Proteomics: the first decade and beyond

[1]  E. Petricoin,et al.  Use of proteomic patterns in serum to identify ovarian cancer , 2002, The Lancet.

[2]  P. O’Farrell.  High resolution two-dimensional electrophoresis of proteins. , 1975, The Journal of biological chemistry.

[3]  International Human Genome Sequencing Consortium.  Initial sequencing and analysis of the human genome , 2001, Nature.

[4]  F C Holstege,et al.  DNA microarrays : raising the profile , 2022 .

[5]  B. Barrell,et al.  Life with 6000 Genes , 1996, Science.

[6]  M. Soares,et al.  Normalization and subtraction: two approaches to facilitate gene discovery. , 1996, Genome research.

[7]  B. Chait,et al.  Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome , 2001, Nature Biotechnology.

[8]  S. Pennington,et al.  Arrays for protein expression profiling: Towards a viable alternative to two‐dimensional gel electrophoresis? , 2001, Proteomics.

[9]  J. Klose.  Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues , 1975, Humangenetik.

[10]  Linda M. Thienpont,et al.  Applications of isotope dilution-mass spectrometry in clinical chemistry, pharmacokinetics, and toxicology , 1992 .

[11]  G. Palomaki,et al.  Reference distributions for α2‐macroglobulin: A comparison of a large cohort to the world's literature , 2004, Journal of clinical laboratory analysis.

[12]  M. Mrksich,et al.  Peptide chips for the quantitative evaluation of protein kinase activity , 2002, Nature Biotechnology.

[13]  P. Mitchell.  A perspective on protein microarrays , 2002, Nature Biotechnology.

[14]  E. Padlan,et al.  Analysis of the structure of naturally processed peptides bound by class I and class II major histocompatibility complex molecules. , 1995, EXS.

[15]  Stanley Fields,et al.  A yeast sensor of ligand binding , 2001, Nature Biotechnology.

[16]  A. Klug,et al.  Designing DNA-binding proteins on the surface of filamentous phage. , 1995, Current opinion in biotechnology.

[17]  S. Fields,et al.  A biochemical genomics approach for identifying genes by the activity of their products. , 1999, Science.

[18]  Yudong D. He,et al.  Gene expression profiling predicts clinical outcome of breast cancer , 2002, Nature.

[19]  M. Stoeckli,et al.  Imaging mass spectrometry: A new technology for the analysis of protein expression in mammalian tissues , 2001, Nature Medicine.

[20]  T. Veenstra,et al.  Quantitative analysis of bacterial and mammalian proteomes using a combination of cysteine affinity tags and 15N-metabolic labeling. , 2001, Analytical chemistry.

[21]  Gary D Bader,et al.  Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry , 2002, Nature.

[22]  Koichi Tanaka,et al.  Detection of high mass molecular ions by laser desorption time-of-flight mass spectrometry. , 1988 .

[23]  J I Garrels,et al.  Transformation-sensitive and growth-related changes of protein synthesis in REF52 cells. A two-dimensional gel analysis of SV40-, adenovirus-, and Kirsten murine sarcoma virus-transformed rat cells using the REF52 protein database. , 1989, The Journal of biological chemistry.

[24]  R. Aebersold,et al.  Equipping scientists for the new biology , 2000, Nature Biotechnology.

[25]  T. Rabilloud,et al.  A comparison between Sypro Ruby and ruthenium II tris (bathophenanthroline disulfonate) as fluorescent stains for protein detection in gels , 2001, Proteomics.

[26]  L. Hood,et al.  Complementary Profiling of Gene Expression at the Transcriptome and Proteome Levels in Saccharomyces cerevisiae*S , 2002, Molecular & Cellular Proteomics.

[27]  Philippe Matherat,et al.  HERMeS: A second generation approach to the automatic analysis of two‐dimensional electrophoresis gels Part I: Data acquisition , 1986 .

[28]  L. Hood,et al.  Internal amino acid sequence analysis of proteins separated by one- or two-dimensional gel electrophoresis after in situ protease digestion on nitrocellulose. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[29]  M E Belov,et al.  Rapid quantitative measurements of proteomes by Fourier transform ion cyclotron resonance mass spectrometry , 2001, Electrophoresis.

