteomicsMike 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... - Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per proteinYasushi 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... - Differential expression profiling of membrane proteins by quantitative proteomics in a human mesenchymal stem cell line undergoing osteoblast differentiationLeonard 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... - Analysis of tyrosine phosphorylation sites in signaling molecules by a phosphotyrosine-specific immonium ion scanning methodHanno 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... - [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 - Top-down protein sequencing and MS3 on a hybrid linear quadrupole ion trap-orbitrap mass spectrometerBoris 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... - Axin-mediated CKI phosphorylation of beta-catenin at Ser 45: a molecular switch for the Wnt pathwaySharon 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... - The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteinsJun Adachi
Department of Proteomics and Signal Transduction, Max-Planck Institute for Biochemistry, Am Klopferspitz, D-82152 Martinsried, Germany
Genome Biol 7:R80. 2006..The urinary proteome is unexpectedly complex and may prove useful in biomarker discovery in the future... - Distinct and overlapping sets of SUMO-1 and SUMO-2 target proteins revealed by quantitative proteomicsAlfred C O Vertegaal
Department of Molecular Cell Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
Mol Cell Proteomics 5:2298-310. 2006.... - Mass spectrometric mapping of linker histone H1 variants reveals multiple acetylations, methylations, and phosphorylation as well as differences between cell culture and tissueJacek 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... - Pseudosubstrate regulation of the SCF(beta-TrCP) ubiquitin ligase by hnRNP-UMatti 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... - Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometryYuen 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... - MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomesYanling 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... - Functional and quantitative proteomics using SILACMatthias 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.... - Tyrosine phosphoproteomics of fibroblast growth factor signaling: a role for insulin receptor substrate-4Anders 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...