Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation.
暂无分享,去创建一个
Richard D. Smith | P. Pevzner | Navdeep Jaitly | V. Bafna | A. Osterman | R. Edwards | J. Adkins | M. Lipton | S. Tanner | Nitin Gupta | M. Romine | N. Jaitly | Stephen W. Tanner | Stephen Tanner
[1] C. Trachsel,et al. Human Blood Plasma Proteins , 2008 .
[2] E. Marcotte,et al. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation , 2007, Nature Biotechnology.
[3] M. Savitski,et al. Extent of Modifications in Human Proteome Samples and Their Effect on Dynamic Range of Analysis in Shotgun Proteomics*S , 2006, Molecular & Cellular Proteomics.
[4] Thierry Meinnel,et al. The Proteomics of N-terminal Methionine Cleavage*S , 2006, Molecular & Cellular Proteomics.
[5] Andrei L Osterman,et al. Comparative Genomics and Experimental Characterization of N-Acetylglucosamine Utilization Pathway of Shewanella oneidensis* , 2006, Journal of Biological Chemistry.
[6] Richard D. Smith,et al. Confirmation of the expression of a large set of conserved hypothetical proteins in Shewanella oneidensis MR-1. , 2006, Journal of microbiological methods.
[7] James P. Reilly,et al. A computational approach toward label-free protein quantification using predicted peptide detectability , 2006, ISMB.
[8] M. Riley,et al. Genomic Analysis of Carbon Source Metabolism of Shewanella oneidensis MR-1: Predictions versus Experiments , 2006, Journal of Bacteriology.
[9] O. Jensen. Interpreting the protein language using proteomics , 2006, Nature Reviews Molecular Cell Biology.
[10] Damian Fermin,et al. Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics , 2006, Genome Biology.
[11] H. Mori,et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection , 2006, Molecular systems biology.
[12] P. Pevzner,et al. Unrestrictive identification of post-translational modifications through peptide mass spectrometry , 2006, Nature Protocols.
[13] Dekel Tsur,et al. Identification of post-translational modifications by blind search of mass spectra , 2005, Nature Biotechnology.
[14] Naryttza N. Diaz,et al. The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes , 2005, Nucleic acids research.
[15] Akhilesh Pandey,et al. Genome annotation of Anopheles gambiae using mass spectrometry-derived data , 2005, BMC Genomics.
[16] Dekel Tsur,et al. Identification of post-translational modifications via blind search of mass-spectra , 2005, 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05).
[17] Rong Wang,et al. Mass spectrometry of the M. smegmatis proteome: protein expression levels correlate with function, operons, and codon bias. , 2005, Genome research.
[18] Matthew E Monroe,et al. Global detection and characterization of hypothetical proteins in Shewanella oneidensis MR‐1 using LC‐MS based proteomics , 2005, Proteomics.
[19] Mark Borodovsky,et al. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses , 2005, Nucleic Acids Res..
[20] Jing-lan Wang,et al. Identification of degradation products formed during performic oxidation of peptides and proteins by high-performance liquid chromatography with matrix-assisted laser desorption/ionization and tandem mass spectrometry. , 2005, Rapid communications in mass spectrometry : RCM.
[21] Gordon A Anderson,et al. Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[22] Vineet Bafna,et al. InsPecT : Fast and accurate identification of post-translationally modified peptides from tandem mass spectra , 2005 .
[23] Matthew E Monroe,et al. Validation of Shewanella oneidensis MR-1 small proteins by AMT tag-based proteome analysis. , 2004, Omics : a journal of integrative biology.
[24] Jacob D. Jaffe,et al. The complete genome and proteome of Mycoplasma mobile. , 2004, Genome research.
[25] S. Brunak,et al. Improved prediction of signal peptides: SignalP 3.0. , 2004, Journal of molecular biology.
[26] Dieter Jahn,et al. PrediSi: prediction of signal peptides and their cleavage positions , 2004, Nucleic Acids Res..
[27] M. Mann,et al. Trypsin Cleaves Exclusively C-terminal to Arginine and Lysine Residues*S , 2004, Molecular & Cellular Proteomics.
[28] D. Creasy,et al. Unimod: Protein modifications for mass spectrometry , 2004, Proteomics.
[29] John S Garavelli,et al. The RESID Database of Protein Modifications as a resource and annotation tool , 2004, Proteomics.
