Summary of Study ST003970

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 PR002486. The data can be accessed directly via it's Project DOI: 10.21228/M89C27 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.

Perform statistical analysis  |  Show all samples  |  Show named metabolites  |  Download named metabolite data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST003970
Study TitleComprehensive multiplatform mass spectrometry-based metabolomics unveils insights into Babesia divergens metabolism.
Study SummaryBabesia divergens is a zoonotic parasite belonging to the apicomplexa phyla causing human babesiosis. However, its metabolism remains poorly understood as scarce biochemical studies have been reported, and no global metabolic network reconstructions have been reported up to date. Comprehensive understanding of the B. divergens metabolism could reveal novel therapeutic targets. We performed a multiplatform analysis combining targeted and non-targeted mass spectrometry based metabolomics of samples (pellets, supernatants) obtained from Babesia divergens-infected erythrocyte cultures and non-infected culture controls, acquired with CE-ESI(+)/MS, GC-CI(+)/MS, LC-ESI(+)/MS, LC-ESI(-)/MS (all non-targeted analyses) and LC-ESI(-)/MS (targeted analysis). Profound metabolite level changes occur in both the B. divergens-RBC system and its supernatant compared to controls, including those related with central carbon metabolism, pyrimidine nucleotide biosynthesis, redox metabolism, glycerophospholipid and sphingolipid metabolism, amino acid metabolism and nucleotide metabolism. This resource serves as a comprehensive dataset describing how the metabolic alterations caused by the intraerythrocytic stage of Babesia divergens are reflected in different metabolite profiles across multiple mass-spectrometry-based platforms.
Institute
CEMBIO
Last NameFernández-García
First NameMiguel
AddressUniversidad San Pablo-CEU, Urbanización Montepríncipe, 28925, Alcorcón, Madrid, Spain
Emailmig.fernandez.ce@ceindo.ceu.es
Phone690090778
Submit Date2022-10-04
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailGC-MS/LC-MS/CE-MS
Release Date2025-10-05
Release Version1
Miguel Fernández-García Miguel Fernández-García
https://dx.doi.org/10.21228/M89C27
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002486
Project DOI:doi: 10.21228/M89C27
Project Title:Evaluation of Babesia divergens metabolism
Project Summary:The project aims to evaluate the metabolism of the piroplasmid apicomplexa Babesia divergens through metabolomics and complementary functional assays involving metabolites.
Institute:Centro Nacional de Microbiología CNM-ISCIII
Last Name:Estrella
First Name:Montero
Address:Ctra. de Pozuelo, 28, 28222 Majadahonda, Madrid, España
Email:estrella.montero@isciii.es
Phone:+34 918 22 36 57

Subject:

