General Information
- Experiment ID
- OEX010850
- Experiment Name
- Bacterial proteomics
- Experiment Type
- Proteomic
- Description
- Roseobacter strains were cultured in modified Silicibacter basal medium, pH ~7.2, added with 10mM DHPS or 15mM acetate, respectively. Cells were harvested via centrifugation at the exponential phase or the stationary phase. A Label-free analyses of total proteins of crude extracts of DHPS- and acetate-grown cells was investigated.
- Protocol
- The cells were washed twice with phosphate-buffered saline (PBS, pH 7.4), then were flash-frozen in liquid nitrogen and stored at − 80 °C. For digestion, the protein solution was reduced with 5 mM dithiothreitol for 30 min at 56 °C and alkylated with 11 mM iodoacetamide for 15 min at room temperature in darkness. The protein sample was then diluted by adding 100 mM TEAB to urea concentration less than 2M. Finally, trypsin was added at 1:50 trypsin-to-protein mass ratio for the first digestion overnight and 1:100 trypsin-to-protein mass ratio for a second 4 h-digestion.
Experiment information
- Attributes
-
enzyme Trypsin/P quantification n/a instrument_type n/a experimental_method Shotgun proteomics fixed_modifications n/a variable_modifications n/a platform Q Exactive Plus - Project
-
1
Project ID Project name Create Date OEP001337 Proteomic characteristics of three Roseobacter strains, DSS-3, DFL12 and OCh114, gowing in DHPS and acetate 2020-12-01 - Samples
-
11
Sample ID Sample Name Organism Tissue Create Date OES055190 OCh114_DHPS_2d Roseobacter denitrificans OCh 114 N/A 2020-12-01 OES055252 OCh114_DHPS_4d Roseobacter denitrificans OCh 114 N/A 2020-12-02 OES055189 DFL12_36h_DHPS Dinoroseobacter shibae DFL 12 = DSM 16493 N/A 2020-12-01 OES055233 DFL12_61h_DHPS Dinoroseobacter shibae DFL 12 = DSM 16493 N/A 2020-12-02 OES055231 DFL12_acetate Dinoroseobacter shibae DFL 12 = DSM 16493 N/A 2020-12-01 OES055232 OCh114_acetate Roseobacter denitrificans OCh 114 N/A 2020-12-01 OES055228 DSS-3_Acetate Ruegeria pomeroyi DSS-3 N/A 2020-12-01 OES055230 DSS-3_R-DHPS Ruegeria pomeroyi DSS-3 N/A 2020-12-01 OES055227 DSS-3_107_DHPS Ruegeria pomeroyi DSS-3 N/A 2020-12-01 OES055188 DSS-3_48h_DHPS Ruegeria pomeroyi DSS-3 N/A 2020-12-01 OES055234 DSS-3_S-DHPS Ruegeria pomeroyi DSS-3 N/A 2020-12-02 - Runs
-
33
Run ID Run Name Sample Data Num Create Date OER090126 OCh114_DHPS_2d_1 OCh114_DHPS_2d 4 2020-12-01 OER090127 OCh114_DHPS_2d_3 OCh114_DHPS_2d 4 2020-12-01 OER090128 OCh114_DHPS_2d_9 OCh114_DHPS_2d 4 2020-12-01 OER090129 OCh114_DHPS_4d_2 OCh114_DHPS_4d 4 2020-12-01 OER090130 OCh114_DHPS_4d_4 OCh114_DHPS_4d 4 2020-12-01 OER090131 OCh114_DHPS_4d_7 OCh114_DHPS_4d 4 2020-12-01 OER090142 DFL12_36h_2 DFL12_36h_DHPS 4 2020-12-02 OER090143 DFL12_36h_4 DFL12_36h_DHPS 4 2020-12-02 OER090144 DFL12_36h_5 DFL12_36h_DHPS 4 2020-12-02 OER090145 DFL12_61h_DHPS DFL12_61h_DHPS 4 2020-12-02 OER090146 DFL12_61h_DHPS_8 DFL12_61h_DHPS 4 2020-12-02 OER090147 DFL12_61h_DHPS_9 DFL12_61h_DHPS 4 2020-12-02 OER090148 DFL12_acetate_1 DFL12_acetate 4 2020-12-02 OER090149 DFL12_acetate_2 DFL12_acetate 4 2020-12-02 OER090150 DFL12_acetate_3 DFL12_acetate 4 2020-12-02 OER090151 OCh114_acetate_1 OCh114_acetate 4 2020-12-02 OER090152 OCh114_acetate_2 OCh114_acetate 4 2020-12-02 OER090153 OCh114_acetate_3 OCh114_acetate 4 2020-12-02 OER090154 DSS-3_Acetate_1 DSS-3_Acetate 4 2020-12-02 OER090155 DSS-3_Acetate_2 DSS-3_Acetate 4 2020-12-02 OER090156 DSS-3_Acetate_3 DSS-3_Acetate 4 2020-12-02 OER090157 DSS-3_R-DHPS_1 DSS-3_R-DHPS 4 2020-12-02 OER090158 DSS-3_R-DHPS_3 DSS-3_R-DHPS 4 2020-12-02 OER090159 DSS-3_R-DHPS_4 DSS-3_R-DHPS 4 2020-12-02 OER090160 DSS-3_DHPS_107_6 DSS-3_107_DHPS 4 2020-12-02 OER090161 DSS-3_DHPS_107_7 DSS-3_107_DHPS 4 2020-12-02 OER090162 DSS-3_DHPS_48h_1 DSS-3_48h_DHPS 4 2020-12-02 OER090163 DSS-3_DHPS_48h_3 DSS-3_48h_DHPS 4 2020-12-02 OER090164 DSS-3_DHPS_48h_5 DSS-3_48h_DHPS 4 2020-12-02 OER090165 DSS-3_S-DHPS_1 DSS-3_S-DHPS 4 2020-12-02 OER090166 DSS-3_S-DHPS_3 DSS-3_S-DHPS 4 2020-12-02 OER090167 DSS-3_S-DHPS_4 DSS-3_S-DHPS 4 2020-12-02 OER090183 DSS-3_DHPS_107_4 DSS-3_107_DHPS 4 2020-12-02 - Analysis
-
3
Analysis ID Analysis Title Analysis Type Data Num Create Date OEZ007030 Proteomic of DSS-3 grown in DHPS and Acetate Sequence Annotation 0 2020-12-02 OEZ007031 Proteomic of DFL12 grown in DHPS and Acetate Sequence Annotation 0 2020-12-02 OEZ007032 Proteomic of OCh114 grown in DHPS and Acetate Sequence Annotation 0 2020-12-02
Author Information
- Create Date
- 2020-12-01
- Last Modified
- 2023-03-13
- Submission
- Xiaofeng Chen
- State Key Laboratory of Marine Environmental Science