{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,8,19]],"date-time":"2023-08-19T16:29:28Z","timestamp":1692462568614},"reference-count":47,"publisher":"Elsevier","license":[{"start":{"date-parts":[[2017,1,1]],"date-time":"2017-01-01T00:00:00Z","timestamp":1483228800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017]]},"DOI":"10.1016\/bs.mie.2016.11.003","type":"book-chapter","created":{"date-parts":[[2017,1,18]],"date-time":"2017-01-18T02:51:20Z","timestamp":1484707880000},"page":"379-411","source":"Crossref","is-referenced-by-count":3,"title":["Rapid Proteomics to Prospect and Validate Novel Bacterial Metabolism Induced by Environmental Burden"],"prefix":"10.1016","author":[{"given":"C.L.","family":"Yu","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"S.","family":"Brooks","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Y.","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"M.","family":"Subramanian","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"R.","family":"Summers","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"M.","family":"Pope","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/bs.mie.2016.11.003_bb0005","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1038\/nprot.2009.21","article-title":"Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics","volume":"4","author":"Boersema","year":"2009","journal-title":"Nature Protocols"},{"key":"10.1016\/bs.mie.2016.11.003_bb0010","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1016\/j.jpba.2015.04.013","article-title":"Stable isotope labelling methods in mass spectrometry-based quantitative proteomics","volume":"113","author":"Chahrour","year":"2015","journal-title":"Journal of Pharmaceutical and Biomedical Analysis"},{"issue":"2","key":"10.1016\/bs.mie.2016.11.003_bb0015","doi-asserted-by":"crossref","first-page":"209","DOI":"10.3390\/ijms17020209","article-title":"Identification of predictive markers for response to neoadjuvant chemoradiation in rectal carcinomas by proteomic isotope coded protein label (ICPL) analysis","volume":"17","author":"Croner","year":"2016","journal-title":"The International Journal of Molecular Sciences"},{"issue":"16","key":"10.1016\/bs.mie.2016.11.003_bb0020","doi-asserted-by":"crossref","first-page":"2153","DOI":"10.1007\/s00018-007-7051-9","article-title":"Caffeine analogs: Biomedical impact","volume":"64","author":"Daly","year":"2007","journal-title":"Cellular and Molecular Life Sciences"},{"issue":"24","key":"10.1016\/bs.mie.2016.11.003_bb0025","doi-asserted-by":"crossref","first-page":"1993","DOI":"10.1007\/s10529-006-9196-2","article-title":"Catabolic pathways and biotechnological applications of microbial caffeine degradation","volume":"28","author":"Dash","year":"2006","journal-title":"Biotechnology Letters"},{"issue":"7","key":"10.1016\/bs.mie.2016.11.003_bb0030","doi-asserted-by":"crossref","first-page":"1382","DOI":"10.1002\/ece3.249","article-title":"Understanding of the impact of chemicals on amphibians: A meta-analytic review","volume":"2","author":"Egea-Serrano","year":"2012","journal-title":"Ecology and Evolution"},{"issue":"16","key":"10.1016\/bs.mie.2016.11.003_bb0035","first-page":"2278","article-title":"Isolation and characterization of high caffeine-tolerant bacterium strains from the soil of tea garden","volume":"5","author":"Fan","year":"2011","journal-title":"African Journal of Microbiology Research"},{"issue":"19","key":"10.1016\/bs.mie.2016.11.003_bb0040","doi-asserted-by":"crossref","first-page":"6426","DOI":"10.1021\/ac050923i","article-title":"Orthogonality of separation in two-dimensional liquid chromatography","volume":"77","author":"Gilar","year":"2005","journal-title":"Analytical Chemistry"},{"issue":"14","key":"10.1016\/bs.mie.2016.11.003_bb0045","doi-asserted-by":"crossref","first-page":"1694","DOI":"10.1002\/jssc.200500116","article-title":"Two-dimensional separation of peptides using RP-RP-HPLC system with different pH in first and second separation dimensions","volume":"28","author":"Gilar","year":"2005","journal-title":"Journal of Separation Science"},{"key":"10.1016\/bs.mie.2016.11.003_bb9000","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1038\/msb.2008.75","article-title":"An integrated workflow for charting the human interaction proteome: Insights into the PP2A system","volume":"5","author":"Glatter","year":"2009","journal-title":"Molecular Systems Biology."