[30]  Roger Y. Tsien,et al.  Seeing the Machinery of Live Cells , 1998, Science.

[31]  G. Hart,et al.  Specific isolation of O-linked N-acetylglucosamine glycopeptides from complex mixtures. , 1995, Analytical biochemistry.

[32]  P Green,et al.  Base-calling of automated sequencer traces using phred. II. Error probabilities. , 1998, Genome research.

[33]  F. Cross,et al.  Accurate quantitation of protein expression and site-specific phosphorylation. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[34]  P. Schellhammer,et al.  Serum protein fingerprinting coupled with a pattern-matching algorithm distinguishes prostate cancer from benign prostate hyperplasia and healthy men. , 2002, Cancer research.

[35]  B. Franza,et al.  The Ref52 Protein Database , 1988 .

[36]  A. Görg,et al.  The current state of two‐dimensional electrophoresis with immobilized pH gradients , 2000, Electrophoresis.

[37]  B. Cravatt,et al.  Profiling serine hydrolase activities in complex proteomes. , 2001, Biochemistry.

[38]  G. Scheele,et al.  Two-dimensional gel analysis of soluble proteins. Charaterization of guinea pig exocrine pancreatic proteins. , 1975, The Journal of biological chemistry.

[39]  C. Watanabe,et al.  Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[40]  X. Yao,et al.  Proteolytic 18O labeling for comparative proteomics: model studies with two serotypes of adenovirus. , 2001, Analytical chemistry.

[41]  James R. Knight,et al.  A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae , 2000, Nature.

[42]  R. Aebersold,et al.  Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry , 2001, Nature Biotechnology.

[43]  D. Botstein,et al.  Singular value decomposition for genome-wide expression data processing and modeling. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[44]  B. Futcher,et al.  A Sampling of the Yeast Proteome , 1999, Molecular and Cellular Biology.

[45]  Ronald W. Davis,et al.  Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray , 1995, Science.

[46]  Ruedi Aebersold,et al.  The study of macromolecular complexes by quantitative proteomics , 2003, Nature Genetics.

[47]  M. Chalfie.  GREEN FLUORESCENT PROTEIN , 1995, Photochemistry and photobiology.

[48]  T. Hunkapiller,et al.  Peptide mass maps: a highly informative approach to protein identification. , 1993, Analytical biochemistry.

[49]  A. Kerlavage,et al.  Complementary DNA sequencing: expressed sequence tags and human genome project , 1991, Science.

[50]  Andrew J. Link,et al.  Proteomics of the Eukaryotic Transcription Machinery: Identification of Proteins Associated with Components of Yeast TFIID by Multidimensional Mass Spectrometry , 2002, Molecular and Cellular Biology.

[51]  P. Tempst,et al.  Internal sequence analysis of proteins separated on polyacrylamide gels at the submicrogram level: Improved methods, applications and gene cloning strategies , 1990, Electrophoresis.

[52]  M. Mann,et al.  Electrospray ionization for mass spectrometry of large biomolecules. , 1989, Science.

[53]  B. Cravatt,et al.  Proteomic profiling of mechanistically distinct enzyme classes using a common chemotype , 2002, Nature Biotechnology.

[54]  M. Mrksich,et al.  Towards quantitative assays with peptide chips: a surface engineering approach. , 2002, Trends in biotechnology.

[55]  T. Hughes,et al.  Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. , 2000, Science.

[56]  John J. Wyrick,et al.  Genome-wide location and function of DNA binding proteins. , 2000, Science.

[57]  T. Rabilloud.  Two‐dimensional gel electrophoresis in proteomics: Old, old fashioned, but it still climbs up the mountains , 2002, Proteomics.

[58]  S. Kingsmore,et al.  Multiplexed protein profiling on microarrays by rolling-circle amplification , 2002, Nature Biotechnology.

[59]  Yudong D. He,et al.  Functional Discovery via a Compendium of Expression Profiles , 2000, Cell.

[60]  A. Mirzabekov,et al.  Massive parallel analysis of the binding specificity of histone-like protein HU to single- and double-stranded DNA with generic oligodeoxyribonucleotide microchips. , 2001, Nucleic acids research.

