Summary of study ST001270

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 PR000855. The data can be accessed directly via it's Project DOI: 10.21228/M85H5H This work is supported by NIH grant, U2C- DK119886.

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Study IDST001270
Study TitleNecrotizing soft-tissue infections (NSTIs) metabolomics
Study SummaryNecrotizing soft-tissue infections (NSTIs) have multiple causes, risk factors, anatomical locations, and pathogenic mechanisms. In patients with NSTI, circulating metabolites may serve as substrate having impact on bacterial adaptation at the site of infection. Metabolic signatures associated with NSTI may reveal potential be useful as diagnostic and prognostic markers, as well as novel targets for therapy. This study used untargeted metabolomics analyses of plasma from NSTI patients (n=34) and healthy (non-infected) controls (n=24) to identify the metabolic signatures and connectivity patterns among metabolites associated with NSTI.
Institute
Wageningen University & Research
Last NameEdoardo
First NameSaccenti
AddressStippeneng 4, 6708 Wageningen, the Netherlands
Emailedoardo.saccenti@wur.nl
Phone+31644482628
Submit Date2019-10-28
Raw Data AvailableYes
Analysis Type DetailGC-MS
Release Date2020-01-06
Release Version1
Saccenti Edoardo Saccenti Edoardo
https://dx.doi.org/10.21228/M85H5H
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000855
Project DOI:doi: 10.21228/M85H5H
Project Title:Necrotizing soft-tissue infections (NSTIs) metabolomics
Project Summary:Necrotizing soft-tissue infections (NSTIs) have multiple causes, risk factors, anatomical locations, and pathogenic mechanisms. In patients with NSTI, circulating metabolites may serve as substrate having impact on bacterial adaptation at the site of infection. Metabolic signatures associated with NSTI may reveal potential be useful as diagnostic and prognostic markers, as well as novel targets for therapy. This study used untargeted metabolomics analyses of plasma from NSTI patients (n=34) and healthy (non-infected) controls (n=24) to identify the metabolic signatures and connectivity patterns among metabolites associated with NSTI.
Institute:Wageningen University & Research
Last Name:Saccenti
First Name:Edoardo
Address:Stippeneng 4, Wageningen, Gelderlad, 6708WE, Netherlands Antilles
Email:edoardo.saccenti@wur.nl
Phone:0031631568602

Subject:

