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Bibliography (104 total) : Review Only   Up

• 2013


• Perez-Riverol Y, Sánchez A, Noda J, Borges D, Carvalho PC, Wang R, Vizcaíno JA, Betancourt L, Ramos Y, Duarte G, Nogueira FC, González LJ, Padrón G, Tabb DL, Hermjakob H, Domont GB, Besada V (2013) HI-bone: a scoring system for identifying phenylisothiocyanate-derivatized peptides based on precursor mass and high intensity fragment ions. Anal Chem 85:3515-20



• Nováková L, Vaast A, Stassen C, Broeckhoven K, De Pra M, Swart R, Desmet G, Eeltink S (2013) High-resolution peptide separations using nano-LC at ultra-high pressure. J Sep Sci 36:1192-9



• Zhu G, Sun L, Yan X, Dovichi NJ (2013) Single-shot proteomics using capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry with production of more than 1250 Escherichia coli peptide identifications in a 50 min separation. Anal Chem 85:2569-73



• Wenger CD, Coon JJ (2013) A proteomics search algorithm specifically designed for high-resolution tandem mass spectra. J Proteome Res 12:1377-86



• Weisbrod CR, Chavez JD, Eng JK, Yang L, Zheng C, Bruce JE (2013) In Vivo Protein Interaction Network Identified with a Novel Real-Time Cross-Linked Peptide Identification Strategy. J Proteome Res :



• Baran R, Bowen BP, Price MN, Arkin AP, Deutschbauer AM, Northen TR (2013) Metabolic footprinting of mutant libraries to map metabolite utilization to genotype. ACS Chem Biol 8:189-99



• Woodruff LB, Pandhal J, Ow SY, Karimpour-Fard A, Weiss SJ, Wright PC, Gill RT (2013) Genome-scale identification and characterization of ethanol tolerance genes in Escherichia coli. Metab Eng 15:124-33



• 2012


• Toh-Boyo GM, Wulff SS, Basile F (2012) Comparison of sample preparation methods and evaluation of intra- and intersample reproducibility in bacteria MALDI-MS profiling. Anal Chem 84:9971-80



• Dolch ME, Hornuss C, Klocke C, Praun S, Villinger J, Denzer W, Schelling G, Schubert S (2012) Volatile compound profiling for the identification of Gram-negative bacteria by ion-molecule reaction-mass spectrometry. J Appl Microbiol 113:1097-105



• Arike L, Valgepea K, Peil L, Nahku R, Adamberg K, Vilu R (2012) Comparison and applications of label-free absolute proteome quantification methods on Escherichia coli. J Proteomics 75:5437-48



• Filiou MD, Varadarajulu J, Teplytska L, Reckow S, Maccarrone G, Turck CW (2012) The (15) N isotope effect in Escherichia coli: A neutron can make the difference. Proteomics :



• Wessels HJ, Bloemberg TG, van Dael M, Wehrens R, Buydens LM, van den Heuvel LP, Gloerich J (2012) A comprehensive full factorial LC-MS/MS proteomics benchmark data set. Proteomics 12:2276-81



• Ye X, Li L (2012) Microwave-assisted protein solubilization for mass spectrometry-based shotgun proteome analysis. Anal Chem 84:6181-91



• Xia S, Tao D, Yuan H, Zhou Y, Liang Z, Zhang L, Zhang Y (2012) Nano-flow multidimensional liquid chromatography platform integrated with combination of protein and peptide separation for proteome analysis. J Sep Sci 35:1764-70



• Austin RJ, Chang DK, Holstein CA, Lee LW, Risler J, Wang JH, Adams L, Krusberski NB, Martin DB (2012) IQcat: multiplexed protein quantification by isoelectric QconCAT. Proteomics 12:2078-83



• Wetzel C, Limbach PA (2012) Global identification of transfer RNAs by liquid chromatography-mass spectrometry (LC-MS). J Proteomics 75:3450-64



• Armengaud J (2012) Microbiology and proteomics, getting the best of both worlds! Environ Microbiol :



