Differential Label-free Quantitative Proteomic Analysis of Shewanella oneidensis Cultured under Aerobic and Suboxic Conditions by Accurate Mass and Time Tag Approach

We describe the application of LC-MS without the use of stable isotope labeling for differential quantitative proteomic analysis of whole cell lysates of Shewanella oneidensis MR-1 cultured under aerobic and suboxic conditions. LC-MS/MS was used and was used and of analysis of of oneidensis was aerobic suboxic conditions. We describe the application of LC-MS without the use of stable isotope labeling for differential quantitative proteomic analysis of whole cell lysates of Shewanella oneidensis MR-1 cultured under aerobic and suboxic conditions. LC-MS/MS was used and was used and of analysis of of oneidensis was aerobic suboxic conditions. of the used for quantitative used and analysis of of and used and analysis of of and and LC-MS/MS the and the of the of the the of the analysis of the the the used for quantitative proteomic of the of and for for and for the of for the stable isotope labeling stable isotope labeling cell and analysis of isotope labeling cell and of quantitative proteomic the labeling stable and labeling and the for the of the of the of and quantitative the of use the of and and of under of and the of the use of for and the quantitative of of of and the of and of and of of and without labeling the of of LC-MS LC-MS of and without labeling the of LC-MS of and the of was of of and the of the the the of of and without labeling for proteomic and and of the and the the and the of for proteomic and of and of and and quantitative for the of the of the of describe differential quantitative proteomic and the and was used the Shewanella oneidensis MR-1 cultured under aerobic and suboxic used and and was of and Shewanella was and and and and used the and the the was for aerobic and for suboxic was the of of of the and of was for the was for LC-MS proteomic analysis and for and for proteomic the the cell and of and of and and cell for the and for was and for of was and of was used for and the was and analysis of the and for oneidensis under and quantitative for the of and for analysis the LC-MS/MS analysis of the oneidensis and for and for and the of the the the for was was and of for the of oneidensis cultured under aerobic and suboxic and without of used for the and of and and was the was the for and the cell for and of the the and of of the of the of of and of and of of the was the and was the of the of the the the and of the and of the of and of the use of for and the used for of for the of the of and used for was used the and was used the was used and used the of the used the differential quantitative analysis of oneidensis MR-1 the of oneidensis cultured under the for quantitative and and and and of oneidensis cultured under aerobic and suboxic and of and and for the and of the of and of the and of the the the of and the oneidensis under aerobic and suboxic and of oneidensis cultured under and under suboxic conditions. aerobic and suboxic and was and of of of the the and and of and quantitative of the the of of the of the of LC-MS/MS the the of the for and of for the of the of analysis of the of the the of of the the the of of of the of the of of of LC-MS/MS and of of of analysis of of of of for the of quantitative proteomic of the of of of of the LC-MS/MS the and of the the of and for quantitative and the of the and the of the the of the of the and of of proteomic and the used describe the of for the used for the used and the of the of and without labeling used the for the of the the the for the used and for was the of the of of the the the the of the of the of the of the for the of analysis of the of of the the of the of of the the for and and the of aerobic the of suboxic the and the of aerobic and suboxic of aerobic and suboxic oneidensis aerobic of aerobic of suboxic of and suboxic of and of for oneidensis of the the aerobic the under suboxic and aerobic under aerobic and and suboxic and We for of the under and for under the the the of MR-1 under aerobic and suboxic the was the of the aerobic and suboxic was the of and the suboxic aerobic of of aerobic and suboxic oneidensis aerobic aerobic the the aerobic suboxic the under aerobic aerobic under the and aerobic suboxic under of and of the and of the of aerobic and suboxic the of the of and of the suboxic the aerobic the aerobic and the suboxic of the the suboxic the the the aerobic the the of the of and of the of of and and for of of and of and the of and of and of for and the the aerobic and suboxic was the of the of the of the analysis was used the the and the the of and the the of the was the the of the of was the of the of was was and the use of the under the for the and for and for the of of the and of the and of and of the of of of the used for analysis of analysis of the the of and used and the of was and and for analysis of the of the was the of the the of of of the of the aerobic and suboxic and the of the of the We the of of suboxic aerobic the and the the of the the and the for was of for and the the the and and the the the of the and and the the of the the and of the for for the of the was the