[30] G. Crooks,et al. WebLogo: a sequence logo generator. , 2004, Genome research.
[31] O. White,et al. Environmental Genome Shotgun Sequencing of the Sargasso Sea , 2004, Science.
[32] Katalin F. Medzihradszky,et al. Factors that contribute to the complexity of protein digests , 2004 .
[33] Jacob D. Jaffe,et al. Proteogenomic mapping as a complementary method to perform genome annotation , 2004, Proteomics.
[34] Kenneth H. Nealson,et al. Breathing metals as a way of life: geobiology in action , 2002, Antonie van Leeuwenhoek.
[35] C. Gualerzi,et al. Cloning and characterization of a gene cluster from Bacillus stearothermophilus comprising infC, rpmI and rplT , 1989, Molecular and General Genetics MGG.
[36] F. Chang. Methylation of ribosomal proteins during ribosome assembly in Escherichia coli , 2004, Molecular and General Genetics MGG.
[37] Eugene V. Koonin,et al. Comparative genomics, minimal gene-sets and the last universal common ancestor , 2003, Nature Reviews Microbiology.
[38] J. W. Campbell,et al. Experimental Determination and System Level Analysis of Essential Genes in Escherichia coli MG1655 , 2003, Journal of bacteriology.
[39] R. Aebersold,et al. Mass spectrometry-based proteomics , 2003, Nature.
[40] T. Tatusova,et al. Reannotation of Shewanella oneidensis genome. , 2003, Omics : a journal of integrative biology.
[41] Raymond F. Gesteland,et al. Recode 2003 , 2003, Nucleic Acids Res..
[42] O. White,et al. Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis , 2002, Nature Biotechnology.
[43] L. Kirsch,et al. The relative rates of glutamine and asparagine deamidation in glucagon fragment 22-29 under acidic conditions. , 2002, Journal of pharmaceutical sciences.
[44] John R Yates,et al. Parallel identification of new genes in Saccharomyces cerevisiae. , 2002, Genome research.
[45] C. James,et al. A New UAG-Encoded Residue in the Structure of a Methanogen Methyltransferase , 2002, Science.
[46] Pavel V Baranov,et al. Recoding: translational bifurcations in gene expression. , 2002, Gene.
[47] J. Boyd,et al. Cyclization of N-terminal S-carbamoylmethylcysteine causing loss of 17 Da from peptides and extra peaks in peptide maps. , 2002, Journal of proteome research.
[48] Måns Ehrenberg,et al. The hemK gene in Escherichia coli encodes the N5‐glutamine methyltransferase that modifies peptide release factors , 2002, The EMBO journal.
[49] M. Paetzel,et al. Signal peptidases. , 2002, Chemical reviews.
[50] Jan Maarten van Dijl,et al. A proteomic view on genome-based signal peptide predictions. , 2001, Genome research.
[51] E. Boja,et al. Overalkylation of a protein digest with iodoacetamide. , 2001, Analytical chemistry.
[52] P. Mortensen,et al. Mass spectrometry allows direct identification of proteins in large genomes , 2001, Proteomics.
[53] P. Demirev,et al. Characterization of intact microorganisms by MALDI mass spectrometry. , 2001, Mass spectrometry reviews.
[54] M. Mann,et al. Use of mass spectrometry-derived data to annotate nucleotide and protein sequence databases. , 2001, Trends in biochemical sciences.
[55] F. Lottspeich,et al. Deamidation as a widespread phenomenon in two‐dimensional polyacrylamide gel electrophoresis of human blood plasma proteins , 2000, Electrophoresis.
[56] V. N. Lapko,et al. Identification of an artifact in the mass spectrometry of proteins derivatized with iodoacetamide. , 2000, Journal of mass spectrometry : JMS.
[57] A Bairoch,et al. High-throughput mass spectrometric discovery of protein post-translational modifications. , 1999, Journal of molecular biology.
[58] J. Reilly,et al. Observation of Escherichia coli ribosomal proteins and their posttranslational modifications by mass spectrometry. , 1999, Analytical biochemistry.
[59] I. Apostol,et al. Carbamylation of cysteine: a potential artifact in peptide mapping of hemoglobins in the presence of urea. , 1999, Analytical biochemistry.
[60] I. Humphery-Smith,et al. Small genes/gene-products in Escherichia coli K-12. , 1998, FEMS microbiology letters.