• Miladinovi? SM, Kozhinov AN, Gorshkov MV, Tsybin YO (2012) On the utility of isotopic fine structure mass spectrometry in protein identification. Anal Chem 84:4042-51



• Singh P, Batth TS, Juminaga D, Dahl RH, Keasling JD, Adams PD, Petzold CJ (2012) Application of targeted proteomics to metabolically engineered Escherichia coli. Proteomics 12:1289-99



• Fritzsche R, Ihling CH, Götze M, Sinz A (2012) Optimizing the enrichment of cross-linked products for mass spectrometric protein analysis. Rapid Commun Mass Spectrom 26:653-8



• Yadav AK, Kumar D, Dash D (2012) Learning from decoys to improve the sensitivity and specificity of proteomics database search results. PLoS One 7:e50651



• Babu M, Kagan O, Guo H, Greenblatt J, Emili A (2012) Identification of protein complexes in Escherichia coli using sequential peptide affinity purification in combination with tandem mass spectrometry. J Vis Exp :



• Batth TS, Keasling JD, Petzold CJ (2012) Targeted proteomics for metabolic pathway optimization. Methods Mol Biol 944:237-49



• Cheung HY, Wong MM, Cheung SH, Liang LY, Lam YW, Chiu SK (2012) Differential actions of chlorhexidine on the cell wall of Bacillus subtilis and Escherichia coli. PLoS One 7:e36659



• Kudlicki A (2012) The optimal exponent base for emPAI is 6.5. PLoS One 7:e32339



• Mata-Gómez MA, Yasui MT, Guerrero-Rangel A, Valdés-Rodríguez S, Winkler R (2012) Accelerated identification of proteins by mass spectrometry by employing covalent pre-gel staining with Uniblue A. PLoS One 7:e31438



• Lomas L, Clarke CH, Thulasiraman V, Fung E (2012) Optimized conditions for a quantitative SELDI TOF MS protein assay. Methods Mol Biol 818:1-10



• 2011


• Ballardini R, Benevento M, Arrigoni G, Pattini L, Roda A (2011) MassUntangler: a novel alignment tool for label-free liquid chromatography-mass spectrometry proteomic data. J Chromatogr A 1218:8859-68



• Stefanopoulou M, Kokoschka M, Sheldrick WS, Wolters DA (2011) Cell response of Escherichia coli to cisplatin-induced stress. Proteomics 11:4174-88



• Wang T, Ma J, Wu S, Yuan H, Zhang L, Liang Z, Zhang Y (2011) Integrated platform of capillary isoelectric focusing, trypsin immobilized enzyme microreactor and nanoreversed-phase liquid chromatography with mass spectrometry for online protein profiling. Electrophoresis 32:2848-56



• Fränzel B, Wolters DA (2011) Advanced MudPIT as a next step toward high proteome coverage. Proteomics 11:3651-6



• Xu M, Li L (2011) Validation of peptide MS/MS spectra using metabolic isotope labeling for spectral matching-based shotgun proteome analysis. J Proteome Res 10:3632-41



• Lauber MA, Reilly JP (2011) Structural analysis of a prokaryotic ribosome using a novel amidinating cross-linker and mass spectrometry. J Proteome Res 10:3604-16



• Polacco BJ, Purvine SO, Zink EM, Lavoie SP, Lipton MS, Summers AO, Miller SM (2011) Discovering mercury protein modifications in whole proteomes using natural isotope distributions observed in liquid chromatography-tandem mass spectrometry. Mol Cell Proteomics 10:M110.004853



• Wu F, Sun D, Wang N, Gong Y, Li L (2011) Comparison of surfactant-assisted shotgun methods using acid-labile surfactants and sodium dodecyl sulfate for membrane proteome analysis. Anal Chim Acta 698:36-43



• Ho MY, Chiou ML, Du WS, Chang FY, Chen YH, Weng YJ, Cheng CC (2011) Inductive properties of polypyridyl ruthenium complexes significantly regulate various protein distributions in Escherichia coli. J Inorg Biochem 105:902-10



