Summary of Study ST001511

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 PR001018. The data can be accessed directly via it's Project DOI: 10.21228/M83T2V This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST001511
Study TitleSymbiotic bacteria-derived organic acids
Study SummaryMetabolomic profiles of six bacteria and K. oxytoca were compared to identify candidate metabolites that may prevent B. bassiana infection of D. antiqua.
Institute
Qilu University of Technology (Shandong Academy of Sciences)
Last NameZhou
First NameFangyuan
AddressNo. 28789 Jingshidong Road, Jinan, Shandong, 250103, China
Emailfangyuan_zhou@163.com
Phone+8618511761347
Submit Date2020-09-10
Raw Data AvailableYes
Raw Data File Type(s)wiff
Analysis Type DetailLC-MS
Release Date2022-01-02
Release Version1
Fangyuan Zhou Fangyuan Zhou
https://dx.doi.org/10.21228/M83T2V
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001018
Project DOI:doi: 10.21228/M83T2V
Project Title:Delia antiqua bacteria-derived organic acids
Project Summary:Metabolomic profiles of six bacteria and K. oxytoca were compared to identify candidate metabolites that may prevent B. bassiana infection of D. antiqua.
Institute:Qilu University of Technology (Shandong Academy of Sciences)
Last Name:Zhou
First Name:Fangyuan
Address:No. 28789 Jingshidong Road, Jinan, Shandong, 250103, China
Email:fangyuan_zhou@163.com
Phone:+8618511761347

Subject:

Subject ID:SU001585
Subject Type:Bacteria
Subject Species:Citrobacter freundii;Enterobacter ludwigii;Pseudomonas protegens;Serratia plymuthica;Sphingobacterium faecium;Stenotrophomonas maltophilia;Klebsiella oxytoca
Taxonomy ID:546;299767;380021;82996;34087;40324;571

Factors:

Subject type: Bacteria; Subject species: Citrobacter freundii;Enterobacter ludwigii;Pseudomonas protegens;Serratia plymuthica;Sphingobacterium faecium;Stenotrophomonas maltophilia;Klebsiella oxytoca (Factor headings shown in green)