[61]  R H Hruban,et al.  Gene expression profiles in normal and cancer cells. , 1997, Science.

[62]  C. López-Otín,et al.  Protease degradomics: A new challenge for proteomics , 2002, Nature Reviews Molecular Cell Biology.

[63]  T. Südhof,et al.  Cartography of neurexins: More than 1000 isoforms generated by alternative splicing and expressed in distinct subsets of neurons , 1995, Neuron.

[64]  A. Nesvizhskii,et al.  Experimental protein mixture for validating tandem mass spectral analysis. , 2002, Omics : a journal of integrative biology.

[65]  L. Staudt,et al.  Molecular features of B-cell lymphoma , 2001, Current opinion in oncology.

[66]  P. Tarroux,et al.  HERMeS: A second generation approach to the automatic analysis of two‐dimensional electrophoresis gels. Part V: Data analysis , 2022 .

[67]  Lucy J. Holt,et al.  The use of recombinant antibodies in proteomics. , 2000, Current opinion in biotechnology.

[68]  R. Wahl,et al.  Towards defining the urinary proteome using liquid chromatography‐tandem mass spectrometry I.Profiling an unfractionated tryptic digest , 2001, Proteomics.

[69]  Philippe Tarroux,et al.  HERMeS: A second generation approach to the automatic analysis of two‐dimensional electrophoresis gels. Part III: Spot list matching , 1987 .

[70]  A. F. Neuwald,et al.  Purification and biochemical characterization of interchromatin granule clusters , 1999, The EMBO journal.

[71]  P. Uetz,et al.  Towards an understanding of complex protein networks. , 2001, Trends in cell biology.

[72]  E Gianazza,et al.  Immobilized pH gradients. , 1988, Trends in biochemical sciences.

[73]  A. McCormack,et al.  Direct Analysis of Protein Mixtures by Tandem Mass Spectrometry , 1997, Journal of protein chemistry.

[74]  M. Vidal,et al.  A protein–protein interaction map of the Caenorhabditis elegans 26S proteasome , 2001, EMBO reports.

[75]  Andrew Emili,et al.  De novo peptide sequencing and quantitative profiling of complex protein mixtures using mass-coded abundance tagging , 2002, Nature Biotechnology.

[76]  Ruedi Aebersold,et al.  Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags. , 2002, Journal of proteome research.

[77]  B. Chait,et al.  The Yeast Nuclear Pore Complex: Composition, Architecture, and Transport Mechanism , 2000 .

[78]  M. Gerstein,et al.  Subcellular localization of the yeast proteome. , 2002, Genes & development.

[79]  S. P. Fodor,et al.  Light-generated oligonucleotide arrays for rapid DNA sequence analysis. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[80]  J I Garrels,et al.  The REF52 protein database. Methods of database construction and analysis using the QUEST system and characterizations of protein patterns from proliferating and quiescent REF52 cells. , 1989, The Journal of biological chemistry.

[81]  H. Lehrach,et al.  Analysis of the mouse proteome. (I) Brain proteins: Separation by two‐dimensional electrophoresis and identification by mass spectrometry and genetic variation , 1999, Electrophoresis.

[82]  R. Hoess,et al.  Tendamistat as a scaffold for conformationally constrained phage peptide libraries. , 1995, Journal of molecular biology.

[83]  H. Lehrach,et al.  Protein arrays for gene expression and molecular interaction screening. , 2000, Current opinion in microbiology.

[84]  J. Garrels.  The QUEST system for quantitative analysis of two-dimensional gels. , 1989, The Journal of biological chemistry.

[85]  D. Mccormick.  Sequence the Human Genome , 1986, Bio/Technology.

[86]  J. Seilhamer,et al.  A comparison of selected mRNA and protein abundances in human liver , 1997, Electrophoresis.

[87]  David Botstein,et al.  SGD: Saccharomyces Genome Database , 1998, Nucleic Acids Res..

[88]  M. Mann,et al.  Proteomics to study genes and genomes , 2000, Nature.

[89]  J. Porath,et al.  Immobilized metal ion affinity chromatography. Effect of solute structure, ligand density and salt concentration on the retention of peptides. , 1990, Journal of chromatography.