• Nandakumar R, Espirito Santo C, Madayiputhiya N, Grass G (2011) Quantitative proteomic profiling of the Escherichia coli response to metallic copper surfaces. Biometals 24:429-44



• Zhang H, Liu Q, Zimmerman LJ, Ham AJ, Slebos RJ, Rahman J, Kikuchi T, Massion PP, Carbone DP, Billheimer D, Liebler DC (2011) Methods for peptide and protein quantitation by liquid chromatography-multiple reaction monitoring mass spectrometry. Mol Cell Proteomics 10:M110.006593



• De Laurentiis EI, Mo F, Wieden HJ (2011) Construction of a fully active Cys-less elongation factor Tu: functional role of conserved cysteine 81. Biochim Biophys Acta 1814:684-92



• Han MJ, Yun H, Lee JW, Lee YH, Lee SY, Yoo JS, Kim JY, Kim JF, Hur CG (2011) Genome-wide identification of the subcellular localization of the Escherichia coli B proteome using experimental and computational methods. Proteomics 11:1213-27



• Rizzello L, Sorce B, Sabella S, Vecchio G, Galeone A, Brunetti V, Cingolani R, Pompa PP (2011) Impact of nanoscale topography on genomics and proteomics of adherent bacteria. ACS Nano 5:1865-76



• Kapellios EA, Karamanou S, Sardis MF, Aivaliotis M, Economou A, Pergantis SA (2011) Using nanoelectrospray ion mobility spectrometry (GEMMA) to determine the size and relative molecular mass of proteins and protein assemblies: a comparison with MALLS and QELS. Anal Bioanal Chem 399:2421-33



• Liao H, Zhang F, Hu X, Liao X (2011) Effects of high-pressure carbon dioxide on proteins and DNA in Escherichia coli. Microbiology 157:709-20



• Strader MB, Costantino N, Elkins CA, Chen CY, Patel I, Makusky AJ, Choy JS, Court DL, Markey SP, Kowalak JA (2011) A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12. Mol Cell Proteomics 10:M110.005199



• Wickström D, Wagner S, Baars L, Ytterberg AJ, Klepsch M, van Wijk KJ, Luirink J, de Gier JW (2011) Consequences of depletion of the signal recognition particle in Escherichia coli. J Biol Chem 286:4598-609



• Mukherjee J, Ow SY, Noirel J, Biggs CA (2011) Quantitative protein expression and cell surface characteristics of Escherichia coli MG1655 biofilms. Proteomics 11:339-51



• Han MJ, Lee JW, Lee SY (2011) Understanding and engineering of microbial cells based on proteomics and its conjunction with other omics studies. Proteomics 11:721-43 Review



• Harris JJ, Duarte CW, Mossing MC (2011) Using protein abundance to indicate underlying mRNA expression levels in E.coli: an SEM modelling approach. Int J Comput Biol Drug Des 4:387-95



• Khan Z, Amini S, Bloom JS, Ruse C, Caudy AA, Kruglyak L, Singh M, Perlman DH, Tavazoie S (2011) Accurate proteome-wide protein quantification from high-resolution 15N mass spectra. Genome Biol 12:R122



• Schilling O, Huesgen PF, Barré O, Overall CM (2011) Identification and relative quantification of native and proteolytically generated protein C-termini from complex proteomes: C-terminome analysis. Methods Mol Biol 781:59-69



• Kramer G, Kasper PT, de Jong L, de Koster CG (2011) Quantitation of newly synthesized proteins by pulse labeling with azidohomoalanine. Methods Mol Biol 753:169-81



• 2010


• Manabe T, Jin Y (2010) Performance of nondenaturing micro 2-DE followed by third-dimension SDS-PAGE in the analysis of Escherichia coli soluble proteins. Electrophoresis :



• Müller SA, Kohajda T, Findeiss S, Stadler PF, Washietl S, Kellis M, von Bergen M, Kalkhof S (2010) Optimization of parameters for coverage of low molecular weight proteins. Anal Bioanal Chem 398:2867-81