mb_sample_id local_sample_id Sample Type
SA126893B505_3PCitrobacter freundii
SA126894B505_2PCitrobacter freundii
SA126895B505_2NCitrobacter freundii
SA126896B505_5PCitrobacter freundii
SA126897B505_1PCitrobacter freundii
SA126898B505_3NCitrobacter freundii
SA126899B505_6NCitrobacter freundii
SA126900B505_5NCitrobacter freundii
SA126901B505_4NCitrobacter freundii
SA126902B505_1NCitrobacter freundii
SA126903B505_6PCitrobacter freundii
SA126904B505_4PCitrobacter freundii
SA126905B424_6PEnterobacter ludwigii
SA126906B424_4PEnterobacter ludwigii
SA126907B424_3PEnterobacter ludwigii
SA126908B424_1NEnterobacter ludwigii
SA126909B424_2NEnterobacter ludwigii
SA126910B424_5NEnterobacter ludwigii
SA126911B424_4NEnterobacter ludwigii
SA126912B424_3NEnterobacter ludwigii
SA126913B424_2PEnterobacter ludwigii
SA126914B424_5PEnterobacter ludwigii
SA126915B424_6NEnterobacter ludwigii
SA126916B424_1PEnterobacter ludwigii
SA126917B313_4PKlebsiella oxytoca
SA126918B313_6PKlebsiella oxytoca
SA126919B313_3PKlebsiella oxytoca
SA126920B313_1PKlebsiella oxytoca
SA126921B313_2PKlebsiella oxytoca
SA126922B313_6NKlebsiella oxytoca
SA126923B313_5NKlebsiella oxytoca
SA126924B313_2NKlebsiella oxytoca
SA126925B313_1NKlebsiella oxytoca
SA126926B313_5PKlebsiella oxytoca
SA126927B313_4NKlebsiella oxytoca
SA126928B313_3NKlebsiella oxytoca
SA126929LB6NLB medium
SA126930LB1NLB medium
SA126931LB5PLB medium
SA126932LB6PLB medium
SA126933LB4PLB medium
SA126934LB3PLB medium
SA126935LB1PLB medium
SA126936LB2PLB medium
SA126937LB2NLB medium
SA126938LB3NLB medium
SA126939LB4NLB medium
SA126940LB5NLB medium
SA126941B108_2NNseudomonas protegens
SA126942B108_6NNseudomonas protegens
SA126943B108_3NNseudomonas protegens
SA126944B108_5NNseudomonas protegens
SA126945B108_1NNseudomonas protegens
SA126946B108_4NNseudomonas protegens
SA126947B108_5PPseudomonas protegens
SA126948B108_2PPseudomonas protegens
SA126949B108_1PPseudomonas protegens
SA126950B108_6PPseudomonas protegens
SA126951B108_3PPseudomonas protegens
SA126952B108_4PPseudomonas protegens
SA126953QC9NQuality Control
SA126954QC8NQuality Control
SA126955QC1NQuality Control
SA126956QC6PQuality Control
SA126957QC7PQuality Control
SA126958QC8PQuality Control
SA126959QC5PQuality Control
SA126960QC4PQuality Control
SA126961QC2PQuality Control
SA126962QC3PQuality Control
SA126963QC7NQuality Control
SA126964QC9PQuality Control
SA126965QC3NQuality Control
SA126966QC2NQuality Control
SA126967QC4NQuality Control
SA126968QC1PQuality Control
SA126969QC5NQuality Control
SA126970QC6NQuality Control
SA126971B585_1NSerratia plymuthica
SA126972B585_1PSerratia plymuthica
SA126973B585_2NSerratia plymuthica
SA126974B585_5NSerratia plymuthica
SA126975B585_2PSerratia plymuthica
SA126976B585_6NSerratia plymuthica
SA126977B585_3NSerratia plymuthica
SA126978B585_4NSerratia plymuthica
SA126979B585_3PSerratia plymuthica
SA126980B585_5PSerratia plymuthica
SA126981B585_6PSerratia plymuthica
SA126982B585_4PSerratia plymuthica
SA126983B253_6PSphingobacterium faecium
SA126984B253_3NSphingobacterium faecium
SA126985B253_6NSphingobacterium faecium
SA126986B253_4NSphingobacterium faecium
SA126987B253_1NSphingobacterium faecium
SA126988B253_2PSphingobacterium faecium
SA126989B253_3PSphingobacterium faecium
SA126990B253_5PSphingobacterium faecium
SA126991B253_4PSphingobacterium faecium
SA126992B253_2NSphingobacterium faecium
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Collection:

Collection ID:CO001580
Collection Summary:Individual bacterial LB cultures (150 rpm/min at 28 °C for 72 h) for each strain including K. oxytoca B313 were centrifuged at 3000 rpm/min for 5 min.
Sample Type:Bacterial cells

Treatment:

Treatment ID:TR001600
Treatment Summary:20 μL of supernatant filtered with a 0.2 μm filter was mixed with 120 μL of precooled 50% methanol (4 °C for 24 h), vortexed for 1 min, and incubated at room temperature for 10 min.

Sample Preparation:

Sampleprep ID:SP001593
Sampleprep Summary:The mixture was then stored overnight at -20 °C and centrifuged at 4,000 ×g for 20 min, and the supernatants were transferred into a new glass vial for the LC-MS analysis.

Combined analysis:

Analysis ID AN002504 AN002505
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Unspecified Unspecified
Column Waters Acquity BEH Amide (150 x 2.1mm,1.7um) Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
MS Type EI EI
MS instrument type Triple TOF Triple TOF
MS instrument name ABI Sciex 5600+ TripleTOF ABI Sciex 5600+ TripleTOF
Ion Mode POSITIVE NEGATIVE
Units peak area peak area

Chromatography:

Chromatography ID:CH001831
Chromatography Summary:All samples from the nine groups were analyzed by a LC-MS system. First, all chromatographic separations were performed using an ultra-performance liquid chromatography (UPLC) system (SCIEX, UK) equipped with an ACQUITY UPLC BEH Amide column (100 mm×2.1 mm, 1.7 µm, Waters, UK) for the reversed-phase separation. The column oven was maintained at 35 °C. The flow rate was 0.4 mL/min and the mobile phase consisted of solvent A (25 mM ammonium acetate) and solvent B (isopropanol: acetonitrile =9:1 + 0.1% formic acid). Gradient elution conditions were set as follows: 0-0.5 min, 95% B; 0.5-9.5 min, 95% to 65% B; 9.5-10.5 min, 65%-40% B; 10.5-12 min, 40% B; 12-12.2 min, 40%-95% B; and 12.2-15 min, 95% B. The injection volume for each sample was 4 µL.
Instrument Name:Unspecified
Column Name:Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
Column Temperature:35
Flow Gradient:0-0.5 min, 95% B; 0.5-9.5 min, 95% to 65% B; 9.5-10.5 min, 65%-40% B; 10.5-12 min, 40% B; 12-12.2 min, 40%-95% B; and 12.2-15 min, 95% B.
Flow Rate:0.4 mL/min
Solvent A:100% water; 25 mM ammonium acetate
Solvent B:90% isopropanol/10% acetonitrile; 0.1% formic acid
Chromatography Type:HILIC

MS:

MS ID:MS002324
Analysis ID:AN002504
Instrument Name:ABI Sciex 5600+ TripleTOF
Instrument Type:Triple TOF
MS Type:EI
MS Comments:A high-resolution tandem mass spectrometer TripleTOF 5600 plus (SCIEX, UK) was used to detect metabolites eluted from the column in both positive and negative ion modes with the curtain gas set to 30 psi, ion source gas1 set to 60 psi, ion source gas2 set to 60 psi, and an interface heater temperature set to 650 °C. The ionspray floating voltage was set to 5000 V for positive ion mode and -4500 V for negative ion mode. The mass spectrometry data were acquired in IDA mode, and the TOF mass range was from 60 to 1200 Da. Ion survey scans were completed in 150 ms, and 12 product ions were collected if they exceeded a threshold of 100 counts per second (counts/s) and with a 1+ charge-state. The total cycle time was set to 0.56 s. Four bins were summed during each scan at a pulser frequency of 11 kHz through the monitoring of the 40 GHz multichannel TDC detector with four-anode/channel detection. Dynamic exclusion was set for 4 s. During mass spectrometry data acquisition, the mass accuracy was calibrated every 10 samples. Furthermore, to maintain the stability of the LC-MS system during the whole analysis, all samples from the nine groups were analyzed in a random sequence, and a QC sample was analyzed every 10 samples.
Ion Mode:POSITIVE
  
MS ID:MS002325
Analysis ID:AN002505
Instrument Name:ABI Sciex 5600+ TripleTOF
Instrument Type:Triple TOF
MS Type:EI
MS Comments:A high-resolution tandem mass spectrometer TripleTOF 5600 plus (SCIEX, UK) was used to detect metabolites eluted from the column in both positive and negative ion modes with the curtain gas set to 30 psi, ion source gas1 set to 60 psi, ion source gas2 set to 60 psi, and an interface heater temperature set to 650 °C. The ionspray floating voltage was set to 5000 V for positive ion mode and -4500 V for negative ion mode. The mass spectrometry data were acquired in IDA mode, and the TOF mass range was from 60 to 1200 Da. Ion survey scans were completed in 150 ms, and 12 product ions were collected if they exceeded a threshold of 100 counts per second (counts/s) and with a 1+ charge-state. The total cycle time was set to 0.56 s. Four bins were summed during each scan at a pulser frequency of 11 kHz through the monitoring of the 40 GHz multichannel TDC detector with four-anode/channel detection. Dynamic exclusion was set for 4 s. During mass spectrometry data acquisition, the mass accuracy was calibrated every 10 samples. Furthermore, to maintain the stability of the LC-MS system during the whole analysis, all samples from the nine groups were analyzed in a random sequence, and a QC sample was analyzed every 10 samples.
Ion Mode:NEGATIVE
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