[90]  Ji Huang,et al.  [Serial analysis of gene expression]. , 2002, Yi chuan = Hereditas.

[91]  R Gras,et al.  Computational aspects of protein identification by mass spectrometry. , 2001, Current opinion in molecular therapeutics.

[92]  P. Bork,et al.  Functional organization of the yeast proteome by systematic analysis of protein complexes , 2002, Nature.

[93]  Joseph J. Pereira,et al.  Proteomic analysis of the human colon carcinoma cell line (LIM 1215): Development of a membrane protein database , 2000, Electrophoresis.

[94]  M. Vidal,et al.  Protein interaction mapping in C. elegans using proteins involved in vulval development. , 2000, Science.

[95]  M. Posewitz,et al.  Immobilized gallium(III) affinity chromatography of phosphopeptides. , 1999, Analytical chemistry.

[96]  U. Alon,et al.  Robustness in bacterial chemotaxis , 2022 .

[97]  M. Gerstein,et al.  Analysis of yeast protein kinases using protein chips , 2000, Nature Genetics.

[98]  R. Aebersold,et al.  Mass spectrometric approaches for the identification of gel‐separated proteins , 1995, Electrophoresis.

[99]  J. Stults,et al.  Electrospray ionization mass spectrometry of phosphopeptides isolated by on-line immobilized metal-ion affinity chromatography , 1993, Journal of the American Society for Mass Spectrometry.

[100]  Timothy D. Veenstra,et al.  AN ACCURATE MASS TAG STRATEGY FOR QUANTITATIVE AND HIGH THROUGHPUT PROTEOME MEASUREMENTS , 2002 .

[101]  J. Yates,et al.  Direct analysis of protein complexes using mass spectrometry , 1999, Nature Biotechnology.

[102]  A. Shevchenko,et al.  Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry , 1996, Nature.

[103]  G. Winter,et al.  Phage antibodies: filamentous phage displaying antibody variable domains , 1990, Nature.

[104]  J. Yates,et al.  Large-scale analysis of the yeast proteome by multidimensional protein identification technology , 2001, Nature Biotechnology.

[105]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[106]  P. Green,et al.  Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.

[107]  A. Tramontano,et al.  The making of the minibody: An engineered β‐protein for the display of conformationally constrained peptides , 1994, Journal of molecular recognition : JMR.

[108]  R. Fleischmann,et al.  Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence. , 1995, Nature.

[109]  D. Hochstrasser,et al.  The dynamic range of protein expression: A challenge for proteomic research , 2000, Electrophoresis.

[110]  S. Gygi,et al.  Quantitative analysis of complex protein mixtures using isotope-coded affinity tags , 1999, Nature Biotechnology.

[111]  R Y Tsien,et al.  Wavelength mutations and posttranslational autoxidation of green fluorescent protein. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[112]  R. Nadon,et al.  Statistical issues with microarrays: processing and analysis. , 2002, Trends in genetics : TIG.

[113]  M. Wilm,et al.  Electrospray and Taylor-Cone theory, Dole's beam of macromolecules at last? , 1994 .

[114]  B. Snel,et al.  Comparative assessment of large-scale data sets of protein–protein interactions , 2002, Nature.

[115]  M. Ünlü,et al.  Difference gel electrophoresis. A single gel method for detecting changes in protein extracts , 1997, Electrophoresis.

[116]  B. Cravatt,et al.  Activity-based protein profiling: the serine hydrolases. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[117]  G. Kroemer,et al.  Simplification of complex peptide mixtures for proteomic analysis: Reversible biotinylation of cysteinyl peptides , 2000, Electrophoresis.

[118]  J. Yates,et al.  An automated multidimensional protein identification technology for shotgun proteomics. , 2001, Analytical chemistry.

[119]  B K Hayes,et al.  Selective detection and site-analysis of O-GlcNAc-modified glycopeptides by beta-elimination and tandem electrospray mass spectrometry. , 1996, Analytical biochemistry.

[120]  Michael Ruogu Zhang,et al.  Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. , 1998, Molecular biology of the cell.

[121]  Jennifer M. Campbell,et al.  The characteristics of peptide collision-induced dissociation using a high-performance MALDI-TOF/TOF tandem mass spectrometer. , 2000, Analytical chemistry.