• Kramer G, Sprenger RR, Nessen MA, Roseboom W, Speijer D, de Jong L, de Mattos MJ, Back J, de Koster CG (2010) Proteome-wide alterations in Escherichia coli translation rates upon anaerobiosis. Mol Cell Proteomics 9:2508-16



• Eeltink S, Dolman S, Detobel F, Swart R, Ursem M, Schoenmakers PJ (2010) High-efficiency liquid chromatography-mass spectrometry separations with 50 mm, 250 mm, and 1 m long polymer-based monolithic capillary columns for the characterization of complex proteolytic digests. J Chromatogr A 1217:6610-5



• Sánchez A, Pérez-Riverol Y, González LJ, Noda J, Betancourt L, Ramos Y, Gil J, Vera R, Padrón G, Besada V (2010) Evaluation of phenylthiocarbamoyl-derivatized peptides by electrospray ionization mass spectrometry: selective isolation and analysis of modified multiply charged peptides for liquid chromatography-tandem mass spectrometry experiments. Anal Chem 82:8492-501



• Price CE, Otto A, Fusetti F, Becher D, Hecker M, Driessen AJ (2010) Differential effect of YidC depletion on the membrane proteome of Escherichia coli under aerobic and anaerobic growth conditions. Proteomics 10:3235-47



• Jehmlich N, Hübschmann T, Gesell Salazar M, Völker U, Benndorf D, Müller S, von Bergen M, Schmidt F (2010) Advanced tool for characterization of microbial cultures by combining cytomics and proteomics. Appl Microbiol Biotechnol 88:575-84



• Kim MS, Kandasamy K, Chaerkady R, Pandey A (2010) Assessment of resolution parameters for CID-based shotgun proteomic experiments on the LTQ-Orbitrap mass spectrometer. J Am Soc Mass Spectrom 21:1606-11



• Schilling O, Barré O, Huesgen PF, Overall CM (2010) Proteome-wide analysis of protein carboxy termini: C terminomics. Nat Methods 7:508-11



• Fagerquist CK, Garbus BR, Williams KE, Bates AH, Harden LA (2010) Covalent attachment and dissociative loss of sinapinic acid to/from cysteine-containing proteins from bacterial cell lysates analyzed by MALDI-TOF-TOF mass spectrometry. J Am Soc Mass Spectrom 21:819-32



• Iwasaki M, Miwa S, Ikegami T, Tomita M, Tanaka N, Ishihama Y (2010) One-dimensional capillary liquid chromatographic separation coupled with tandem mass spectrometry unveils the Escherichia coli proteome on a microarray scale. Anal Chem 82:2616-20



• Impens F, Colaert N, Helsens K, Plasman K, Van Damme P, Vandekerckhove J, Gevaert K (2010) MS-driven protease substrate degradomics. Proteomics 10:1284-96 Review



• Jones LN, Baldwin SA, Henderson PJ, Ashcroft AE (2010) Defining topological features of membrane proteins by nanoelectrospray ionisation mass spectrometry. Rapid Commun Mass Spectrom 24:276-84



• Arike L, Nahku R, Borrisova M, Adamberg K, Vilu R (2010) Identification and relative quantification of proteins in Escherichia coli proteome by "up-front" collision-induced dissociation. Eur J Mass Spectrom (Chichester, Eng) 16:227-35



• 2009


• de Sousa Abreu R, Penalva LO, Marcotte EM, Vogel C (2009) Global signatures of protein and mRNA expression levels. Mol Biosyst 5:1512-26 Review



• Eeltink S, Dolman S, Swart R, Ursem M, Schoenmakers PJ (2009) Optimizing the peak capacity per unit time in one-dimensional and off-line two-dimensional liquid chromatography for the separation of complex peptide samples. J Chromatogr A 1216:7368-74



• Sherman J, McKay MJ, Ashman K, Molloy MP (2009) Unique ion signature mass spectrometry, a deterministic method to assign peptide identity. Mol Cell Proteomics 8:2051-62



• Zerck A, Nordhoff E, Resemann A, Mirgorodskaya E, Suckau D, Reinert K, Lehrach H, Gobom J (2009) An iterative strategy for precursor ion selection for LC-MS/MS based shotgun proteomics. J Proteome Res 8:3239-51



