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.

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Study IDST000267
Study TitleActivity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv3722c
Study Typetimecourse
Study SummaryThese 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
DepartmentMicrobiology and Immunology
Last NameRhee
First NameKyu
AddressDepartment of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, NY
Emailkyr9001@med.cornell.edu
Submit Date2015-11-13
Study CommentsThe 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 AvailableNo
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2016-12-22
Release Version2
Release CommentsUpdated study design factors
Kyu Rhee Kyu Rhee
https://dx.doi.org/10.21228/M8388M
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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)
SA0120663722c_A_00
SA0120693722c_B_00
SA0120723722c_C_00
SA0120673722c_A_1515
SA0120703722c_B_1515
SA0120733722c_C_1515
SA0120683722c_A_3030
SA0120713722c_B_3030
SA0120743722c_C_3030
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
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