},{"key":"10.1016\/bs.mie.2016.11.003_bb0050","doi-asserted-by":"crossref","first-page":"1417","DOI":"10.1016\/j.procbio.2005.12.018","article-title":"Kinetics of cell growth and caffeine utilization by Pseudomonas sp. GSC 1182","volume":"41","author":"Gokulakrishnan","year":"2006","journal-title":"Process Biochemistry"},{"issue":"2","key":"10.1016\/bs.mie.2016.11.003_bb0055","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1007\/s00253-011-3737-x","article-title":"Physiology, biochemistry and possible applications of microbial caffeine degradation","volume":"93","author":"Gummadi","year":"2012","journal-title":"Applied Microbiology Biotechnology"},{"issue":"17","key":"10.1016\/bs.mie.2016.11.003_bb0060","doi-asserted-by":"crossref","first-page":"9390","DOI":"10.1073\/pnas.160270797","article-title":"Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology","volume":"97","author":"Gygi","year":"2000","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"10.1016\/bs.mie.2016.11.003_bb0065","doi-asserted-by":"crossref","first-page":"6843","DOI":"10.1021\/ac0348625","article-title":"Stable-isotope dimethyl labeling for quantitative proteomics","volume":"75","author":"Hsu","year":"2003","journal-title":"Analytical Chemistry"},{"issue":"12","key":"10.1016\/bs.mie.2016.11.003_bb0070","doi-asserted-by":"crossref","first-page":"3899","DOI":"10.1002\/pmic.200400872","article-title":"- Identification of proteins induced by polycyclic aromatic hydrocarbon in Mycobacterium vanbaalenii PYR-1 using two dimensional polyacrylamide gel electrophoresis and de novo sequencing methods","volume":"4","author":"Kim","year":"2004","journal-title":"Proteomics"},{"key":"10.1016\/bs.mie.2016.11.003_bb0075","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1128\/JB.01310-06","article-title":"Complete and integrated pyrene degradation pathway in Mycobacterium vanbaalenii PYR-1 based on system biology","volume":"189","author":"Kim","year":"2007","journal-title":"Journal of Bacteriology"},{"issue":"4","key":"10.1016\/bs.mie.2016.11.003_bb0080","doi-asserted-by":"crossref","first-page":"991","DOI":"10.1007\/s00216-012-6070-z","article-title":"Applications of stable isotope dimethyl labeling in quantitative proteomics","volume":"404","author":"Kovanich","year":"2012","journal-title":"Analytical and Bioanalytical Chemistry"},{"key":"10.1016\/bs.mie.2016.11.003_bb0085","doi-asserted-by":"crossref","first-page":"3828","DOI":"10.1128\/JB.185.13.3828-3841.2003","article-title":"Identification of pyrene-induced proteins in Mycobacterium spp. strain 6PY1: Evidence for two ring-hydroxylating dioxygenases","volume":"185","author":"Krivobok","year":"2003","journal-title":"Journal of Bacteriology"},{"key":"10.1016\/bs.mie.2016.11.003_bb0090","doi-asserted-by":"crossref","first-page":"1493","DOI":"10.1128\/JB.187.4.1493-1503.2005","article-title":"Substrate-dependent regulation of anaerobic degradation pathways for toluene and ethylbenzene in a denitrifying bacterium, strain EbN1","volume":"187","author":"Kuhner","year":"2005","journal-title":"Journal of Bacteriology"},{"key":"10.1016\/bs.mie.2016.11.003_bb0095","doi-asserted-by":"crossref","first-page":"3330","DOI":"10.1021\/es0489801","article-title":"Plot and field studies on bioremediation of p-nitrophenol contaminated soil using Arthrobacter protophormiae RKJ100","volume":"39","author":"Labana","year":"2005","journal-title":"Environmental Science & Technology"},{"issue":"12","key":"10.1016\/bs.mie.2016.11.003_bb0100","doi-asserted-by":"crossref","first-page":"952","DOI":"10.1038\/nrm2067","article-title":"Functional and quantitative proteomics using SILAC","volume":"7","author":"Mann","year":"2006","journal-title":"Nature Reviews Molecular Cell Biology"},{"issue":"15","key":"10.1016\/bs.mie.2016.11.003_bb0105","doi-asserted-by":"crossref","first-page":"3872","DOI":"10.1128\/JB.00597-12","article-title":"Delineation of the caffeine C-8 oxidation pathway in Pseudomonas sp. strain CBB1 via characterization of a new trimethyluric acid monooxygenase and genes involved in trimethyluric acid metabolism","volume":"194","author":"Mohanty","year":"2012","journal-title":"Journal of Bacteriology"},{"issue":"8","key":"10.1016\/bs.mie.2016.11.003_bb0110","doi-asserted-by":"crossref","first-page":"1375","DOI":"10.1007\/s00018-013-1497-8","article-title":"The buzz on caffeine in invertebrates: Effects on behavior and molecular mechanisms","volume":"71","author":"Mustard","year":"2014","journal-title":"Cellular and Molecular Life