Summary of Study ST000262

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 IDST000262
Study TitleActivity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv1713
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
Num Groups3 replicates X 3 timepoints X with/without GTP
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:SU000282
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) co-factor added to lysate
SA0120131mMGTP1713_A_00 1mM GTP
SA0120191mMGTP1713_B_00 1mM GTP
SA0120251mMGTP1713_C_00 1mM GTP
SA0120121713_A_00 None
SA0120181713_B_00 None
SA0120241713_C_00 None
SA0120151mMGTP1713_A_1515 1mM GTP
SA0120211mMGTP1713_B_1515 1mM GTP
SA0120271mMGTP1713_C_1515 1mM GTP
SA0120141713_A_1515 None
SA0120201713_B_1515 None
SA0120261713_C_1515 None
SA0120171mMGTP1713_A_3030 1mM GTP
SA0120231mMGTP1713_B_3030 1mM GTP
SA0120291mMGTP1713_C_3030 1mM GTP
SA0120161713_A_3030 None
SA0120221713_B_3030 None
SA0120281713_C_3030 None
Showing results 1 to 18 of 18

Collection:

Collection ID:CO000276
Collection Summary:protein expression
Collection Protocol ID:Rv1713 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:TR000296

Sample Preparation:

Sampleprep ID:SP000290
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 AN000417 AN000418
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:CH000294
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:MS000358
Analysis ID:AN000417
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:MS000359
Analysis ID:AN000418
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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