- MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
Department for Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
Nat Biotechnol 26:1367-72. 2008
..MaxQuant automatically quantifies several hundred thousand peptides per SILAC-proteome experiment and allows statistically robust identification and quantification of >4,000 proteins in mammalian ..
- Initial sequencing and analysis of the human genome
E S Lander
Whitehead Institute for Biomedical Research, Center for Genome Research, Cambridge, Massachusetts 02142, USA
Nature 409:860-921. 2001
..We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence...
- Lysine acetylation targets protein complexes and co-regulates major cellular functions
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...
- Universal sample preparation method for proteome analysis
Jacek R Wisniewski
Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
Nat Methods 6:359-62. 2009
..We completely solubilized the proteome in sodium dodecyl sulfate, which we then exchanged by urea on a standard filtration device...
- Expansion of the eukaryotic proteome by alternative splicing
Timothy W Nilsen
Center for RNA Molecular Biology, Department of Biochemistry, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
Nature 463:457-63. 2010
..It is now clear that the 'missing' information is in large part provided by alternative splicing, the process by which multiple different functional messenger RNAs, and therefore proteins, can be synthesized from a single gene...
- Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
Science 329:533-8. 2010
..At high expression levels, the distributions are dominated by extrinsic noise. We found that a single cell's protein and mRNA copy numbers for any given gene are uncorrelated...
- Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
Joshua E Elias
Department of Cell Biology, 240 Longwood Avenue, Harvard Medical School, Boston, Massachusetts 02115, USA
Nat Methods 4:207-14. 2007
..As most sequence search engines return results even for 'unmatchable' spectra, proteome researchers must devise ways to distinguish correct from incorrect peptide identifications...
- A mitochondrial protein compendium elucidates complex I disease biology
David J Pagliarini
Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
Cell 134:112-23. 2008
..Our results have important implications for understanding CI function and pathogenesis and, more generally, illustrate how our compendium can serve as a foundation for systematic investigations of mitochondria...
- Systematic and quantitative assessment of the ubiquitin-modified proteome
Department of Cell Biology, Harvard Medical School, Boston, MA, USA
Mol Cell 44:325-40. 2011
..To globally characterize the human ubiquitin-modified proteome (ubiquitinome), we utilized a monoclonal antibody that recognizes diglycine (diGly)-containing isopeptides ..
- Functional profiling of the Saccharomyces cerevisiae genome
Stanford Genome Technology Center, Stanford University, Palo Alto, California 94304, USA
Nature 418:387-91. 2002
..Our results validate the yeast gene-deletion collection as a valuable resource for functional genomics...
- Global analysis of protein expression in yeast
Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California 94143 2240, USA
Nature 425:737-41. 2003
..We find that about 80% of the proteome is expressed during normal growth conditions, and, using additional sequence information, we systematically ..
- Deep proteome and transcriptome mapping of a human cancer cell line
Department for Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
Mol Syst Biol 7:548. 2011
..peptides identified 10 255 different human proteins encoded by 9207 human genes, providing a lower limit on the proteome in this cancer cell line. Deep transcriptome sequencing revealed transcripts for nearly all detected proteins...
- Global analysis of protein localization in budding yeast
Won Ki Huh
Howard Hughes Medical Institute, University of California San Francisco, Department of Biochemistry and Biophysics, 600 16th Street, San Francisco, California 94143 2240, USA
Nature 425:686-91. 2003
..We classify these proteins, representing 75% of the yeast proteome, into 22 distinct subcellular localization categories, and provide localization information for 70% of previously ..
- The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes
Institute for Bioinformatics MIPS, GSF National Research Center for Environment and Health, Ingolstaedter Landstrasse 1, D 85764 Neuherberg, Germany
Nucleic Acids Res 32:5539-45. 2004
..Over the last decade, the FunCat has been established as a robust and stable annotation scheme that offers both, meaningful and manageable functional classification as well as ease of perception...
- The human plasma proteome: history, character, and diagnostic prospects
N Leigh Anderson
Plasma Proteome Institute, Washington, DC 20009 3450, USA
Mol Cell Proteomics 1:845-67. 2002
The human plasma proteome holds the promise of a revolution in disease diagnosis and therapeutic monitoring provided that major challenges in proteomics and related disciplines can be addressed...