[122]  R. Cortese,et al.  Coupling protein design and in vitro selection strategies: improving specificity and affinity of a designed beta-protein IL-6 antagonist. , 1996, Journal of molecular biology.

[123]  J Thornton,et al.  Structural genomics takes off. , 2001, Trends in biochemical sciences.

[124]  M. Marton,et al.  Identification of genes over-expressed in small cell lung carcinoma using suppression subtractive hybridization and cDNA microarray expression analysis , 2002, Oncogene.

[125]  T. Haystead,et al.  Gamma-phosphate-linked ATP-sepharose for the affinity purification of protein kinases. Rapid purification to homogeneity of skeletal muscle mitogen-activated protein kinase kinase. , 1993, European journal of biochemistry.

[126]  J. Wojcik,et al.  The protein–protein interaction map of Helicobacter pylori , 2001, Nature.

[127]  S. Gygi,et al.  Correlation between Protein and mRNA Abundance in Yeast , 1999, Molecular and Cellular Biology.

[128]  Benjamin F. Cravatt,et al.  Chemical strategies for the global analysis of protein function. , 2000 .

[129]  D. Barford,et al.  Development of "substrate-trapping" mutants to identify physiological substrates of protein tyrosine phosphatases. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[130]  M. Wickens,et al.  Yeast three-hybrid system to detect and analyze RNA-protein interactions. , 2000, Methods in enzymology.

[131]  John R. Yates,et al.  A STRATEGY FOR THE IDENTIFICATION OF PROTEINS LOCALIZED TO SUBCELLULAR SPACES : APPLICATION TO E. COLI PERIPLASMIC PROTEINS , 1997 .

[132]  Ljiljana Paša-Tolić,et al.  An accurate mass tag strategy for quantitative and high‐throughput proteome measurements , 2002, Proteomics.

[133]  G. Gonnet,et al.  Protein identification by mass profile fingerprinting. , 1993, Biochemical and biophysical research communications.

[134]  John R Yates,et al.  Analysis of quantitative proteomic data generated via multidimensional protein identification technology. , 2002, Analytical chemistry.

[135]  G. Palomaki,et al.  Reference distributions for the negative acute‐phase proteins, albumin, transferrin, and transthyretin: A comparison of a large cohort to the world's literature , 1999, Journal of clinical laboratory analysis.

[136]  N. Anderson,et al.  Proteomics: applications in basic and applied biology. , 2000, Current opinion in biotechnology.

[137]  S. Patterson,et al.  Identification and Characterization of proSAAS, a Granin-Like Neuroendocrine Peptide Precursor that Inhibits Prohormone Processing , 2000, The Journal of Neuroscience.

[138]  J. Porath.  Immobilized metal ion affinity chromatography. , 1992, Protein expression and purification.

[139]  Jilin Sun,et al.  Identification of incompletely processed potential Carboxypeptidase E substrates from CpEfat/CpEfat mice , 2001, Proteomics.

[140]  C. Mirkin,et al.  Protein Nanoarrays Generated By Dip-Pen Nanolithography , 2002, Science.

[141]  M. Uhlén,et al.  A combinatorial library of an α-helical bacterial receptor domain , 1995 .

[142]  Koichi Tanaka,et al.  Protein and polymer analyses up to m/z 100 000 by laser ionization time-of-flight mass spectrometry , 1988 .

[143]  M. Uhlén,et al.  Anti‐idiotypic protein domains selected from protein A‐based affibody libraries , 2002, Proteins.

[144]  Sunny Shin,et al.  Substrate binding and sequence preference of the proteasome revealed by active-site-directed affinity probes. , 1998, Chemistry & biology.

[145]  T. Ito,et al.  Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[146]  B. Cravatt,et al.  Profiling the specific reactivity of the proteome with non-directed activity-based probes. , 2001, Chemistry & biology.

[147]  Roger E Bumgarner,et al.  Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. , 2001, Science.

[148]  R. Aebersold,et al.  Current Problems and Technical Solutions in Protein Biochemistry , 1998 .