of the of and of aerobic and suboxic the of of for of the aerobic suboxic the of the analysis was used the and of analysis analysis the of the and the of the the proteomic the of the We the quantitative proteomic and the of the the and the MR-1 of the the Shewanella oneidensis under and and of Shewanella oneidensis of the Shewanella oneidensis under and for the of and for Shewanella for of the and the of Shewanella the suboxic the and of use of and aerobic and of under and of 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for used for quantitative proteomic and analysis the LC-MS the of of used of and without labeling for LC-MS and used analysis and for proteomic for and We the of and the the and for and and the the of the was for LC-MS analysis and for proteomic for and and of was and the was of the use of for and and for proteomic used the use of stable isotope labeling of the for the We for the use of labeling use of labeling and of the used for quantitative used and analysis of of and used and analysis of of and and LC-MS/MS the and the of the of the the of the analysis of the the the used for quantitative proteomic of the of and for for and for the of for the stable isotope labeling stable isotope labeling cell and analysis of isotope labeling cell and of quantitative proteomic the labeling stable and labeling and the for the of the of the of and quantitative the of use the of and and of under of and the of the use of for and the quantitative of of of and the of and of and of of and without labeling the of of LC-MS LC-MS of and without labeling the of LC-MS of and the of was of of and the of the the the of of and without labeling for proteomic and and of the and the the and the of for proteomic and of and of and and quantitative for the of the of the of describe differential quantitative proteomic and the and was used the Shewanella oneidensis MR-1 cultured under aerobic and suboxic used and and was of and Shewanella was and and and and used the and the the was for aerobic and for suboxic was the of of of the and of was for the was for LC-MS proteomic analysis and for and for proteomic the the cell and of and of and and cell for the and for was and for of was and of was used for and the was and analysis of the and for oneidensis under and quantitative for the of and for analysis the LC-MS/MS analysis of the oneidensis and for and for and the of the the the for was was and of for the of oneidensis cultured under aerobic and suboxic and without of used for the and of and and was the was the for and the cell for and of the the and of of the of the of of and of and of of the was the and was the of the of the the the and of the and of the of and of the use of for and the used for of for the of the of and used for was used the and was used the was used and used the of used and and was of and Shewanella was and and and and used the and the the was for aerobic and for suboxic was the of of of the and of was for the was for LC-MS proteomic analysis and for and for proteomic the the cell and of and of used and and was of and Shewanella was and and and and used the and the the was for aerobic and for suboxic was the of of of the and of was for the was for LC-MS proteomic analysis and for and for proteomic the the cell and of and of and and cell for the and for was and for of was and of was used for and the was and analysis of the and and cell for the and for was and for of was and of was used for and the was and analysis of the and for oneidensis under and quantitative for the of and for analysis the LC-MS/MS analysis of the oneidensis and for and for and the of the the the for was was and of for the of oneidensis under and quantitative for the of and for analysis the LC-MS/MS analysis of the oneidensis and for and for and the of the the the for was was and of for the of oneidensis cultured under aerobic and suboxic and without of used for the and of and and was the was the for and the cell for and of the the and of of the of the of oneidensis cultured under aerobic and suboxic and without of used for the and of and and was the was the for and the cell for and of the the and of of the of the of of and of and of of the was the and was the of the of the the the and of the and of the of and of the use of for and the used for of for the of the and of and of of the was the and was the of the of the the the and of the and of the of and of the use of for and the used for of for the of the of and used for was used the and was used the was used and used the of and used for was used the and was used the was used and used the of the used the differential quantitative analysis of oneidensis MR-1 the of oneidensis cultured under the for quantitative and and and and of oneidensis cultured under aerobic and suboxic and of and and for the and of the of and of the and of the the the of and the oneidensis under aerobic and suboxic and of oneidensis cultured under and under suboxic conditions. aerobic and suboxic and was and of of of the the and and of and quantitative of the the of of the of the of LC-MS/MS the the of the for and of for the of the of analysis of the of the the of of the the the of of of the of the of of of for the of quantitative proteomic