- 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
..We applied high-resolution mass spectrometry-based proteomics to investigate the proteome and phosphoproteome of the human cell cycle on a global scale and quantified 6027 proteins and 20,443 unique ..
- Discovering regulatory and signalling circuits in molecular interaction networks
Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA Institute for Systems Biology, Seattle, WA 98103, USA
Bioinformatics 18:S233-40. 2002
..The method we present here combines a rigorous statistical measure for scoring subnetworks with a search algorithm for identifying subnetworks with high score...
- The quantitative proteome of a human cell line
European Molecular Biology Laboratory, Heidelberg, Germany
Mol Syst Biol 7:549. 2011
..Here, we provide a quantitative description of the proteome of a commonly used human cell line in two functional states, interphase and mitosis...
- Regulation of cellular metabolism by protein lysine acetylation
School of Life Sciences, Fudan University, Shanghai 20032, China
Science 327:1000-4. 2010
..Our study reveals that acetylation plays a major role in metabolic regulation...
- Genome sequence of the human malaria parasite Plasmodium falciparum
Malcolm J Gardner
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
Nature 419:498-511. 2002
..The genome sequence provides the foundation for future studies of this organism, and is being exploited in the search for new drugs and vaccines to fight malaria...
- Next-generation proteomics: towards an integrative view of proteome dynamics
A F Maarten Altelaar
Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
Nat Rev Genet 14:35-48. 2013
..The proteome is extremely multifaceted owing to splicing and protein modifications, and this is further amplified by the ..
- Characterization of mammalian selenoproteomes
Gregory V Kryukov
Department of Biochemistry, University of Nebraska, Lincoln, NE 68588 0664, USA
Science 300:1439-43. 2003
..The human selenoproteome consists of 25 selenoproteins...
- 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...
- A human protein atlas for normal and cancer tissues based on antibody proteomics
Department of Biotechnology, AlbaNova University Center, Royal Institute of Technology KTH, SE 106 91 Stockholm, Sweden
Mol Cell Proteomics 4:1920-32. 2005
Antibody-based proteomics provides a powerful approach for the functional study of the human proteome involving the systematic generation of protein-specific affinity reagents...
- The Chlamydomonas genome reveals the evolution of key animal and plant functions
Sabeeha S Merchant
Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA
Science 318:245-50. 2007
- Analysis of the myosin-II-responsive focal adhesion proteome reveals a role for β-Pix in negative regulation of focal adhesion maturation
Jean Cheng Kuo
Cell Biology and Physiology Centre, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland 20892, USA
Nat Cell Biol 13:383-93. 2011
..459 of which changed in abundance with myosin II inhibition, defining the myosin-II-responsive focal adhesion proteome. The abundance of 73% of the proteins in the myosin-II-responsive focal adhesion proteome was enhanced by ..
- AT_CHLORO, a comprehensive chloroplast proteome database with subplastidial localization and curated information on envelope proteins
INSERM, Laboratoire d Etude de Dynamique des Protéomes, U880, France
Mol Cell Proteomics 9:1063-84. 2010
..This is especially true for envelope proteins. We went a step further into the knowledge of the chloroplast proteome by focusing, in the same set of experiments, on the localization of proteins in the stroma, the thylakoids, and ..
- COPASI--a COmplex PAthway SImulator
Virginia Bioinformatics Institute, Virginia Tech, Washington St 0477, Blacksburg, VA 24061, USA
Bioinformatics 22:3067-74. 2006
..Therefore, there is a big need for software tools that allow access to diverse simulation and modeling methods as well as support for the usage of these methods...
- The importance of intrinsic disorder for protein phosphorylation
Lilia M Iakoucheva
School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
Nucleic Acids Res 32:1037-49. 2004
- Comparative analysis of proteome and transcriptome variation in mouse
Department of Medicine Division of Cardiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
PLoS Genet 7:e1001393. 2011
..In light of the widespread use of high-throughput technologies in both clinical and basic research, the results presented have practical as well as basic implications...
- UniProt: the Universal Protein knowledgebase
The EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Nucleic Acids Res 32:D115-9. 2004
..The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). The scientific community is encouraged to submit data for inclusion in UniProt...