[149]  A. Burlingame,et al.  Epoxide electrophiles as activity-dependent cysteine protease profiling and discovery tools. , 2000, Chemistry & biology.

[150]  R. Caprioli,et al.  Molecular imaging of biological samples: localization of peptides and proteins using MALDI-TOF MS. , 1997, Analytical chemistry.

[151]  P. Højrup,et al.  Rapid identification of proteins by peptide-mass fingerprinting , 1993, Current Biology.

[152]  M. Elowitz,et al.  Combinatorial Synthesis of Genetic Networks , 2002, Science.

[153]  M. Karas,et al.  Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. , 1988, Analytical chemistry.

[154]  R. Kobayashi,et al.  Identification of the Cell Cycle Regulator VCP (p97/CDC48) as a Substrate of the Band 4.1-related Protein-tyrosine Phosphatase PTPH1* , 1999, The Journal of Biological Chemistry.

[155]  Yudong D. He,et al.  Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer , 2001, Nature Biotechnology.

[156]  C. Ball,et al.  Saccharomyces Genome Database. , 2002, Methods in enzymology.

[157]  S. Gygi,et al.  Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[158]  M. Van Montagu,et al.  Protein-blotting on Polybrene-coated glass-fiber sheets. A basis for acid hydrolysis and gas-phase sequencing of picomole quantities of protein previously separated on sodium dodecyl sulfate/polyacrylamide gel. , 1985, European journal of biochemistry.

[159]  G. Kroemer,et al.  Mass spectrometric identification of proteins released from mitochondria undergoing permeability transition , 2000, Cell Death and Differentiation.

[160]  R. Henderson,et al.  HLA-A2.1-associated peptides from a mutant cell line: a second pathway of antigen presentation. , 1992, Science.

[161]  J. Craig Venter,et al.  3,400 new expressed sequence tags identify diversity of transcripts in human brain , 1993, Nature Genetics.

[162]  Richard D. Smith,et al.  Phosphoprotein isotope-coded affinity tag approach for isolating and quantitating phosphopeptides in proteome-wide analyses. , 2001, Analytical chemistry.

[163]  D. Hochstrasser,et al.  Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. , 1996, Biotechnology & genetic engineering reviews.

[164]  S. Fields,et al.  A novel genetic system to detect protein–protein interactions , 1989, Nature.

[165]  S. Withers,et al.  Approaches to labeling and identification of active site residues in glycosidases , 1995, Protein science : a publication of the Protein Society.

[166]  R. Ozawa,et al.  A comprehensive two-hybrid analysis to explore the yeast protein interactome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[167]  M. Diehn.  Large-scale identification of secreted and membrane-associated gene products using DNA microarrays , 1999, Nature Genetics.

[168]  P. Højrup,et al.  Use of mass spectrometric molecular weight information to identify proteins in sequence databases. , 1993, Biological mass spectrometry.

[169]  S. Ishii,et al.  Affinity chromatography on immobilized anhydrotrypsin: general utility for selective isolation of C-terminal peptides from protease digests of proteins. , 1987, Journal of biochemistry.

[170]  M Wilm,et al.  Automated de novo sequencing of proteins using the differential scanning technique , 2001, Proteomics.

[171]  R. Henderson,et al.  Characterization of peptides bound to the class I MHC molecule HLA-A2.1 by mass spectrometry. , 1992, Science.

[172]  J. Betts,et al.  Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling , 2002, Molecular microbiology.

[173]  F. Tureček.  Mass spectrometry in coupling with affinity capture-release and isotope-coded affinity tags for quantitative protein analysis. , 2002, Journal of mass spectrometry : JMS.

[174]  B. Collings,et al.  Resonance shifts in the excitation of the n = 0, K = 1 to 6 quadrupolar resonances for ions confined in a linear ion trap , 2002, Journal of the American Society for Mass Spectrometry.

[175]  J. Shabanowitz,et al.  Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae , 2002, Nature Biotechnology.

[176]  P. Roepstorff,et al.  Quantitation of peptides and proteins by matrix-assisted laser desorption/ionization mass spectrometry using (18)O-labeled internal standards. , 2000, Rapid communications in mass spectrometry : RCM.

[177]  Ronald W. Davis,et al.  Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. , 1999, Science.

