Comprehensive Phosphoproteome Analysis of INS-1 Pancreatic Beta-Cells using Various Digestion Strategies Coupled with Liquid Chromatography-Tandem Mass Spectrometry. Han, D., Moon, S., Kim, Y., Ho, W.K., Kim, K., Kang, Y., Jun, H., & Kim, Y. J. Proteome Res., 11(4):2206–2223, 2012. doi abstract bibtex Type 2 diabetes results from aberrant regulation of the phosphorylation cascade in beta-cells. Phosphorylation in pancreatic beta-cells has not been examd. extensively, except with regard to subcellular phosphoproteomes using mitochondria. Thus, robust, comprehensive anal. strategies are needed to characterize the many phosphorylated proteins that exist, because of their low abundance, the low stoichiometry of phosphorylation, and the dynamic regulation of phosphoproteins. In this study, the authors attempted to generate data on a large-scale phosphoproteome from the INS-1 rat pancreatic beta-cell line using linear ion trap MS/MS. To profile the phosphoproteome in-depth, the authors used comprehensive phosphoproteomic strategies, including detergent-based protein extn. (SDS and SDC), differential sample prepn. (in-gel, in-soln. digestion, and FASP), TiO2 enrichment, and MS replicate analyses (MS2-only and multiple-stage activation). All spectra were processed and validated by stringent multiple filtering using target and decoy databases. The authors identified 2467 distinct phosphorylation sites on 1419 phosphoproteins using 4 mg of INS-1 cell lysate in 24 LC-MS/MS runs, of which 683 (27.7%) were considered novel phosphorylation sites that have not been characterized in human, mouse, or rat homologs. The authors' informatics data constitute a rich bioinformatics resource for investigating the function of reversible phosphorylation in pancreatic beta-cells. In particular, novel phosphorylation sites on proteins that mediate the pathol. of type 2 diabetes, such as Pdx-1, Nkx.2, and Srebf1, will be valuable targets in ongoing phosphoproteomics studies. [on SciFinder(R)]
@article{ han_comprehensive_2012,
title = {Comprehensive Phosphoproteome Analysis of {INS-1} Pancreatic Beta-Cells using Various Digestion Strategies Coupled with Liquid Chromatography-Tandem Mass Spectrometry.},
volume = {11},
issn = {1535-3893},
doi = {10.1021/pr200990b},
abstract = {Type 2 diabetes results from aberrant regulation of the phosphorylation cascade in beta-cells. Phosphorylation in pancreatic beta-cells has not been examd. extensively, except with regard to subcellular phosphoproteomes using mitochondria. Thus, robust, comprehensive anal. strategies are needed to characterize the many phosphorylated proteins that exist, because of their low abundance, the low stoichiometry of phosphorylation, and the dynamic regulation of phosphoproteins. In this study, the authors attempted to generate data on a large-scale phosphoproteome from the {INS-1} rat pancreatic beta-cell line using linear ion trap {MS/MS.} To profile the phosphoproteome in-depth, the authors used comprehensive phosphoproteomic strategies, including detergent-based protein extn. ({SDS} and {SDC)}, differential sample prepn. (in-gel, in-soln. digestion, and {FASP)}, {TiO2} enrichment, and {MS} replicate analyses ({MS2-only} and multiple-stage activation). All spectra were processed and validated by stringent multiple filtering using target and decoy databases. The authors identified 2467 distinct phosphorylation sites on 1419 phosphoproteins using 4 mg of {INS-1} cell lysate in 24 {LC-MS/MS} runs, of which 683 (27.7%) were considered novel phosphorylation sites that have not been characterized in human, mouse, or rat homologs. The authors' informatics data constitute a rich bioinformatics resource for investigating the function of reversible phosphorylation in pancreatic beta-cells. In particular, novel phosphorylation sites on proteins that mediate the pathol. of type 2 diabetes, such as Pdx-1, Nkx.2, and Srebf1, will be valuable targets in ongoing phosphoproteomics studies. [on {SciFinder(R)]}},
number = {4},
journal = {J. Proteome Res.},
author = {Han, Dohyun and Moon, Sungyoon and Kim, Yikwon and Ho, Won-Kyung and Kim, Kyunggon and Kang, Yup and Jun, Heesook and Kim, Youngsoo.},
year = {2012},
keywords = {{HPLC}, {INS1}, beta, cell, digestion, mass, pancreatic, phosphoproteomics, spectrometry},
pages = {2206–2223}
}