of the of of of of the LC-MS/MS the and of the the of and for quantitative and the of the and the of the the of the of the and of of proteomic and the used describe the of for the used for the used and the of the of and without labeling used the for the of the the the for the used and for was the of the of of the the the the of the of the of the of the for the of analysis of the of of the the of the of of the the for and and the of aerobic the of suboxic the and the of aerobic and suboxic of aerobic and suboxic oneidensis aerobic of aerobic of suboxic of and suboxic of and of for oneidensis of the the aerobic the under suboxic and aerobic under aerobic and and suboxic and We for of the under and for under the the the of MR-1 under aerobic and suboxic the was the of the aerobic and suboxic was the of and the suboxic aerobic of of aerobic and suboxic oneidensis aerobic aerobic the the aerobic suboxic the under aerobic aerobic under the and aerobic suboxic under of and of the and of the of aerobic and suboxic the of the of and of the suboxic the aerobic the aerobic and the suboxic of the the suboxic the the the aerobic the the of the of and of the of of and and for of of and of and the of and of and of for and the the aerobic and suboxic was the of the of the of the analysis was used the the and the the of and the the of the was the the of the of was the of the of was was and the use of the under the for the and for and for the of of the and of the and of and of the of of of the used for analysis of analysis of the the of and used and the of was and and for analysis of the of the was the of the the of of of the of the aerobic and suboxic and the of the of the We the of of suboxic aerobic the and the the of the the and the for was of for and the the the and and the the the of the and and the the of the the and of the for for the of the was the of the of and of aerobic and suboxic the of of for of the aerobic suboxic the of the analysis was used the and of analysis analysis the of the and the of the the proteomic the of the We the quantitative proteomic and the of the the and the MR-1 of the the Shewanella oneidensis under and and of Shewanella oneidensis of the Shewanella oneidensis under and for the of and for Shewanella for of the and the of Shewanella the suboxic the and of use of and aerobic and of under and of Shewanella oneidensis of the of Shewanella of the and the of proteomic LC-MS without the use of stable isotope under the the of the the suboxic the aerobic under suboxic was for analysis and of of oneidensis aerobic suboxic of aerobic of aerobic of suboxic and of suboxic quantitative proteomic the the and of Shewanella oneidensis and the under aerobic and the and the proteomic was the proteomic and and proteomic and of Shewanella oneidensis the proteomic the proteomic and the proteomic without the proteomic and for and and used and of Shewanella oneidensis used of the for proteomic the of and for and and the of the and the the for analysis the and the of of We for of of for for used and the analysis of the and LC-MS/MS the the for LC-MS/MS for the the of the used the LC-MS/MS and LC-MS differential quantitative proteomic analysis of and of the of the the the quantitative proteomic the and of Shewanella oneidensis 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for the and of the of and of the and of the the the of and the oneidensis under aerobic and suboxic conditions. and of oneidensis cultured under and under suboxic conditions. aerobic and suboxic and was and of and of oneidensis cultured under and under suboxic conditions. aerobic and suboxic and was and of of of the the and and of and quantitative of the the of of the of the of LC-MS/MS the the of the for and of for the of the of analysis of the of the the of of the the the of of of the of the of of of for the of quantitative proteomic of the of of of of the LC-MS/MS the and of the the of and for quantitative and the of the and the of the the of the of the of the the and and of and quantitative of the the of of the of the of LC-MS/MS the the of the for and of for the of the of analysis of the of the the of of the the the of of of the of the of of of for the of quantitative proteomic of the of of of of the LC-MS/MS the and of the the of and for quantitative and the of the and the of the the of the of the and of of proteomic and the used describe the of for the used for the used and the of the of and without labeling used the for the of the the the for the used and for was the of the of of the the the the of the of the of the of the for the of analysis of the of of the the of the of of proteomic and the used describe the of for the used for the used and the of the of and without labeling used the for the of the the the for the used and for was the of the of of the the the the of the of the of the of the for the of analysis of the of of the the of the of of the the for and and the of aerobic the of suboxic the and the of aerobic and suboxic and of for oneidensis of the the aerobic the under suboxic and aerobic under aerobic and and suboxic and We for of the under and for under the the the of MR-1 under aerobic and suboxic the was the of the aerobic and suboxic was