[178]  Stanley Fields,et al.  A protein linkage map of Escherichia coli bacteriophage T7 , 1996, Nature Genetics.

[179]  S. Schreiber,et al.  Printing proteins as microarrays for high-throughput function determination. , 2000, Science.

[180]  G. Scheele.  Two-Dimensional Gel Analysis of Soluble Proteins , 1975 .

[181]  James I. Garrels,et al.  YPD-A database for the proteins of Saccharomyces cerevisiae , 1996, Nucleic Acids Res..

[182]  J Taylor,et al.  Global approaches to quantitative analysis of gene-expression patterns observed by use of two-dimensional gel electrophoresis. , 1984, Clinical chemistry.

[183]  M. Natan,et al.  Solution and chip arrays in protein profiling. , 2001, Trends in biotechnology.

[184]  J. Hopfield,et al.  From molecular to modular cell biology , 1999, Nature.

[185]  Ruedi Aebersold,et al.  Quantitative Proteome Analysis by Solid-phase Isotope Tagging and Mass Spectrometry Beads Photocleavable Linker Isotope Tag Reactive Group , 2022 .

[186]  M. Münchbach,et al.  Quantitation and facilitated de novo sequencing of proteins by isotopic N-terminal labeling of peptides with a fragmentation-directing moiety. , 2000, Analytical chemistry.

[187]  N G Anderson,et al.  The Human Protein Index. , 1981, Clinical chemistry.

[188]  P. Brown,et al.  Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions , 2001, Genome Biology.

[189]  A. Burlingame,et al.  Chemical Approaches for Functionally Probing the Proteome* , 2002, Molecular & Cellular Proteomics.

[190]  J. Yates,et al.  An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database , 1994, Journal of the American Society for Mass Spectrometry.

[191]  Ruedi Aebersold,et al.  Quantitative proteomic analysis of Myc oncoprotein function , 2002, The EMBO journal.

[192]  Peter Aldhous.  Raising the profile , 1991, Nature.

[193]  M. Schummer,et al.  Messenger RNA translation state: the second dimension of high-throughput expression screening. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[194]  A. Marshall,et al.  Fourier transform ion cyclotron resonance mass spectrometry: a primer. , 1998, Mass spectrometry reviews.

[195]  J. Yates,et al.  Proteasomal proteomics: identification of nucleotide-sensitive proteasome-interacting proteins by mass spectrometric analysis of affinity-purified proteasomes. , 2000, Molecular biology of the cell.

[196]  A Sette,et al.  Peptides presented to the immune system by the murine class II major histocompatibility complex molecule I-Ad. , 1992, Science.

[197]  B Herbert,et al.  Advances in protein solubilisation for two‐dimensional electrophoresis , 1999, Electrophoresis.

[198]  J. Yates,et al.  Charting the Protein Complexome in Yeast by Mass Spectrometry* , 2002, Molecular & Cellular Proteomics.

[199]  S. Fields,et al.  Genome-wide analysis of vaccinia virus protein-protein interactions. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[200]  Laboratory Course on High Resolution Two Dimensional Gel Electrophoresis Of Proteins , 2022 .

[201]  H. Kantarjian,et al.  Prognostic value of plasma interleukin‐6 levels in patients with chronic lymphocytic leukemia , 2002, Cancer.

[202]  S. Patterson,et al.  Automated LC-LC-MS-MS platform using binary ion-exchange and gradient reversed-phase chromatography for improved proteomic analyses. , 2001, Journal of chromatography. B, Biomedical sciences and applications.

[203]  D. Cahill,et al.  Protein and antibody arrays and their medical applications. , 2001, Journal of immunological methods.

[204]  L. Gold,et al.  The use of aptamers in large arrays for molecular diagnostics. , 1999, Molecular diagnosis : a journal devoted to the understanding of human disease through the clinical application of molecular biology.

[205]  Erkki Ruoslahti,et al.  Phage Libraries Displaying Cyclic Peptides with Different Ring Sizes: Ligand Specificities of the RGD-Directed Integrins , 1995, Bio/Technology.

[206]  R. Aebersold,et al.  A systematic approach to the analysis of protein phosphorylation , 2001, Nature Biotechnology.