- Proteome analysis of erythrocytes lacking AMP-activated protein kinase reveals a role of PAK2 kinase in eryptosis
Department of Physiology, University of Tübingen, Germany
J Proteome Res 10:1690-7. 2011
..To determine the link between AMPK and the eryptotic phenotype, we performed a global proteome analysis of erythrocytes from ampk(-/-) mice and wild-type mice using high-accuracy mass spectrometry and label-..
- Feature-based prediction of non-classical and leaderless protein secretion
Jannick Dyrløv Bendtsen
Center for Biological Sequence Analysis BioCentrum DTU, Building 208, Technical University of Denmark, DK 2800 Lyngby, Denmark
Protein Eng Des Sel 17:349-56. 2004
..By scanning the entire human proteome we identified new proteins potentially undergoing non-classical secretion. Predictions can be made at http://www...
- HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot
Swiss Prot group, Swiss Institute of Bioinformatics, 1 rue Michel Servet, 1211 Geneva 4, Switzerland
Nucleic Acids Res 37:D471-8. 2009
..The HAMAP system is composed of two databases, the proteome database and the family database, and of an automatic annotation pipeline...
- De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics
Max Delbruck Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Robert Rossle Strasse 10, Berlin, Germany
Genome Res 21:1193-200. 2011
..However, the characterization of its transcriptome is far from complete. Furthermore, not a single proteome of the entire phylum has been assayed on a genome-wide level...
- Plant proteome changes under abiotic stress--contribution of proteomics studies to understanding plant stress response
Department of Genetics and Plant Breeding, Crop Research Institute, Drnovská Street 507, 161 06 Prague 6 Ruzyne, The Czech Republic
J Proteomics 74:1301-22. 2011
Plant acclimation to stress is associated with profound changes in proteome composition...
- A quantitative analysis of kinase inhibitor selectivity
Mazen W Karaman
Ambit Biosciences, 4215 Sorrento Valley Blvd, San Diego, California 92121, USA
Nat Biotechnol 26:127-32. 2008
..We further investigate the impact of panel size and find that small assay panels do not provide a robust measure of selectivity...
- Aneuploidy confers quantitative proteome changes and phenotypic variation in budding yeast
Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, Missouri 64110, USA
Nature 468:321-5. 2010
..results provide strong evidence that aneuploidy directly affects gene expression at both the transcriptome and proteome levels and can generate significant phenotypic variation that could bring about fitness gains under diverse ..
- PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites
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...
- ProteoWizard: open source software for rapid proteomics tools development
Spielberg Family Center for Applied Proteomics, Cedars Sinai Medical Center, USA
Bioinformatics 24:2534-6. 2008
..In addition to the library, we also introduce a rapidly growing set of companion tools whose implementation helps to illustrate the simplicity of developing applications on top of the ProteoWizard library...
- Decoding signalling networks by mass spectrometry-based proteomics
The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
Nat Rev Mol Cell Biol 11:427-39. 2010
..Large-scale proteomics-based signalling research will fundamentally change our understanding of signalling networks...
- Initial sequencing and comparative analysis of the mouse genome
Robert H Waterston
Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
Nature 420:520-62. 2002
- Mass spectrometry in high-throughput proteomics: ready for the big time
Research Institute of the McGill University Health Centre, McGill University, Montreal, Quebec, Canada
Nat Methods 7:681-5. 2010
Mass spectrometry has evolved and matured to a level where it is able to assess the complexity of the human proteome. We discuss some of the expected challenges ahead and promising strategies for success.
- High-quality binary protein interaction map of the yeast interactome network
Center for Cancer Systems Biology CCSB, Dana Farber Cancer Institute, Boston, MA 02115, USA
Science 322:104-10. 2008
..Rather than correlating with essentiality, protein connectivity correlates with genetic pleiotropy...
- Mapping intact protein isoforms in discovery mode using top-down proteomics
John C Tran
Department of Chemistry and Biochemistry, and the Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
Nature 480:254-8. 2011
A full description of the human proteome relies on the challenging task of detecting mature and changing forms of protein molecules in the body...