Sciences"},{"issue":"1","key":"10.1016\/bs.mie.2016.11.003_bb0115","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1016\/j.bbr.2012.04.014","article-title":"Consumption of an acute dose of caffeine reduces acquisition but not memory in the honey bee","volume":"232","author":"Mustard","year":"2012","journal-title":"Behavioural Brain Research"},{"key":"10.1016\/bs.mie.2016.11.003_bb0120","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1126\/science.6207592","article-title":"Caffeine and related methylxanthines, possible naturally occurring pesticides","volume":"226","author":"Nathanson","year":"1984","journal-title":"Science"},{"issue":"5","key":"10.1016\/bs.mie.2016.11.003_bb0125","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1074\/mcp.M200025-MCP200","article-title":"Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics","volume":"1","author":"Ong","year":"2002","journal-title":"Molecular & Cellular Proteomics"},{"key":"10.1016\/bs.mie.2016.11.003_bb0130","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1016\/j.jprot.2013.05.020","article-title":"Proteogenomic insights into salt tolerance by a halotolerant alpha-proteobacterium isolated from an Andean saline spring","volume":"97","author":"Rubiano-Labrador","year":"2014","journal-title":"Journal of Proteomics"},{"key":"10.1016\/bs.mie.2016.11.003_bb0135","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1016\/S0167-7799(02)01943-1","article-title":"Polycyclic aromatic hydrocarbons: Environmental pollution and bioremediation","volume":"20","author":"Samanta","year":"2002","journal-title":"Trends in Biotechnology"},{"key":"10.1016\/bs.mie.2016.11.003_bb0140","first-page":"149","article-title":"Methylxanthine composition and consumption patterns of cocoa and chocolate products","volume":"158","author":"Shively","year":"1984","journal-title":"Progress in Clinical Biological Research"},{"key":"10.1016\/bs.mie.2016.11.003_bb0145","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1016\/j.jprot.2014.07.006","article-title":"Comprehensive proteome analysis of the response of Pseudomonas putida KT2440 to the flavor compound vanillin","volume":"109","author":"Simon","year":"2014","journal-title":"Journal of Proteomics"},{"issue":"4","key":"10.1016\/bs.mie.2016.11.003_bb0150","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1093\/bfgp\/eli006","article-title":"Transcriptomics, proteomics and interactomics: Unique approaches to track the insights of bioremediation","volume":"4","author":"Singh","year":"2006","journal-title":"Briefings in Functional Genomics & Proteomics"},{"issue":"8","key":"10.1016\/bs.mie.2016.11.003_bb0155","doi-asserted-by":"crossref","first-page":"2041","DOI":"10.1128\/JB.06637-11","article-title":"Novel, highly specific N-demethylases enable bacteria to live on caffeine and related purine alkaloids","volume":"194","author":"Summers","year":"2012","journal-title":"Journal of Bacteriology"},{"issue":"Pt 2","key":"10.1016\/bs.mie.2016.11.003_bb0160","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1099\/mic.0.043612-0","article-title":"Characterization of a broad-specificity non-haem iron N-demethylase from Pseudomonas putida CBB5 capable of utilizing several purine alkaloids as sole carbon and nitrogen source","volume":"157","author":"Summers","year":"2011","journal-title":"Microbiology"},{"issue":"17","key":"10.1016\/bs.mie.2016.11.003_bb0170","doi-asserted-by":"crossref","first-page":"3933","DOI":"10.1128\/JB.00585-13","article-title":"Caffeine junkie, an unprecedented glutathione S-transferase-dependent oxygenase required for caffeine degradation by Pseudomonas putida CBB5","volume":"195","author":"Summers","year":"2013","journal-title":"Journal of Bacteriology"},{"issue":"8","key":"10.1016\/bs.mie.2016.11.003_bb0175","doi-asserted-by":"crossref","first-page":"1895","DOI":"10.1021\/ac0262560","article-title":"Tandem mass tags: A novel quantification strategy for comparative analysis of complex protein mixtures by MS\/MS","volume":"75","author":"Thompson","year":"2003","journal-title":"Analytical Chemistry"},{"key":"10.1016\/bs.mie.2016.11.003_bb0180","doi-asserted-by":"crossref","first-page":"S119","DOI":"10.1002\/pmic.200500422","article-title":"Proteomic and transcriptional characterization of aromatic degradation pathways in Rhodococcus sp. strain TFB","volume":"6","author":"Tom\u00e1s-Gallardo","year":"2006","journal-title":"Proteomics"},{"issue":"7","key":"10.1016\/bs.mie.2016.11.003_bb0185","doi-asserted-by":"crossref","first-page":"1771","DOI":"10.1002\/pmic.200800642","article-title":"Identification