Summary of Study ST002763

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 PR001721. The data can be accessed directly via it's Project DOI: 10.21228/M87X4W 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 IDST002763
Study TitleMetabolomic and lipidomic characterization of Haemophilus influenzae Rd KW20
Study SummaryThis study aims to comprehensively characterize the polar metabolome and the phosphlipidome of Haemophilus influenzae Rd Kw20, to provide an improved understanding of this bacterial metabolome by comparison with data inferred from genome annotation data.
Institute
Universidad CEU San Pablo
Last NameGarcía
First NameAntonia
AddressCentro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, Urbanización Montepríncipe, 28660, Boadilla del Monte, España
Emailmiguel.fernandezgarcia@ceu.es
Phone913724711
Submit Date2023-06-25
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailGC-MS/LC-MS
Release Date2024-01-01
Release Version1
Antonia García Antonia García
https://dx.doi.org/10.21228/M87X4W
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001721
Project DOI:doi: 10.21228/M87X4W
Project Title:Multi-omics of Haemophilus influenzae Rd KW20
Project Summary:This project aims to characterize at different levels the modifications ocurring during compensatory evolution of bacteria upon plasmid transformation and to characterize the metabolome of H. influenzae at a global level.
Institute:Universidad CEU San Pablo
Last Name:García
First Name:Antonia
Address:Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, Urbanización Montepríncipe, 28660, Boadilla del Monte, España
Email:miguel.fernandezgarcia@ceu.es
Phone:913724711

Subject:

Subject ID:SU002870
Subject Type:Bacteria
Subject Species:Haemophilus influenzae
Genotype Strain:Rd KW20

Factors:

Subject type: Bacteria; Subject species: Haemophilus influenzae (Factor headings shown in green)

mb_sample_id local_sample_id Population
SA291570A3_CE-MSA
SA291571A4_CE-MSA
SA291572A2_CE-MSA
SA291573A1_LC-MSposA
SA291574A2_GC-MSA
SA291575A5_CE-MSA
SA291576A1_LC-MSnegA
SA291577A5_LC-MSnegA
SA291578A4_LC-MSnegA
SA291579A3_LC-MSnegA
SA291580A2_LC-MSnegA
SA291581A3_LC-MSposA
SA291582A2_LC-MSposA
SA291583A5_GC-MSA
SA291584A1_GC-MSA
SA291585A4_LC-MSposA
SA291586A1_CE-MSA
SA291587A4_GC-MSA
SA291588A3_GC-MSA
SA291589A5_LC-MSposA
SA291590B5_CE-MSB
SA291591B4_CE-MSB
SA291592B3_CE-MSB
SA291593B1_CE-MSB
SA291594B1_LC-MSposB
SA291595B5_LC-MSnegB
SA291596B2_LC-MSposB
SA291597B3_LC-MSposB
SA291598B5_LC-MSposB
SA291599B4_LC-MSposB
SA291600B2_CE-MSB
SA291601B4_LC-MSnegB
SA291602B2_GC-MSB
SA291603B2_LC-MSnegB
SA291604B1_LC-MSnegB
SA291605B4_GC-MSB
SA291606B5_GC-MSB
SA291607B3_LC-MSnegB
SA291608B1_GC-MSB
SA291609B3_GC-MSB
SA291610C4_LC-MSposC
SA291611C5_LC-MSposC
SA291612C5_GC-MSC
SA291613C2_GC-MSC
SA291614C1_LC-MSposC
SA291615C1_GC-MSC
SA291616C3_GC-MSC
SA291617C4_GC-MSC
SA291618C5_CE-MSC
SA291619C4_LC-MSnegC
SA291620C3_LC-MSnegC
SA291621C2_LC-MSnegC
SA291622C1_LC-MSnegC
SA291623C5_LC-MSnegC
SA291624C1_CE-MSC
SA291625C2_LC-MSposC
SA291626C4_CE-MSC
SA291627C3_CE-MSC
SA291628C2_CE-MSC
SA291629C3_LC-MSposC
SA291630D5_LC-MSposD
SA291631D4_CE-MSD
SA291632D1_CE-MSD
SA291633D2_CE-MSD
SA291634D3_CE-MSD
SA291635D4_LC-MSposD
SA291636D5_CE-MSD
SA291637D2_LC-MSposD
SA291638D1_LC-MSnegD
SA291639D2_LC-MSnegD
SA291640D3_LC-MSnegD
SA291641D4_LC-MSnegD
SA291642D5_GC-MSD
SA291643D3_GC-MSD
SA291644D1_GC-MSD
SA291645D3_LC-MSposD
SA291646D2_GC-MSD
SA291647D5_LC-MSnegD
SA291648D4_GC-MSD
SA291649D1_LC-MSposD
SA291650E2_CE-MSE
SA291651E1_CE-MSE
SA291652E3_LC-MSposE
SA291653E4_LC-MSposE
SA291654E1_LC-MSnegE
SA291655E5_LC-MSposE
SA291656E2_LC-MSposE
SA291657E5_CE-MSE
SA291658E4_CE-MSE
SA291659E1_LC-MSposE
SA291660E3_CE-MSE
SA291661E5_LC-MSnegE
SA291662E3_LC-MSnegE
SA291663E2_LC-MSnegE
SA291664E5_GC-MSE
SA291665E4_LC-MSnegE
SA291666E4_GC-MSE
SA291667E1_GC-MSE
SA291668E2_GC-MSE
SA291669E3_GC-MSE
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Collection:

Collection ID:CO002863
Collection Summary:H. influenzae Rd KW20 (NC_000907.1) was cultured in HTM broth and bacterial pellets were obtained by centrifugation.
Sample Type:Bacterial cells

Treatment:

Treatment ID:TR002879
Treatment Summary:In this case, samples were not treated as the study is a characterization. We performed independent evolution of five biological replicate populations.

Sample Preparation:

Sampleprep ID:SP002876
Sampleprep Summary:Sample preparation was performed following Ares-Arroyo, M. et al. (https://doi.org/10.1128/msphere.00184-22)

Combined analysis:

Analysis ID AN004492 AN004493 AN004494 AN004495 AN004496 AN004497
Analysis type MS MS MS MS MS MS
Chromatography type GC CE Reversed phase Reversed phase Reversed phase Reversed phase
Chromatography system Agilent 7890B Agilent 7100 CE Agilent 1290 Infinity Agilent 1290 Infinity Agilent 1290 Infinity Agilent 1290 Infinity
Column Agilent DB5-MS (30m x 0.25mm, 0.25um) fused silica capillary (70 cm; 50 um i.d.), Agilent Technologies Agilent InfinityLab Poroshell 120 EC-C18 (100 x 3mm,2.7um) Agilent InfinityLab Poroshell 120 EC-C18 (100 x 3mm,2.7um) Agilent InfinityLab Poroshell 120 EC-C18 (100 x 3mm,2.7um) Agilent InfinityLab Poroshell 120 EC-C18 (100 x 3mm,2.7um)
MS Type EI ESI ESI ESI ESI ESI
MS instrument type QTOF TOF QTOF QTOF QTOF QTOF
MS instrument name Agilent 7250 Agilent 6224 TOF Agilent 6545 QTOF Agilent 6545 QTOF Agilent 6545 QTOF Agilent 6545 QTOF
Ion Mode UNSPECIFIED POSITIVE POSITIVE NEGATIVE POSITIVE NEGATIVE
Units raw abundance raw abundance raw abundance raw abundance raw abundance

Chromatography:

Chromatography ID:CH003377
Chromatography Summary:Chromatography was performed according to DOI: 10.1385/1-59745-003-0:439
Instrument Name:Agilent 7890B
Column Name:Agilent DB5-MS (30m x 0.25mm, 0.25um)
Column Temperature:According to temperature gradient. DOI: 10.1385/1-59745-003-0:439
Flow Gradient:N/A for GC
Flow Rate:0.85 mL/min
Internal Standard:Tricosane
Sample Injection:2 uL
Solvent A:N/A for GC
Solvent B:N/A for GC
Chromatography Type:GC
Solvent C:N/A for GC
  
Chromatography ID:CH003378
Chromatography Summary:Separation was performed according to DOI: 10.1128/msphere.00184-22
Instrument Name:Agilent 7100 CE
Column Name:fused silica capillary (70 cm; 50 um i.d.), Agilent Technologies
Column Temperature:RT
Flow Gradient:N/A for CE-MS
Flow Rate:N/A for CE-MS
Internal Standard:Methionine sulfone
Sample Injection:hydrodynamic injection: 50 mbar for 100 s
Solvent A:N/A for CE-MS
Solvent B:N/A for CE-MS
Capillary Voltage:30 kV
Running Buffer:1M HCOOH in MeOH:H2O 1:9 (v/v) (BGE)
Chromatography Type:CE
Solvent C:N/A for CE-MS
  