• White CA, Oey N, Emili A (2009) Global quantitative proteomic profiling through 18O-labeling in combination with MS/MS spectra analysis. J Proteome Res 8:3653-65



• Kramer G, Sprenger RR, Back J, Dekker HL, Nessen MA, van Maarseveen JH, de Koning LJ, Hellingwerf KJ, de Jong L, de Koster CG (2009) Identification and quantitation of newly synthesized proteins in Escherichia coli by enrichment of azidohomoalanine-labeled peptides with diagonal chromatography. Mol Cell Proteomics 8:1599-611



• Iwasaki M, Masuda T, Tomita M, Ishihama Y (2009) Chemical cleavage-assisted tryptic digestion for membrane proteome analysis. J Proteome Res 8:3169-75



• Ramakrishnan SR, Vogel C, Prince JT, Li Z, Penalva LO, Myers M, Marcotte EM, Miranker DP, Wang R (2009) Integrating shotgun proteomics and mRNA expression data to improve protein identification. Bioinformatics 25:1397-403



• Zhou P, Tian F, Lv F, Shang Z (2009) Comprehensive comparison of eight statistical modelling methods used in quantitative structure-retention relationship studies for liquid chromatographic retention times of peptides generated by protease digestion of the Escherichia coli proteome. J Chromatogr A 1216:3107-16



• Tao D, Zhu G, Sun L, Ma J, Liang Z, Zhang W, Zhang L, Zhang Y (2009) Serially coupled microcolumn reversed phase liquid chromatography for shotgun proteomic analysis. Proteomics 9:2029-36



• Ahrends R, Pieper S, Neumann B, Scheler C, Linscheid MW (2009) Metal-coded affinity tag labeling: a demonstration of analytical robustness and suitability for biological applications. Anal Chem 81:2176-84



• Geromanos SJ, Vissers JP, Silva JC, Dorschel CA, Li GZ, Gorenstein MV, Bateman RH, Langridge JI (2009) The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependant LC-MS/MS. Proteomics 9:1683-95



• Gharib M, Marcantonio M, Lehmann SG, Courcelles M, Meloche S, Verreault A, Thibault P (2009) Artifactual sulfation of silver-stained proteins: implications for the assignment of phosphorylation and sulfation sites. Mol Cell Proteomics 8:506-18



• Liu J, Huang TY, McLuckey SA (2009) Top-down protein identification/characterization of a priori unknown proteins via ion trap collision-induced dissociation and ion/ion reactions in a quadrupole/time-of-flight tandem mass spectrometer. Anal Chem 81:1433-41



• Haegler K, Mueller NS, Maccarrone G, Hunyadi-Gulyas E, Webhofer C, Filiou MD, Zhang Y, Turck CW (2009) QuantiSpec--Quantitative mass spectrometry data analysis of (15)N-metabolically labeled proteins. J Proteomics 71:601-8



• Wood TK (2009) Insights on Escherichia coli biofilm formation and inhibition from whole-transcriptome profiling. Environ Microbiol 11:1-15 Review



• 2008


• Szájli E, Fehér T, Medzihradszky KF (2008) Investigating the quantitative nature of MALDI-TOF MS. Mol Cell Proteomics 7:2410-8



• Becker GW (2008) Stable isotopic labeling of proteins for quantitative proteomic applications. Brief Funct Genomic Proteomic 7:371-82 Review



• Dowell JA, Frost DC, Zhang J, Li L (2008) Comparison of two-dimensional fractionation techniques for shotgun proteomics. Anal Chem 80:6715-23



• Ramos Y, Gutierrez E, Machado Y, Sánchez A, Castellanos-Serra L, González LJ, Fernández-de-Cossio J, Pérez-Riverol Y, Betancourt L, Gil J, Padrón G, Besada V (2008) Proteomics based on peptide fractionation by SDS-free PAGE. J Proteome Res 7:2427-34



• Everley RA, Croley TR (2008) Ultra-performance liquid chromatography/mass spectrometry of intact proteins. J Chromatogr A 1192:239-47