of proteins of Neisseria meningitidis induced under iron-limiting conditions using the isobaric tandem mass tag (TMT) labeling approach","volume":"9","author":"van Ulsen","year":"2009","journal-title":"Proteomics"},{"key":"10.1016\/bs.mie.2016.11.003_bb0190","doi-asserted-by":"crossref","first-page":"2204","DOI":"10.1002\/(SICI)1522-2683(19990801)20:11<2204::AID-ELPS2204>3.0.CO;2-I","article-title":"Differential protein expression by Pseudomonas fragi submitted to various stresses","volume":"20","author":"Vasseur","year":"1999","journal-title":"Electrophoresis"},{"key":"10.1016\/bs.mie.2016.11.003_bb9005","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1016\/j.ab.2016.05.011","article-title":"Comparison and optimization of methods for the simultaneous extraction of DNA, RNA, proteins, and metabolites","volume":"508","author":"Vorreiter","year":"2016","journal-title":"Analytical Biochemistry"},{"key":"10.1016\/bs.mie.2016.11.003_bb0195","first-page":"3396","article-title":"Altered protein expression of Streptococcus oralis cultured at low pH revealed by two-dimensional gel electrophoresis","volume":"67","author":"Wilkins","year":"2001","journal-title":"Applied Microbiology Biotechnology"},{"issue":"8","key":"10.1016\/bs.mie.2016.11.003_bb0200","doi-asserted-by":"crossref","first-page":"2186","DOI":"10.1111\/j.1462-2920.2011.02467.x","article-title":"Defining the response of a microorganism to temperatures that span its complete growth temperature range (-2\u00b0C to 28\u00b0C) using multiplex quantitative proteomics","volume":"13","author":"Williams","year":"2011","journal-title":"Environmental Microbiology"},{"issue":"2","key":"10.1016\/bs.mie.2016.11.003_bb0205","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1128\/JB.01390-07","article-title":"A novel caffeine dehydrogenase in Pseudomonas sp. strain CBB1 oxidizes caffeine to trimethyluric acid","volume":"190","author":"Yu","year":"2008","journal-title":"Journal of Bacteriology"},{"issue":"14","key":"10.1016\/bs.mie.2016.11.003_bb0210","doi-asserted-by":"crossref","first-page":"4624","DOI":"10.1128\/JB.00409-09","article-title":"Two distinct pathways for metabolism of theophylline and caffeine are coexpressed in Pseudomonas putida CBB5","volume":"191","author":"Yu","year":"2009","journal-title":"Journal of Bacteriology"},{"issue":"1","key":"10.1016\/bs.mie.2016.11.003_bb0215","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1021\/pr500751w","article-title":"Rapid identification and quantitative validation of a caffeine-degrading pathway in Pseudomonas sp. CES","volume":"14","author":"Yu","year":"2015","journal-title":"Journal of Proteome Research"},{"issue":"3","key":"10.1016\/bs.mie.2016.11.003_bb0220","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0091162","article-title":"Proteomic strategy for the analysis of the polychlorobiphenyl-degrading cyanobacterium Anabaena PD-1 exposed to Aroclor 1254","volume":"9","author":"Zhang","year":"2014","journal-title":"PLoS One"},{"issue":"4","key":"10.1016\/bs.mie.2016.11.003_bb0225","doi-asserted-by":"crossref","first-page":"874","DOI":"10.1002\/pmic.200701005","article-title":"Insights into environmental bioremediation by microorganisms through functional genomics and proteomics","volume":"8","author":"Zhao","year":"2008","journal-title":"Proteomics"},{"key":"10.1016\/bs.mie.2016.11.003_bb0230","doi-asserted-by":"crossref","first-page":"1868","DOI":"10.1002\/pmic.200401081","article-title":"Proteome investigation of the global regulatory role of sigma 54 in response to gentisate induction in Pseudomonas alcaligenes NCIMB 9867","volume":"5","author":"Zhao","year":"2005","journal-title":"Proteomics"}],"container-title":["Methods in Enzymology","Proteomics in Biology, Part B"],"original-title":[],"link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0076687916304220?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0076687916304220?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2018,9,5]],"date-time":"2018-09-05T01:53:05Z","timestamp":1536112385000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0076687916304220"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017]]},"references-count":47,"URL":"https:\/\/doi.org\/10.1016\/bs.mie.2016.11.003","relation":{},"ISSN":["0076-6879"],"issn-type":[{"value":"0076-6879","type":"print"}],"subject":[],"published":{"date-parts":[[2017]]}}}