- Proteomic analysis of proteins associated with lipid droplets of basal and lipolytically stimulated 3T3-L1 adipocytes
Dawn L Brasaemle
Department of Nutritional Sciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA
J Biol Chem 279:46835-42. 2004
- The Arabidopsis thaliana chloroplast proteome reveals pathway abundance and novel protein functions
Institute of Plant Sciences and Functional Genomics Center Zurich, Swiss Federal Institute of Technology, ETH Zentrum, LFW E51 1, Universitatstrasse 2, CH 8092 Zurich, Switzerland
Curr Biol 14:354-62. 2004
..Since protein targeting is difficult to predict, many nuclear-encoded plastid proteins are still to be discovered...
- Quantitative, high-resolution proteomics for data-driven systems biology
Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried D 82152, Germany
Annu Rev Biochem 80:273-99. 2011
..It is used to quantify proteins between different proteome states, including the temporal variation of the proteome, to determine the complete primary structure of proteins ..
- PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows
Eric W Deutsch
Institute for Systems Biology, 1441 N 34th Street, Seattle, Washington 98103, USA
EMBO Rep 9:429-34. 2008
..Here, we describe the PeptideAtlas Project, its contents and components, and show how together they provide a unique platform to select and validate mass spectrometry targets, thereby allowing the next revolution in proteomics...
- Mass spectrometry and protein analysis
Institute of Molecular Systems Biology, ETH Zurich, CH 8093 Zurich, Switzerland
Science 312:212-7. 2006
..Here we review recent advances in mass spectrometry instrumentation in the context of current and emerging research strategies in protein science...
- Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs
John C Obenauer
Center for Cancer Research, E18 580, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
Nucleic Acids Res 31:3635-41. 2003
..In addition, a new series of Sequence Match programs for non-quantitative user-defined motifs has been implemented. Scansite is available via the World Wide Web at http://scansite.mit.edu...
- Proteome-wide analysis of disease-associated SNPs that show allele-specific transcription factor binding
Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
PLoS Genet 8:e1002982. 2012
..Here we apply PWAS ("proteome-wide analysis of SNPs"), a methodology based on quantitative mass spectrometry that enables rapid screening of ..
- The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium
Richard G Côté
Proteomics Services Team, EMBL Outstation, European Bioinformatics Institute EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Mol Cell Proteomics 11:1682-9. 2012
..The PRIDE Converter 2 tool suite will thus become a cornerstone in the submission process to PRIDE and, by extension, to the ProteomeXchange consortium of MS-proteomics data repositories...
- The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins
Institut für Genomforschung, Universitat Bielefeld, Universitatsstrasse 25, D 33615 Bielefeld, Germany
J Biotechnol 104:5-25. 2003
..As an example for biotechnological application the complete genome sequence was used to reconstruct the metabolic flow of carbon into a number of industrially important products derived from the amino acid L-aspartate...
- A roadmap to generate renewable protein binders to the human proteome
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
Nat Methods 8:551-8. 2011
..is often hindered by their inconsistent validation, their poor performance and the inadequate coverage of the proteome. These issues could be addressed by systematic, genome-wide efforts to generate and validate renewable protein ..
- Comprehensive proteomics
European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, Germany
Curr Opin Biotechnol 22:3-8. 2011
Extensive proteome discovery projects using a variety of mass spectrometric techniques have identified proteins matching to 50-70% of the predicted gene models of various species...
- Defining the protein complex proteome of plant mitochondria
Institute for Plant Genetics, Faculty of Natural Sciences, Leibniz Universitat Hannover, D 30419 Hannover, Germany
Plant Physiol 157:587-98. 2011
..tandem mass spectrometry and up-to-date computer technology to characterize the mitochondrial "protein complex proteome" of Arabidopsis (Arabidopsis thaliana) in so far unrivaled depth...
- iRefIndex: a consolidated protein interaction database with provenance
The Biotechnology Centre of Oslo, University of Oslo, PO Box 1125 Blindern, 0317 Oslo, Norway
BMC Bioinformatics 9:405. 2008
..We set out to create a unifying index that would facilitate searching for these data and that would group together redundant interaction data while recording the methods used to perform this grouping...