[61] R. Macnab,et al. Translation of the Flagellar Gene fliO ofSalmonella typhimurium from Putative Tandem Starts , 1998, Journal of bacteriology.
[62] Terry D. Lee,et al. The identification of peptide modifications derived from gel‐separated proteins using electrospray triple quadrupole and ion trap analyses , 1998, Electrophoresis.
[63] D. Volkin,et al. Degradative covalent reactions important to protein stability , 1997, Molecular biotechnology.
[64] S. Brunak,et al. SHORT COMMUNICATION Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites , 1997 .
[65] George M. Church,et al. Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K‐12 , 1997, Electrophoresis.
[66] J. Kowalak,et al. β‐Methylthio‐aspartic acid: Identification of a novel posttranslational modification in ribosomal protein S12 from escherichia coli , 1996, Protein science : a publication of the Protein Society.
[67] M. Springer,et al. The role of the AUU initiation codon in the negative feedback regulation of the gene for translation initiation factor IF3 in Escherichia coli , 1996, Molecular microbiology.
[68] R. Simons,et al. Escherichia coli translation initiation factor 3 discriminates the initiation codon in vivo , 1996, Molecular microbiology.
[69] M. van de Weert,et al. Identification of oxidized methionine in peptides. , 1996, Rapid communications in mass spectrometry : RCM.
[70] J. Yates,et al. Mining genomes: correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases. , 1995, Analytical chemistry.
[71] J. J. Schwartz,et al. Molecular cloning and sequencing of infC, the gene encoding translation initiation factor IF3, from four enterobacterial species. , 1993, FEMS microbiology letters.
[72] W. S. Hu,et al. Identification of a putative infC-rpmI-rplT operon flanked by long inverted repeats in Mycoplasma fermentans (incognitus strain). , 1993, Gene.
[73] J. Tobias,et al. The N-end rule in bacteria. , 1991, Science.
[74] S. Aizawa,et al. Amino acids responsible for flagellar shape are distributed in terminal regions of flagellin. , 1991, Journal of molecular biology.
[75] F. Dahlquist,et al. Sites of deamidation and methylation in Tsr, a bacterial chemotaxis sensory transducer. , 1991, The Journal of biological chemistry.
[76] H. H. Sørensen,et al. Strategies for determination of disulphide bridges in proteins using plasma desorption mass spectrometry. , 1990, Biomedical & environmental mass spectrometry.
[77] B. Chait,et al. Influence of ions on cyclization of the amino terminal glutamine residues of tryptic peptides of streptococcal PepM49 protein. Resolution of cyclized peptides by HPLC and characterization by mass spectrometry. , 2009, International journal of peptide and protein research.
[78] P. Dessen,et al. Extent of N-terminal methionine excision from Escherichia coli proteins is governed by the side-chain length of the penultimate amino acid. , 1989, Proceedings of the National Academy of Sciences of the United States of America.
[79] K. Soda,et al. Selenocysteine. , 2020, Methods in enzymology.
[80] K. Myambo,et al. Processing of the initiation methionine from proteins: properties of the Escherichia coli methionine aminopeptidase and its gene structure , 1987, Journal of bacteriology.
[81] F. Dahlquist,et al. Multiple covalent modifications of Trg, a sensory transducer of Escherichia coli. , 1983, The Journal of biological chemistry.
[82] M Grunberg-Manago,et al. Sequence of a 1.26‐kb DNA fragment containing the structural gene for E.coli initiation factor IF3: presence of an AUU initiator codon. , 1982, The EMBO journal.
[83] M. Ross,et al. Purified human growth hormone from E. coli is biologically active , 1981, Nature.
[84] R. Laursen,et al. Location of the site of methylation in elongation factor Tu , 1979, FEBS letters.
[85] J. Adler,et al. Isolation of glutamic acid methyl ester from an Escherichia coli membrane protein involved in chemotaxis. , 1977, The Journal of biological chemistry.
[86] A. Yaron. [50] Dipeptidyl carboxypeptidase from Escherichia coli , 1976 .
[87] A. Yaron. Dipeptidyl carboxypeptidase from Escherichia coli. , 1976, Methods in enzymology.
[88] J. Shine,et al. The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. , 1974, Proceedings of the National Academy of Sciences of the United States of America.
[89] S. Tronick,et al. Methylation of the Flagellin of Salmonella typhimurium , 1971, Journal of bacteriology.