the of and the suboxic aerobic of of aerobic and suboxic oneidensis aerobic aerobic the the aerobic suboxic the under aerobic aerobic under the and aerobic suboxic under of and of the and of the the for and and the of aerobic the of suboxic the and the of aerobic and suboxic and of for oneidensis of the the aerobic the under suboxic and aerobic under aerobic and and suboxic and We for of the under and for under the the the of MR-1 under aerobic and suboxic the was the of the aerobic and suboxic was the of and the suboxic aerobic of and of the and of the of aerobic and suboxic the of the of and of the suboxic the aerobic the aerobic and the suboxic of the the suboxic the the the aerobic the the and and for of of and of and the of and of and the of aerobic and suboxic the of the of and of the suboxic the aerobic the aerobic and the suboxic of the the suboxic the the the aerobic the the and and for of of and of and the of and of and of for and the the aerobic and suboxic was the of the of the of the analysis was used the the and the the of and the the of the was the the of the of was the of the of was was and the use of the under the for the and for and for the of of the and of the the the aerobic and suboxic was the of the of the of the analysis was used the the and the the of and the the of the was the the of the of was the of the of was was and the use of the under the for the and for and for the of of the and of the and of and of the of of of the used for analysis of analysis of the the of and used and the of was and and for analysis of the of the was the of the the of of of the of the aerobic and suboxic and the of the of the We the of of suboxic aerobic the and the the of the the and the for was of for and the the the and and the the the of the and and the the of the the and of the for for the of the was the of the and of the of of of the used for analysis of analysis of the the of and We used and the of was and and for analysis of the of the was the of the the of of of the of the aerobic and suboxic and the of the of the We the of of suboxic aerobic the and the the of the the and the for was of for and the the We the and and the the the of the and and the the of the the and of the for for the of the was the of the analysis analysis the of the and the of the the proteomic the of the We the quantitative proteomic and the of the the and the MR-1 of the the Shewanella oneidensis under and and of Shewanella oneidensis of the Shewanella oneidensis under and for the of and for Shewanella for of the and the of Shewanella the suboxic the and of use of and aerobic and of under and of Shewanella oneidensis of the of Shewanella of the and the of proteomic LC-MS without the use of stable isotope under the the of the the suboxic the aerobic under suboxic was for analysis and quantitative proteomic the the and of Shewanella oneidensis and the under aerobic and the and the proteomic was the proteomic and and proteomic and of Shewanella oneidensis the proteomic the proteomic and the proteomic without the proteomic and for and and used and of Shewanella oneidensis used analysis analysis the of the and the of the the proteomic the of the We the quantitative proteomic and the of the the and the MR-1 of the the Shewanella oneidensis under and and of Shewanella oneidensis of the Shewanella oneidensis under and for the of and for Shewanella for of the and the of Shewanella the suboxic the and of use of and aerobic and of under and of Shewanella oneidensis of the of Shewanella of the and the of proteomic LC-MS without the use of stable isotope under the the of the the suboxic the aerobic under suboxic was for analysis and quantitative proteomic the the and of Shewanella oneidensis and the under aerobic and the and the proteomic was the proteomic and and proteomic and of Shewanella oneidensis the proteomic the proteomic and the proteomic without the proteomic and for and and used and of Shewanella oneidensis used of the for proteomic the of and for and and the of the and the the for analysis the and the of of We for of of for for used and the analysis of the and LC-MS/MS the the for LC-MS/MS for the the of the used the LC-MS/MS and the for proteomic the of and for and and the of the and the the for analysis the and the of of We for of of for for used and the analysis of the and LC-MS/MS the the for LC-MS/MS for the the of the used the LC-MS/MS and LC-MS differential quantitative proteomic analysis of and of the of the the the quantitative proteomic the and of Shewanella oneidensis the proteomic for and and the used used and for and analysis of for and for used for quantitative proteomic and analysis the LC-MS the of of used of and without labeling for LC-MS and used analysis and for proteomic for and We the of and the the and for and and the the of the was for LC-MS analysis and for proteomic for and and of was and the was of the use of for and and for proteomic used the use of stable isotope labeling of the for the We for the use of labeling use of labeling and LC-MS differential quantitative proteomic analysis of and of the of the the the quantitative proteomic the and of Shewanella oneidensis the proteomic for and and the used used and for and analysis of