- Quantitative mass spectrometry in proteomics: a critical review
Cellzome AG, Meyerhofstrasse 1, 69254, Heidelberg, Germany
Anal Bioanal Chem 389:1017-31. 2007
..In this review, we critically examine the more commonly used quantitative mass spectrometry methods for their individual merits and discuss challenges in arriving at meaningful interpretations of quantitative proteomic data...
- Temporal proteome and lipidome profiles reveal hepatitis C virus-associated reprogramming of hepatocellular metabolism and bioenergetics
Deborah L Diamond
Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington, USA
PLoS Pathog 6:e1000719. 2010
- A dynamic model of proteome changes reveals new roles for transcript alteration in yeast
M Violet Lee
Department of Chemistry, University of Wisconsin Madison, Madison, WI, USA
Mol Syst Biol 7:514. 2011
The transcriptome and proteome change dynamically as cells respond to environmental stress; however, prior proteomic studies reported poor correlation between mRNA and protein, rendering their relationships unclear...
- The genome sequence of the malaria mosquito Anopheles gambiae
Robert A Holt
Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA
Science 298:129-49. 2002
..An expressed sequence tag analysis of genes regulated by blood feeding provided insights into the physiological adaptations of a hematophagous insect...
- A proteomics approach to understanding protein ubiquitination
Department of Cell Biology, 240 Longwood Avenue, Harvard Medical School, Boston, Massachusetts 02115, USA
Nat Biotechnol 21:921-6. 2003
..The methodology described here provides a general tool for the large-scale analysis and characterization of protein ubiquitination...
- Reverse engineering of regulatory networks in human B cells
Institute for Cancer Genetics, 1300 St Nicholas Avenue, Room 912, New York, New York 10032, USA
Nat Genet 37:382-90. 2005
..The newly identified MYC targets include some major hubs. This approach can be generally useful for the analysis of normal and pathologic networks in mammalian cells...
- Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise
John R S Newman
Howard Hughes Medical Institute, San Francisco, California, USA
Nature 441:840-6. 2006
..Thus, these studies reveal a remarkable structure to biological noise and suggest that protein noise levels have been selected to reflect the costs and potential benefits of this variation...
- The ciliary proteome database: an integrated community resource for the genetic and functional dissection of cilia
Nat Genet 38:961-2. 2006
- Defining the transcriptome and proteome in three functionally different human cell lines
Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden
Mol Syst Biol 6:450. 2010
..Thus, this study shows a path to characterize the transcriptome and proteome in human cells from different origins.
- Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation
Department of Computer Science, University of British Columbia, Vancouver, British Columbia, Canada
Bioinformatics 23:1040-2. 2007
..Cerebral scales well to networks containing thousands of nodes. AVAILABILITY: http://www.pathogenomics.ca/cerebral..
- Modeling interactome: scale-free or geometric?
Department of Computer Science, University of Toronto, Toronto, M5S 3G4, Canada
Bioinformatics 20:3508-15. 2004
..Since incorrect models lead to incorrect predictions, it is vital to have as accurate a model as possible. As a result, new techniques and models for analyzing and modeling real-world networks have recently been introduced...
- OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups
Department of Chemistry, Center for Bioinformatics, Penn Genomics Institute, University of Pennsylvania, Philadelphia, PA 19104 6018, USA
Nucleic Acids Res 34:D363-8. 2006
..was used to cluster proteins based on sequence similarity, using an all-against-all BLAST search of each species' proteome, followed by normalization of inter-species differences, and Markov clustering. A total of 511,797 proteins (81...
- Quantification of mRNA and protein and integration with protein turnover in a bacterium
EMBL CRG Systems Biology Research Unit, Centre for Genomic Regulation and UPF, Dr Aiguader 88, Barcelona, Spain
Mol Syst Biol 7:511. 2011
..b>Proteome composition changes in response to cellular perturbations reveal specific stress response strategies...
- A global protein kinase and phosphatase interaction network in yeast
Centre for Systems Biology, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario, M5G 1X5, Canada
Science 328:1043-6. 2010
..An extensive backbone of kinase-kinase interactions cross-connects the proteome and may serve to coordinate diverse cellular responses.