Subject ID:SU001338
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Category Bacterial sp
SA092233111_1.cdfNSTI Gr. A strep
SA092234108_1.cdfNSTI Gr. A strep
SA092235113_1.cdfNSTI Gr. A strep
SA092236118_1.cdfNSTI Gr. A strep
SA092237122_1.cdfNSTI Gr. A strep
SA092238176_1.cdfNSTI Gr. A strep
SA092239116_1.cdfNSTI Gr. A strep
SA092240101_1.cdfNSTI Gr. A strep
SA09224191_1.cdfNSTI Gr. A strep
SA09224289_1.cdfNSTI Gr. A strep
SA09224393_1.cdfNSTI Gr. A strep
SA09224495_1.cdfNSTI Gr. A strep
SA092245193_1.cdfNSTI Gr. A strep
SA09224698_1.cdfNSTI Gr. A strep
SA092247103_1.cdfNSTI Gr. A strep
SA092248132_1.cdfNSTI Gr. A strep
SA092249160_1.cdfNSTI Gr. A strep
SA092250187_1.cdfNSTI Gr. A strep
SA092251185_1.cdfNSTI Gr. A strep
SA092252166_1.cdfNSTI Gr. A strep
SA092253171_1.cdfNSTI Gr. A strep
SA092254181_1.cdfNSTI Gr. A strep
SA0922551_1.cdfNSTI Gr. A strep
SA092256154_1.cdfNSTI Gr. A strep
SA092257191_1.cdfNSTI Gr. A strep
SA09225887_1.cdfNSTI Gr. A strep
SA092259137_1.cdfNSTI Gr. A strep
SA092260142_1.cdfNSTI Gr. A strep
SA092261148_1.cdfNSTI Gr. A strep
SA092262189_1.cdfNSTI Gr. A strep
SA092263127_1.cdfNSTI Gr. A strep
SA092264106_1.cdfNSTI Gr. A strep
SA09226531_1.cdfNSTI Gr. A strep
SA09226663_1.cdfNSTI Gr. A strep
SA09226767_1.cdfNSTI Gr. A strep
SA09226826_1.cdfNSTI Gr. A strep
SA092269195_1.cdfNSTI Gr. A strep
SA09227059_1.cdfNSTI Gr. A strep
SA09227155_1.cdfNSTI Gr. A strep
SA09227285_1.cdfNSTI Gr. A strep
SA09227351_1.cdfNSTI Gr. A strep
SA09227441_1.cdfNSTI Gr. A strep
SA09227536_1.cdfNSTI Gr. A strep
SA09227646_1.cdfNSTI Gr. A strep
SA09227721_1.cdfNSTI Gr. A strep
SA09227877_1.cdfNSTI Gr. A strep
SA09227971_1.cdfNSTI Gr. A strep
SA0922806_1.cdfNSTI Gr. A strep
SA09228179_1.cdfNSTI Gr. A strep
SA09228281_1.cdfNSTI Gr. A strep
SA09228383_1.cdfNSTI Gr. A strep
SA09228475_1.cdfNSTI Gr. A strep
SA09228516_1.cdfNSTI Gr. A strep
SA092286198_1.cdfNSTI Gr. A strep
SA09228711_1.cdfNSTI Gr. A strep
SA092288136_1.cdfNSTI Gr. G strep
SA09228943_1.cdfNSTI Gr. G strep
SA092290170_1.cdfNSTI Gr. G strep
SA092291165_1.cdfNSTI Gr. G strep
SA092292194_1.cdfNSTI Gr. G strep
SA092293131_1.cdfNSTI Gr. G strep
SA09229470_1.cdfNSTI Gr. G strep
SA092295112_1.cdfNSTI Gr. G strep
SA09229669_1.cdfNSTI Gr. G strep
SA09229773_1.cdfNSTI Gr. G strep
SA09229874_1.cdfNSTI Gr. G strep
SA09229997_1.cdfNSTI Gr. G strep
SA092300100_1.cdfNSTI Gr. G strep
SA092301121_1.cdfNSTI Gr. G strep
SA092302117_1.cdfNSTI Gr. G strep
SA09230348_1.cdfNSTI Gr. G strep
SA092304126_1.cdfNSTI Gr. G strep
SA092305129_1.cdfNSTI Polymicrob.
SA092306102_1.cdfNSTI Polymicrob.
SA092307150_1.cdfNSTI Polymicrob.
SA092308180_1.cdfNSTI Polymicrob.
SA092309175_1.cdfNSTI Polymicrob.
SA092310139_1.cdfNSTI Polymicrob.
SA092311107_1.cdfNSTI Polymicrob.
SA092312144_1.cdfNSTI Polymicrob.
SA092313134_1.cdfNSTI Polymicrob.
SA092314124_1.cdfNSTI Polymicrob.
SA092315159_1.cdfNSTI Polymicrob.
SA092316153_1.cdfNSTI Polymicrob.
SA092317147_1.cdfNSTI S. anginous
SA092318141_1.cdfNSTI S. anginous
SA092319155_1.cdfNSTI S. aureus
SA092320123_1.cdfNSTI S. aureus
SA092321133_1.cdfNSTI S. aureus
SA09232233_1.cdfNSTI S. aureus
SA09232313_1.cdfNSTI S. aureus
SA0923243_1.cdfNSTI S. aureus
SA092325143_1.cdfNSTI S. aureus
SA09232623_1.cdfNSTI S. aureus
SA092327172_1.cdfNSTI S. aureus
SA092328167_1.cdfNSTI S. aureus
SA092329156_1.cdfNSTI Stap+Strep
SA092330177_1.cdfNSTI Stap+Strep
SA092331186_1.cdfNSTI Stap+Strep
SA092332190_1.cdfNSTI Stap+Strep
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Collection:

Collection ID:CO001332
Collection Summary:EDTA plasma samples from 34 NSTI patients prospectively enrolled in the FP7 project, INFECT (Clinicaltrials.gov, NCT01790698)3 were included in this study. The patients were enrolled at 5 different clinical sites; Rigshospitalet (Copenhagen, Denmark), Karolinska University Hospital (Stockholm, Sweden), Blekingesjukhuset (Karlskrona, Sweden), Sahlgrenska University Hospital (Gothenburg, Sweden) and Haukeland University Hospital (Bergen, Norway). Sampling was done following standardized operating procedures as reported in Madsen, M. B.; Skrede, S.; Bruun, T.; Arnell, P.; Rosén, A.; Nekludov, M.; Karlsson, Y.; Bergey, F.; Saccenti, E.; Martins dos Santos, V. A. P.; et al. Necrotizing Soft Tissue Infections - a Multicentre, Prospective Observational Study (INFECT): Protocol and Statistical Analysis Plan. Acta Anaesthesiol. Scand. 2018, 62 (2), 272–279. https://doi.org/10.1111/aas.13024.
Sample Type:Blood (plasma)