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{"_id":{"_str":"53732dcfb3aa042605001b2a"},"__v":0,"authorIDs":[],"author_short":["Han, D.","Moon, S.","Kim, Y.","Ho, W.K.","Kim, K.","Kang, Y.","Jun, H.","Kim, Y."],"bibbaseid":"han-moon-kim-ho-kim-kang-jun-kim-comprehensivephosphoproteomeanalysisofins1pancreaticbetacellsusingvariousdigestionstrategiescoupledwithliquidchromatographytandemmassspectrometry-2012","bibdata":{"downloads":0,"keyword":["HPLC","INS1","beta","cell","digestion","mass","pancreatic","phosphoproteomics","spectrometry"],"bibbaseid":"han-moon-kim-ho-kim-kang-jun-kim-comprehensivephosphoproteomeanalysisofins1pancreaticbetacellsusingvariousdigestionstrategiescoupledwithliquidchromatographytandemmassspectrometry-2012","urls":{},"role":"author","year":"2012","volume":"11","type":"article","title":"Comprehensive Phosphoproteome Analysis of INS-1 Pancreatic Beta-Cells using Various Digestion Strategies Coupled with Liquid Chromatography-Tandem Mass Spectrometry.","pages":"2206–2223","number":"4","keywords":"HPLC, INS1, beta, cell, digestion, mass, pancreatic, phosphoproteomics, spectrometry","key":"han_comprehensive_2012","journal":"J. Proteome Res.","issn":"1535-3893","id":"han_comprehensive_2012","doi":"10.1021/pr200990b","bibtype":"article","bibtex":"@article{ han_comprehensive_2012,\n title = {Comprehensive Phosphoproteome Analysis of {INS-1} Pancreatic Beta-Cells using Various Digestion Strategies Coupled with Liquid Chromatography-Tandem Mass Spectrometry.},\n volume = {11},\n issn = {1535-3893},\n doi = {10.1021/pr200990b},\n abstract = {Type 2 diabetes results from aberrant regulation of the phosphorylation cascade in beta-cells. Phosphorylation in pancreatic beta-cells has not been examd. extensively, except with regard to subcellular phosphoproteomes using mitochondria. Thus, robust, comprehensive anal. strategies are needed to characterize the many phosphorylated proteins that exist, because of their low abundance, the low stoichiometry of phosphorylation, and the dynamic regulation of phosphoproteins. In this study, the authors attempted to generate data on a large-scale phosphoproteome from the {INS-1} rat pancreatic beta-cell line using linear ion trap {MS/MS.} To profile the phosphoproteome in-depth, the authors used comprehensive phosphoproteomic strategies, including detergent-based protein extn. ({SDS} and {SDC)}, differential sample prepn. (in-gel, in-soln. digestion, and {FASP)}, {TiO2} enrichment, and {MS} replicate analyses ({MS2-only} and multiple-stage activation). All spectra were processed and validated by stringent multiple filtering using target and decoy databases. The authors identified 2467 distinct phosphorylation sites on 1419 phosphoproteins using 4 mg of {INS-1} cell lysate in 24 {LC-MS/MS} runs, of which 683 (27.7%) were considered novel phosphorylation sites that have not been characterized in human, mouse, or rat homologs. The authors' informatics data constitute a rich bioinformatics resource for investigating the function of reversible phosphorylation in pancreatic beta-cells. In particular, novel phosphorylation sites on proteins that mediate the pathol. of type 2 diabetes, such as Pdx-1, Nkx.2, and Srebf1, will be valuable targets in ongoing phosphoproteomics studies. [on {SciFinder(R)]}},\n number = {4},\n journal = {J. Proteome Res.},\n author = {Han, Dohyun and Moon, Sungyoon and Kim, Yikwon and Ho, Won-Kyung and Kim, Kyunggon and Kang, Yup and Jun, Heesook and Kim, Youngsoo.},\n year = {2012},\n keywords = {{HPLC}, {INS1}, beta, cell, digestion, mass, pancreatic, phosphoproteomics, spectrometry},\n pages = {2206–2223}\n}","author_short":["Han, D.","Moon, S.","Kim, Y.","Ho, W.K.","Kim, K.","Kang, Y.","Jun, H.","Kim, Y."],"author":["Han, Dohyun","Moon, Sungyoon","Kim, Yikwon","Ho, Won-Kyung","Kim, Kyunggon","Kang, Yup","Jun, Heesook","Kim, Youngsoo."],"abstract":"Type 2 diabetes results from aberrant regulation of the phosphorylation cascade in beta-cells. Phosphorylation in pancreatic beta-cells has not been examd. extensively, except with regard to subcellular phosphoproteomes using mitochondria. Thus, robust, comprehensive anal. strategies are needed to characterize the many phosphorylated proteins that exist, because of their low abundance, the low stoichiometry of phosphorylation, and the dynamic regulation of phosphoproteins. In this study, the authors attempted to generate data on a large-scale phosphoproteome from the INS-1 rat pancreatic beta-cell line using linear ion trap MS/MS. To profile the phosphoproteome in-depth, the authors used comprehensive phosphoproteomic strategies, including detergent-based protein extn. (SDS and SDC), differential sample prepn. (in-gel, in-soln. digestion, and FASP), TiO2 enrichment, and MS replicate analyses (MS2-only and multiple-stage activation). All spectra were processed and validated by stringent multiple filtering using target and decoy databases. The authors identified 2467 distinct phosphorylation sites on 1419 phosphoproteins using 4 mg of INS-1 cell lysate in 24 LC-MS/MS runs, of which 683 (27.7%) were considered novel phosphorylation sites that have not been characterized in human, mouse, or rat homologs. The authors' informatics data constitute a rich bioinformatics resource for investigating the function of reversible phosphorylation in pancreatic beta-cells. In particular, novel phosphorylation sites on proteins that mediate the pathol. of type 2 diabetes, such as Pdx-1, Nkx.2, and Srebf1, will be valuable targets in ongoing phosphoproteomics studies. 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