• Han KY, Park JS, Seo HS, Ahn KY, Lee J (2008) Multiple stressor-induced proteome responses of Escherichia coli BL21(DE3). J Proteome Res 7:1891-903



• Bunger MK, Cargile BJ, Ngunjiri A, Bundy JL, Stephenson JL (2008) Automated proteomics of E. coli via top-down electron-transfer dissociation mass spectrometry. Anal Chem 80:1459-67



• Hauser NJ, Basile F (2008) Online microwave D-cleavage LC-ESI-MS/MS of intact proteins: site-specific cleavages at aspartic acid residues and disulfide bonds. J Proteome Res 7:1012-26



• Finney GL, Blackler AR, Hoopmann MR, Canterbury JD, Wu CC, MacCoss MJ (2008) Label-free comparative analysis of proteomics mixtures using chromatographic alignment of high-resolution muLC-MS data. Anal Chem 80:961-71



• Eboigbodin KE, Biggs CA (2008) Characterization of the extracellular polymeric substances produced by Escherichia coli using infrared spectroscopic, proteomic, and aggregation studies. Biomacromolecules 9:686-95



• Masuda T, Tomita M, Ishihama Y (2008) Phase transfer surfactant-aided trypsin digestion for membrane proteome analysis. J Proteome Res 7:731-40



• Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008) Protein abundance profiling of the Escherichia coli cytosol. BMC Genomics 9:102



• 2007


• Fälth M, Savitski MM, Nielsen ML, Kjeldsen F, Andren PE, Zubarev RA (2007) SwedCAD, a database of annotated high-mass accuracy MS/MS spectra of tryptic peptides. J Proteome Res 6:4063-7



• Timmer JC, Enoksson M, Wildfang E, Zhu W, Igarashi Y, Denault JB, Ma Y, Dummitt B, Chang YH, Mast AE, Eroshkin A, Smith JW, Tao WA, Salvesen GS (2007) Profiling constitutive proteolytic events in vivo. Biochem J 407:41-8



• Lu CY, Wu CY, Lin CH (2007) Protein identification by syringe pump-driven reversed-phase LC-MS/MS. Anal Biochem 368:123-9



• Yang Y, Zhang S, Howe K, Wilson DB, Moser F, Irwin D, Thannhauser TW (2007) A comparison of nLC-ESI-MS/MS and nLC-MALDI-MS/MS for GeLC-based protein identification and iTRAQ-based shotgun quantitative proteomics. J Biomol Tech 18:226-37



• Matthiesen R (2007) Methods, algorithms and tools in computational proteomics: a practical point of view. Proteomics 7:2815-32 Review



• Tripet B, Renuka Jayadev M, Blow D, Nguyen C, Hodges R, Cios K (2007) Proteomic data mining using predicted peptide chromatographic retention times. Int J Bioinform Res Appl 3:431-45



• Yamaguchi M, Obama T, Kuyama H, Nakayama D, Ando E, Okamura TA, Ueyama N, Nakazawa T, Norioka S, Nishimura O, Tsunasawa S (2007) Specific isolation of N-terminal fragments from proteins and their high-fidelity de novo sequencing. Rapid Commun Mass Spectrom 21:3329-36



• 2004


• Noble WS (2004) Data hoarding is harming proteomics. Nat Biotechnol 22:1209; discussion 1209 Comment



• Prince JT, Carlson MW, Wang R, Lu P, Marcotte EM (2004) The need for a public proteomics repository. Nat Biotechnol 22:471-2



• 2002


• Gevaert K, Van Damme J, Goethals M, Thomas GR, Hoorelbeke B, Demol H, Martens L, Puype M, Staes A, Vandekerckhove J (2002) Chromatographic isolation of methionine-containing peptides for gel-free proteome analysis: identification of more than 800 Escherichia coli proteins. Mol Cell Proteomics 1:896-903



• Reid GE, Shang H, Hogan JM, Lee GU, McLuckey SA (2002) Gas-phase concentration, purification, and identification of whole proteins from complex mixtures. J Am Chem Soc 124:7353-62