- Expanding the proteome: disordered and alternatively folded proteins
H Jane Dyson
Department of Molecular Biology MB2, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
Q Rev Biophys 44:467-518. 2011
- 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
..Stable-isotope labelling by amino acids in cell culture (SILAC) quantification was very accurate across the proteome, as demonstrated by one-to-one ratios of most yeast proteins...
- A Proteome-wide screen for mammalian SxIP motif-containing microtubule plus-end tracking proteins
Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
Curr Biol 22:1800-7. 2012
..Here, we performed a proteome-wide search for mammalian SxIP-containing +TIPs by combining biochemical and bioinformatics approaches...
- Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis
Department of Molecular Biology, University of Geneva, Geneva, Switzerland
Genes Dev 23:1929-43. 2009
..This demonstrates that Sch9 is a master regulator of protein synthesis...
- Structural disorder in eukaryotes
VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium
PLoS ONE 7:e34687. 2012
..We conclude that protists have been the evolutionary hot-bed of experimentation with structural disorder, in a period when structural disorder was actively invented and the major functional classes of disordered proteins established...
- Proteome-wide identification of poly(ADP-Ribosyl)ation targets in different genotoxic stress responses
Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
Mol Cell 52:272-85. 2013
- The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
Genomatica, Inc, Bioprocessing Division, 5405 Morehouse Drive, Suite 210, San Diego, CA 92121, USA
Metab Eng 5:264-76. 2003
..These methods also provide an efficient and robust method to calculate the range of flux distributions that can be derived from quantitative fermentation data...
- Characterization of the proteome, diseases and evolution of the human postsynaptic density
Genes to Cognition Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire, UK
Nat Neurosci 14:19-21. 2011
..The hPSD is an important structure for nervous system disease and behavior...
- Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks
Department of Biology, Eidgenossische Technische Hochschule Zurich, 8092 Zurich, Switzerland
Plant Physiol 150:889-903. 2009
..We propose that ATP synthase is regulated in cooperation with 14-3-3 proteins by CKII-mediated phosphorylation of ATP synthase beta-subunit in the dark...
- Analysis of the Aspergillus fumigatus proteome reveals metabolic changes and the activation of the pseurotin A biosynthesis gene cluster in response to hypoxia
Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute and Friedrich Schiller University, Jena, Germany
J Proteome Res 10:2508-24. 2011
..fumigatus. Therefore, we aimed at obtaining a comprehensive overview about this process on the proteome level...
- Origin and evolution of the mitochondrial proteome
C G Kurland
Department of Molecular Evolution, Evolutionary Biology Centre, University of Uppsala, Uppsala SE 752 36, Lund University, Lund SE 223 62, Sweden
Microbiol Mol Biol Rev 64:786-820. 2000
..The three identifiable ancestral sources to the proteome of mitochondria are proteins descended from the ancestral alpha-proteobacteria symbiont, proteins with no ..
- Mass spectrometry-based proteomics in cell biology
Tobias C Walther
Organelle Architecture and Dynamics and 2 Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
J Cell Biol 190:491-500. 2010
- A sensitive predictor for potential GPI lipid modification sites in fungal protein sequences and its application to genome-wide studies for Aspergillus nidulans, Candida albicans, Neurospora crassa, Saccharomyces cerevisiae and Schizosaccharomyces pombe
Research Institute of Molecular Pathology IMP, Dr Bohr Gasse 7, A 1030 Vienna, Austria
J Mol Biol 337:243-53. 2004
..Lists of potentially GPI lipid anchored proteins for five fungal proteomes have been generated and the hits have been functionally classified. The fungal big-Pi prediction WWW server as well as precursor lists are available at..
- Proteome-wide identification of poly(ADP-ribose) binding proteins and poly(ADP-ribose)-associated protein complexes
Jean Philippe Gagné
Laval University Medical Research Center, CHUQ, Faculty of Medicine, Laval University, Quebec, Canada
Nucleic Acids Res 36:6959-76. 2008
..In this study, refined in silico prediction of pADPr binding proteins and large-scale mass spectrometry-based proteome analysis of pADPr binding proteins were used to establish a comprehensive repertoire of pADPr-associated proteins...