Treatment:

Treatment ID:TR001353
Treatment Summary:Sample preparation was performed according to A et al (A et al. 2005). In detail, 900 uL of extraction buffer (90/10 v/v methanol:water) including internal standards were added to 100 uL of sample material. The sample was shaken at 30 Hz for 3 minutes in a mixer mill and proteins were precipitated at +4 °C on ice. The sample was centrifuged at +4 °C, 14 000 rpm, for 10 minutes. 200 uL of supernatant were transferred to a micro vial and solvents were evaporated. **** Derivatization was performed according to A et al (A et al. 2005). In detail 30 uL of methoxyamine (15 ug/uL in pyridine) were added to the dry sample and the sample was shaken vigorously for 10 minutes. The reaction was begun by keeping the sample at +70 °C for 1 hour before letting the reaction proceed in room temperature for 16 hours. 30 uL of MSTFA were thenceforth added, the sample was shaken and left to react for 1 hour in room temperature. 30 μL of methyl stearate (15 ng/uL in heptane) were added before analysis. *** REFERENCES A, J., et al. (2005), 'Extraction and GC/MS Analysis of the Human Blood Plasma Metabolome', Anal. Chem., 77 (24), 8086-94.
Treatment Protocol Filename:Analytical_parameters_Sleipner_10m_column_P0287_plasma.pdf

Sample Preparation:

Sampleprep ID:SP001346
Sampleprep Summary:GCMS analysis was performed as described previously (A et al. 2005; Gullberg et al. 2004). In detail, 1 μL of the derivatized sample was injected in splitless mode by a CTC Combi Pal autosampler (CTC Analytics AG, Switzerland) into an Agilent 6890 gas chromatograph equipped with a 10 m x 0.18 mm fused silica capillary column with a chemically bonded 0.18 μm DB 5-MS UI stationary phase (J&W Scientific). The injector temperature was 270 °C, the purge flow rate was 20 mL min-1 and the purge was turned on after 60 seconds. The gas flow rate through the column was 1 mL min-1, the column temperature was held at 70 °C for 2 minutes, then increased by 40 °C min-1 to 320 °C, and held there for 2 minutes. The column effluent was introduced into the ion source of a Pegasus III time-of-flight mass spectrometer, GC/TOFMS (Leco Corp., St Joseph, MI, USA). The transfer line and the ion source temperatures were 250 °C and 200 °C, respectively. Ions were generated by a 70 eV electron beam at an ionization current of 2.0 mA, and 30 spectra s-1 were recorded in the mass range m/z 50 - 800. The acceleration voltage was turned on after a solvent delay of 150 seconds. The detector voltage was 1500-2000 V.
Sampleprep Protocol ID:Analytical_parameters_Sleipner_10m_column_P0287_plasma.pdf

Combined analysis:

Analysis ID AN002110
Analysis type MS
Chromatography type GC
Chromatography system Leco Pegasus III GC
Column Agilent DB 5-MS (10 m x 0.18 mm x 0.18 um)
MS Type EI
MS instrument type GC-TOF
MS instrument name Leco Pegasus III GC TOF
Ion Mode POSITIVE
Units Peak area

Chromatography:

Chromatography ID:CH001540
Instrument Name:Leco Pegasus III GC
Column Name:Agilent DB 5-MS (10 m x 0.18 mm x 0.18 um)
Chromatography Type:GC

MS:

MS ID:MS001961
Analysis ID:AN002110
Instrument Name:Leco Pegasus III GC TOF
Instrument Type:GC-TOF
MS Type:EI
MS Comments:Raw data from MS-files were exported from the ChromaTOF software in NetCDF format to Matlab (Mathworks, Natick, MA, USA) format; data pre-processing, such as baseline correction, chromatogram alignment, data compression and Multivariate Curve Resolution were performed using in-house custom Matlab scripts. The extracted mass spectra were identified by comparisons of their retention index and mass spectra with libraries of retention time indices and mass spectra. Mass spectra and retention index comparison was performed using NIST MS 2.0 software. Annotation of mass spectra was based on reverse and forward searches in the library. Masses and ratio between masses indicative for a derivatized metabolite were especially notified.
Ion Mode:POSITIVE
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