Summary of Study ST000264
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000187. The data can be accessed directly via it's Project DOI: 10.21228/M8388M This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000264 |
| Study Title | Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv3280 |
| Study Type | timecourse |
| Study Summary | These experiments involve incubating various proteins of unknown function in the M. tuberculosis genome with whole-cell lysate and assaying changes in metabolite levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might catalyze. |
| Institute | Weill Cornell Medicine |
| Department | Microbiology and Immunology |
| Last Name | Rhee |
| First Name | Kyu |
| Address | Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, NY |
| kyr9001@med.cornell.edu | |
| Submit Date | 2015-11-13 |
| Num Groups | 3 replicates X 3 timepoints |
| Study Comments | The timepoints in the datafiles refer the amount of time (in minutes) that each protein was incubated with lysate.The units for 'mzmed' are mass/charge. The units for 'rtmed' are seconds (retention time). The units for all the other data columns in the spreadsheets are arbitrary; they are integrated peak counts. In this study, Rv1713 was incubated with lysate with and without 1mM GTP added as a co-factor. |
| Raw Data Available | No |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2016-12-22 |
| Release Version | 2 |
| Release Comments | Updated study design factors |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000187 |
| Project DOI: | doi: 10.21228/M8388M |
| Project Title: | FLUTE: Functionalizing Lists of Unknown TB Entities |
| Project Type: | NIH U19 |
| Project Summary: | functional genomics of proteins of unknown function in M. tuberculosis |
| Institute: | Weill Cornell Medicine |
| Department: | Microbiology and Immunology |
| Last Name: | Rhee |
| First Name: | Kyu |
| Address: | #N/A |
| Email: | kyr9001@med.cornell.edu |
Subject:
| Subject ID: | SU000284 |
| Subject Type: | Bacterial cells |
| Subject Species: | Mycobacterium tuberculosis H37Rv |
| Taxonomy ID: | 83332 |
| Genotype Strain: | Mycobacterium tuberculosis H37Rv, taxid: |
| Species Group: | Microorganism |
Factors:
Subject type: Bacterial cells; Subject species: Mycobacterium tuberculosis H37Rv (Factor headings shown in green)
| mb_sample_id | local_sample_id | timepoint (min) |
|---|---|---|
| SA012039 | Rv3280_A_0 | 0 |
| SA012042 | Rv3280_B_0 | 0 |
| SA012045 | Rv3280_C_0 | 0 |
| SA012040 | Rv3280_A_15 | 15 |
| SA012043 | Rv3280_B_15 | 15 |
| SA012046 | Rv3280_C_15 | 15 |
| SA012041 | Rv3280_A_30 | 30 |
| SA012044 | Rv3280_B_30 | 30 |
| SA012047 | Rv3280_C_30 | 30 |
| Showing results 1 to 9 of 9 |
Collection:
| Collection ID: | CO000278 |
| Collection Summary: | protein expression |
| Collection Protocol ID: | Rv3280 from M. tuberculosis H37Rv was expressed in E. coli cells and purified... |
| Sample Type: | Bacterial cells |
| Collection Vials: | polypropylene microfuge tubes |
| Storage Vials: | Agilent polypropylene conical bottom vials |
Treatment:
| Treatment ID: | TR000298 |
Sample Preparation:
| Sampleprep ID: | SP000292 |
| Sampleprep Summary: | 10 uM enzyme incubated at 25C in M. bovis whole-cell extract |
| Processing Method: | extract was lyophilized and resuspended in 20 mM Tris-HCL pH 8.0 |
| Processing Storage Conditions: | cell pellet frozen at -80C |
| Extraction Method: | 70% acetonitrile |
| Extract Cleanup: | centrifugation followed by aspiration of supernatant and lyophilization |
| Extract Storage: | frozen at -80C |
Combined analysis:
| Analysis ID | AN000421 | AN000422 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Normal phase | Normal phase |
| Chromatography system | Agilent 1290 | Agilent 1290 |
| Column | Microsolv Diamond hydride (150mm,4um) | Microsolv Diamond hydride (150mm,4um) |
| MS Type | ESI | ESI |
| MS instrument type | TOF | TOF |
| MS instrument name | Agilent 6220 TOF | Agilent 6220 TOF |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | integrated peak counts | integrated peak counts |
Chromatography:
| Chromatography ID: | CH000296 |
| Chromatography Summary: | Aqueous normal phase diamond hydride |
| Methods Filename: | ANPpos ANP_neg |
| Instrument Name: | Agilent 1290 |
| Column Name: | Microsolv Diamond hydride (150mm,4um) |
| Flow Rate: | 0.4 ml/min |
| Solvent A: | 100% water; 0.2% formic acid |
| Solvent B: | 100% acetonitrile; 0.2% formic acid |
| Analytical Time: | 24 minutes |
| Washing Buffer: | 50% methanol |
| Chromatography Type: | Normal phase |
MS:
| MS ID: | MS000362 |
| Analysis ID: | AN000421 |
| Instrument Name: | Agilent 6220 TOF |
| Instrument Type: | TOF |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| Capillary Voltage: | 3500 |
| Dry Gas Flow: | 10 l/min |
| Dry Gas Temp: | 250 |
| Fragment Voltage: | 135V |
| Mass Accuracy: | 5 ppm |
| Nebulizer: | 35 |
| Octpole Voltage: | 400 |
| Scan Range Moverz: | 50-1200 |
| Scanning Cycle: | 1.4 |
| Skimmer Voltage: | 65 |
| MS ID: | MS000363 |
| Analysis ID: | AN000422 |
| Instrument Name: | Agilent 6220 TOF |
| Instrument Type: | TOF |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
| Capillary Voltage: | 3500 |
| Dry Gas Flow: | 10 l/min |
| Dry Gas Temp: | 250 |
| Fragment Voltage: | 135V |
| Mass Accuracy: | 5 ppm |
| Nebulizer: | 35 |
| Octpole Voltage: | 400 |
| Scan Range Moverz: | 50-1200 |
| Scanning Cycle: | 1.4 |
| Skimmer Voltage: | 65 |
