Summary of Study ST000267
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 | ST000267 |
Study Title | Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv3722c |
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 |
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: | SU000287 |
Subject Type: | Bacterial cells |
Subject Species: | Mycobacterium tuberculosis H37Rv |
Taxonomy ID: | 83332 |
Genotype Strain: | Mycobacterium tuberculosis H37Rv, Rv3722c |
Species Group: | Bacteria |
Factors:
Subject type: Bacterial cells; Subject species: Mycobacterium tuberculosis H37Rv (Factor headings shown in green)
mb_sample_id | local_sample_id | timepoint (min) |
---|---|---|
SA012066 | 3722c_A_0 | 0 |
SA012069 | 3722c_B_0 | 0 |
SA012072 | 3722c_C_0 | 0 |
SA012067 | 3722c_A_15 | 15 |
SA012070 | 3722c_B_15 | 15 |
SA012073 | 3722c_C_15 | 15 |
SA012068 | 3722c_A_30 | 30 |
SA012071 | 3722c_B_30 | 30 |
SA012074 | 3722c_C_30 | 30 |
Showing results 1 to 9 of 9 |
Collection:
Collection ID: | CO000281 |
Collection Summary: | protein expression |
Collection Protocol ID: | Rv3722c 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: | TR000301 |
Sample Preparation:
Sampleprep ID: | SP000295 |
Sampleprep Summary: | 8 uM enzyme incubated at 37C 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 | AN000427 | AN000428 |
---|---|---|
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 | peak height |
Chromatography:
Chromatography ID: | CH000299 |
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: | MS000368 |
Analysis ID: | AN000427 |
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: | MS000369 |
Analysis ID: | AN000428 |
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 |