- A universal molecular clock of protein folds and its power in tracing the early history of aerobic metabolism and planet oxygenation
Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana Champaign, USA
Mol Biol Evol 28:567-82. 2011
..The clock also extends the standard concept that was specific to molecules and their timescales and turns it into a universal timescale-generating tool...
- Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma
Terri A Addona
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Nat Biotechnol 27:633-41. 2009
..We provide data and benchmarks against which individual laboratories can compare their performance and evaluate new technologies for biomarker verification in plasma...
- 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
..However, in global proteome studies, low cellular abundance of protein kinases often results in rather minor peptide species that are ..
- High-throughput generation of selected reaction-monitoring assays for proteins and proteomes
Institute of Molecular Systems Biology, Swiss Federal Institute of Technology, Zurich, Switzerland
Nat Methods 7:43-6. 2010
..We illustrate the power of the approach by generating and applying validated SRM assays for all Saccharomyces cerevisiae kinases and phosphatases...
- Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome
Jacek R Wisniewski
Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
J Proteome Res 8:5674-8. 2009
..To extend proteome coverage, we developed a simple anion exchange fractionation method in a StageTip format...
- Functional and topological characterization of protein interaction networks
Soon Hyung Yook
Department of Physics, University of Notre Dame, Notre Dame, IN 46556, USA
Proteomics 4:928-42. 2004
- A genecentric Human Protein Atlas for expression profiles based on antibodies
Department of Proteomics, School of Biotechnology, AlbaNova University Center, Royal Institute of Technology, Stockholm, Sweden
Mol Cell Proteomics 7:2019-27. 2008
..The new version of the protein atlas thus is a resource for many areas of biomedical research, including protein science and biomarker discovery...
- The International Protein Index: an integrated database for proteomics experiments
Paul J Kersey
EMBL Outstation, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
Proteomics 4:1985-8. 2004
..IPI (the International Protein Index) has been developed to address these issues and offers complete nonredundant data sets representing the human, mouse and rat proteomes, built from the Swiss-Prot, TrEMBL, Ensembl and RefSeq databases...
- PrediSi: prediction of signal peptides and their cleavage positions
Institut fur Mikrobiologie, Technische Universitat Braunschweig, Spielmannstrasse 7, D 38106 Braunschweig, Germany
Nucleic Acids Res 32:W375-9. 2004
..PrediSi allows the evaluation of whole proteome datasets, which are currently accumulating as a result of numerous genome projects and proteomics experiments...
- iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates
Institute for Systems Biology, Seattle, WA, USA
Mol Cell Proteomics 10:M111.007690. 2011
..performance of iProphet is demonstrated on two publicly available data sets: data from a human whole cell lysate proteome profiling experiment representative of typical proteomic data sets, and from a set of Streptococcus pyogenes ..
- Mapping the Arabidopsis organelle proteome
Tom P J Dunkley
Department of Biochemistry, University of Cambridge, Downing Site, Cambridge CB2 1QW, United Kingdom
Proc Natl Acad Sci U S A 103:6518-23. 2006
..Consequently, genuine organelle residents have been distinguished from contaminating proteins and proteins in transit through the secretory pathway...
- Discovery of a cytokine and its receptor by functional screening of the extracellular proteome
Five Prime Therapeutics, Inc, 1650 Owens Street, Suite 200, San Francisco, CA 94158, USA
Science 320:807-11. 2008
..This systematic approach is thus useful for discovering new ligands and receptors and assessing the functional selectivity of extracellular regulatory proteins...
- Rapid transcriptome and proteome profiling of a non-model marine invertebrate, Bugula neritina
Department of Biology, Hong Kong University of Science and Technology, Hong Kong SAR, P R China
Proteomics 10:2972-81. 2010
..In this study, we applied a tandem transcriptome and proteome profiling on a non-model marine fouling organism, Bugula neritina...
- Large-scale analysis of the yeast proteome by multidimensional protein identification technology
M P Washburn
Syngenta Agricultural Discovery Institute, 3115 Merryfield Row, Suite 100, San Diego, CA 92121, USA
Nat Biotechnol 19:242-7. 2001
We describe a largely unbiased method for rapid and large-scale proteome analysis by multidimensional liquid chromatography, tandem mass spectrometry, and database searching by the SEQUEST algorithm, named multidimensional protein ..
- 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