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.
Study ID | ST002763 |
Study Title | Metabolomic and lipidomic characterization of Haemophilus influenzae Rd KW20 |
Study Summary | This 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 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 |
miguel.fernandezgarcia@ceu.es | |
Phone | 913724711 |
Submit Date | 2023-06-25 |
Raw Data Available | Yes |
Raw Data File Type(s) | mzML |
Analysis Type Detail | GC-MS/LC-MS |
Release Date | 2024-01-01 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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 |
Species Group: | Bacteria |
Factors:
Subject type: Bacteria; Subject species: Haemophilus influenzae (Factor headings shown in green)
mb_sample_id | local_sample_id | Population |
---|---|---|
SA291570 | A3_CE-MS | A |
SA291571 | A4_CE-MS | A |
SA291572 | A2_CE-MS | A |
SA291573 | A1_LC-MSpos | A |
SA291574 | A2_GC-MS | A |
SA291575 | A5_CE-MS | A |
SA291576 | A1_LC-MSneg | A |
SA291577 | A5_LC-MSneg | A |
SA291578 | A4_LC-MSneg | A |
SA291579 | A3_LC-MSneg | A |
SA291580 | A2_LC-MSneg | A |
SA291581 | A3_LC-MSpos | A |
SA291582 | A2_LC-MSpos | A |
SA291583 | A5_GC-MS | A |
SA291584 | A1_GC-MS | A |
SA291585 | A4_LC-MSpos | A |
SA291586 | A1_CE-MS | A |
SA291587 | A4_GC-MS | A |
SA291588 | A3_GC-MS | A |
SA291589 | A5_LC-MSpos | A |
SA291590 | B5_CE-MS | B |
SA291591 | B4_CE-MS | B |
SA291592 | B3_CE-MS | B |
SA291593 | B1_CE-MS | B |
SA291594 | B1_LC-MSpos | B |
SA291595 | B5_LC-MSneg | B |
SA291596 | B2_LC-MSpos | B |
SA291597 | B3_LC-MSpos | B |
SA291598 | B5_LC-MSpos | B |
SA291599 | B4_LC-MSpos | B |
SA291600 | B2_CE-MS | B |
SA291601 | B4_LC-MSneg | B |
SA291602 | B2_GC-MS | B |
SA291603 | B2_LC-MSneg | B |
SA291604 | B1_LC-MSneg | B |
SA291605 | B4_GC-MS | B |
SA291606 | B5_GC-MS | B |
SA291607 | B3_LC-MSneg | B |
SA291608 | B1_GC-MS | B |
SA291609 | B3_GC-MS | B |
SA291610 | C4_LC-MSpos | C |
SA291611 | C5_LC-MSpos | C |
SA291612 | C5_GC-MS | C |
SA291613 | C2_GC-MS | C |
SA291614 | C1_LC-MSpos | C |
SA291615 | C1_GC-MS | C |
SA291616 | C3_GC-MS | C |
SA291617 | C4_GC-MS | C |
SA291618 | C5_CE-MS | C |
SA291619 | C4_LC-MSneg | C |
SA291620 | C3_LC-MSneg | C |
SA291621 | C2_LC-MSneg | C |
SA291622 | C1_LC-MSneg | C |
SA291623 | C5_LC-MSneg | C |
SA291624 | C1_CE-MS | C |
SA291625 | C2_LC-MSpos | C |
SA291626 | C4_CE-MS | C |
SA291627 | C3_CE-MS | C |
SA291628 | C2_CE-MS | C |
SA291629 | C3_LC-MSpos | C |
SA291630 | D5_LC-MSpos | D |
SA291631 | D4_CE-MS | D |
SA291632 | D1_CE-MS | D |
SA291633 | D2_CE-MS | D |
SA291634 | D3_CE-MS | D |
SA291635 | D4_LC-MSpos | D |
SA291636 | D5_CE-MS | D |
SA291637 | D2_LC-MSpos | D |
SA291638 | D1_LC-MSneg | D |
SA291639 | D2_LC-MSneg | D |
SA291640 | D3_LC-MSneg | D |
SA291641 | D4_LC-MSneg | D |
SA291642 | D5_GC-MS | D |
SA291643 | D3_GC-MS | D |
SA291644 | D1_GC-MS | D |
SA291645 | D3_LC-MSpos | D |
SA291646 | D2_GC-MS | D |
SA291647 | D5_LC-MSneg | D |
SA291648 | D4_GC-MS | D |
SA291649 | D1_LC-MSpos | D |
SA291650 | E2_CE-MS | E |
SA291651 | E1_CE-MS | E |
SA291652 | E3_LC-MSpos | E |
SA291653 | E4_LC-MSpos | E |
SA291654 | E1_LC-MSneg | E |
SA291655 | E5_LC-MSpos | E |
SA291656 | E2_LC-MSpos | E |
SA291657 | E5_CE-MS | E |
SA291658 | E4_CE-MS | E |
SA291659 | E1_LC-MSpos | E |
SA291660 | E3_CE-MS | E |
SA291661 | E5_LC-MSneg | E |
SA291662 | E3_LC-MSneg | E |
SA291663 | E2_LC-MSneg | E |
SA291664 | E5_GC-MS | E |
SA291665 | E4_LC-MSneg | E |
SA291666 | E4_GC-MS | E |
SA291667 | E1_GC-MS | E |
SA291668 | E2_GC-MS | E |
SA291669 | E3_GC-MS | E |
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 |