Chromatography ID:CH003379
Chromatography Summary:Chromatography was performed according to DOI: 10.1128/msphere.00184-22
Instrument Name:Agilent 1290 Infinity
Column Name:Agilent InfinityLab Poroshell 120 EC-C18 (100 x 3mm,2.7um)
Column Temperature:50 ºC
Flow Gradient:70%B held 1 min; then increase up to 86 %B at 3.5 min; then hold 10 min; Next, incerase in %B up to 100 %B at 11 min; then, held for 6 min. Then, switched to initial conditions (1.84 min of re-equilibration time)
Flow Rate:0.6 mL/min
Sample Injection:2 uL (ESI+, MS1, ITMS with default inj. volume) and 5 uL (ESI-, MS1, ITMS with default inj. volume), 7 uL (ESI+ ITMS with increased inj. volume), 10 uL (ESI- ITMS with increased inj. volume)
Solvent A:10 mM Ammonium acetate and 0.2 mM ammonium fluoride in 9:1 H2O:MeOH (v/v)
Solvent B:10 mM Ammonium acetate and 0.2 mM ammonium fluoride in 2:3:5 ACN:MeOH:IPA (v/v)
Chromatography Type:Reversed phase
Solvent C:N/A

MS:

MS ID:MS004239
Analysis ID:AN004492
Instrument Name:Agilent 7250
Instrument Type:QTOF
MS Type:EI
MS Comments:70 eV EI source, Full MS scan, m/z range from 45 to 650. Acquisition rate of 6.67 spectra/s Data processed using Agilent MassHunter Unknowns Analysis and Agilent MassHunter Quantitative Analysis. Feature assignment performed by comparison with Fiehn exact mass, NIST, and in-house exact mass libraries.
Ion Mode:UNSPECIFIED
  
MS ID:MS004240
Analysis ID:AN004493
Instrument Name:Agilent 6224 TOF
Instrument Type:TOF
MS Type:ESI
MS Comments:drying gas T = 200 ºC; drying gas flow rate = 10 L/min; nebulizer pressure = 10 psi; capillary V = 5500 V; fragmentor V = 125 V; skimmer V = 65 V; octopole RFV = 650 V; Acquisition mode: Full-MS scan, m/z range from 70 to 1000; acquisition rate = 1.36 spectra/s. Data processed with Agilent MassHunter Profinder B.10.00, feature assignment performed with CEU Mass Mediator Exp RMT Search and CEU Mass Mediator Batch Search.
Ion Mode:POSITIVE
  
MS ID:MS004241
Analysis ID:AN004494
Instrument Name:Agilent 6545 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Drying gas T = 300 ºC; drying gas flow rate = 12 L/min; Capillary V = 3500 V; fragmentor V = 150 V; skimmer V = 65 V; octopole RFV = 750 V. MS acquisition mode = Full MS scan, mz range = 50 to 3000; acquisition rate = 3.5 spectra/s. Data processed with Agilent MassHunter Profinder B.10.00 and Agilent MassHunter Qualitative Analysis (B.08.00). Feature annotation performed with Agilent MassHunter Lipid Annotator (v.1.0) and CEU Mass Mediator Batch Search.
Ion Mode:POSITIVE
  
MS ID:MS004242
Analysis ID:AN004495
Instrument Name:Agilent 6545 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Drying gas T = 300 ºC; drying gas flow rate = 12 L/min; Capillary V = 3500 V; fragmentor V = 150 V; skimmer V = 65 V; octopole RFV = 750 V. MS acquisition mode = Auto MS/MS, mz range = 50 to 3000; acquisition rate = 3.5 spectra/s. Data processed with Agilent MassHunter Profinder B.10.00 and Agilent MassHunter Qualitative Analysis (B.08.00). Feature annotation performed with Agilent MassHunter Lipid Annotator (v.1.0) and CEU Mass Mediator Batch Search.
Ion Mode:NEGATIVE
  
MS ID:MS004243
Analysis ID:AN004496
Instrument Name:Agilent 6545 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Drying gas T = 300 ºC; drying gas flow rate = 12 L/min; Capillary V = 3500 V; fragmentor V = 150 V; skimmer V = 65 V; octopole RFV = 750 V. MS acquisition mode = Auto MS/MS, isolation width = narrow (1.3 Da); collision energy (ramp) = 3.8; offset (ramp) = 4 6. Data processed with Agilent MassHunter Profinder B.10.00 and Agilent MassHunter Qualitative Analysis (B.08.00). Feature annotation performed with Agilent MassHunter Lipid Annotator (v.1.0)
Ion Mode:POSITIVE
  
MS ID:MS004244
Analysis ID:AN004497
Instrument Name:Agilent 6545 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Drying gas T = 300 ºC; drying gas flow rate = 12 L/min; Capillary V = 3500 V; fragmentor V = 150 V; skimmer V = 65 V; octopole RFV = 750 V. MS acquisition mode = Iterative auto MS/MS, isolation width = narrow (1.3 Da); collision energy (ramp) = 3.8; offset (ramp) = 4 6. Data processed with Agilent MassHunter Profinder B.10.00 and Agilent MassHunter Qualitative Analysis (B.08.00). Feature annotation performed with Agilent MassHunter Lipid Annotator (v.1.0)
Ion Mode:NEGATIVE
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