Subject ID:SU004107
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

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

mb_sample_id local_sample_id Sample source Sample type
SA453186iRBC3_LC-QTOF-MSnegerythrocyte culture infected RBC
SA453187iRBC1_LC-QTOF-MSposerythrocyte culture infected RBC
SA453188iRBC2_LC-QTOF-MSposerythrocyte culture infected RBC
SA453189iRBC3_LC-QTOF-MSposerythrocyte culture infected RBC
SA453190iRBC4_LC-QTOF-MSposerythrocyte culture infected RBC
SA453191iRBC5_LC-QTOF-MSposerythrocyte culture infected RBC
SA453192iRBC2_CE-TOF-MSerythrocyte culture infected RBC
SA453193iRBC1_LC-QTOF-MSnegerythrocyte culture infected RBC
SA453194iRBC2_LC-QTOF-MSnegerythrocyte culture infected RBC
SA453195iRBC4_LC-QTOF-MSnegerythrocyte culture infected RBC
SA453196iRBC4_GC-QTOF-MSerythrocyte culture infected RBC
SA453197iRBC5_LC-QTOF-MSnegerythrocyte culture infected RBC
SA453198iRBC3_LC-QqQ-MS Aerythrocyte culture infected RBC
SA453199iRBC4_LC-QqQ-MS Aerythrocyte culture infected RBC
SA453200iRBC5_LC-QqQ-MS Aerythrocyte culture infected RBC
SA453201iRBC1_LC-QqQ-MS Berythrocyte culture infected RBC
SA453202iRBC3_LC-QqQ-MS Berythrocyte culture infected RBC
SA453203iRBC4_LC-QqQ-MS Berythrocyte culture infected RBC
SA453204iRBC5_LC-QqQ-MS Berythrocyte culture infected RBC
SA453205iRBC5_GC-QTOF-MSerythrocyte culture infected RBC
SA453206iRBC1_CE-TOF-MSerythrocyte culture infected RBC
SA453207iRBC3_GC-QTOF-MSerythrocyte culture infected RBC
SA453208iRBC1_GC-QTOF-MSerythrocyte culture infected RBC
SA453209iRBC3_CE-TOF-MSerythrocyte culture infected RBC
SA453210iRBC4_CE-TOF-MSerythrocyte culture infected RBC
SA453211iRBC5_CE-TOF-MSerythrocyte culture infected RBC
SA453212iRBC2_GC-QTOF-MSerythrocyte culture infected RBC
SA453213iS1_LC-QqQ-MS Aerythrocyte culture supernatant from infected RBC
SA453214iS3_LC-QTOF-MSposerythrocyte culture supernatant from infected RBC
SA453215iS5_CE-TOF-MSerythrocyte culture supernatant from infected RBC
SA453216iS5_LC-QTOF-MSposerythrocyte culture supernatant from infected RBC
SA453217iS4_CE-TOF-MSerythrocyte culture supernatant from infected RBC
SA453218iS3_CE-TOF-MSerythrocyte culture supernatant from infected RBC
SA453219iS2_CE-TOF-MSerythrocyte culture supernatant from infected RBC
SA453220iS1_CE-TOF-MSerythrocyte culture supernatant from infected RBC
SA453221iS4_LC-QqQ-MS Aerythrocyte culture supernatant from infected RBC
SA453222iS2_LC-QqQ-MS Aerythrocyte culture supernatant from infected RBC
SA453223iS3_LC-QqQ-MS Aerythrocyte culture supernatant from infected RBC
SA453224iS1_LC-QTOF-MSposerythrocyte culture supernatant from infected RBC
SA453225iS5_LC-QqQ-MS Aerythrocyte culture supernatant from infected RBC
SA453226iS1_LC-QqQ-MS Berythrocyte culture supernatant from infected RBC
SA453227iS2_LC-QqQ-MS Berythrocyte culture supernatant from infected RBC
SA453228iS3_LC-QqQ-MS Berythrocyte culture supernatant from infected RBC
SA453229iS4_LC-QqQ-MS Berythrocyte culture supernatant from infected RBC
SA453230iS5_LC-QqQ-MS Berythrocyte culture supernatant from infected RBC
SA453231iS2_LC-QTOF-MSposerythrocyte culture supernatant from infected RBC
SA453232iS4_LC-QTOF-MSposerythrocyte culture supernatant from infected RBC
SA453233iS2_GC-QTOF-MSerythrocyte culture supernatant from infected RBC
SA453234iS4_GC-QTOF-MSerythrocyte culture supernatant from infected RBC
SA453235iS5_GC-QTOF-MSerythrocyte culture supernatant from infected RBC
SA453236iS1_GC-QTOF-MSerythrocyte culture supernatant from infected RBC
SA453237iS3_GC-QTOF-MSerythrocyte culture supernatant from infected RBC
SA453238uS2_LC-QqQ-MS Berythrocyte culture supernatant from uninfected RBC
SA453239uS5_LC-QqQ-MS Aerythrocyte culture supernatant from uninfected RBC
SA453240uS4_LC-QqQ-MS Aerythrocyte culture supernatant from uninfected RBC
SA453241uS3_LC-QqQ-MS Aerythrocyte culture supernatant from uninfected RBC
SA453242uS2_LC-QqQ-MS Aerythrocyte culture supernatant from uninfected RBC
SA453243uS1_LC-QqQ-MS Aerythrocyte culture supernatant from uninfected RBC
SA453244uS2_GC-QTOF-MSerythrocyte culture supernatant from uninfected RBC
SA453245uS4_GC-QTOF-MSerythrocyte culture supernatant from uninfected RBC
SA453246uS1_LC-QqQ-MS Berythrocyte culture supernatant from uninfected RBC
SA453247uS3_GC-QTOF-MSerythrocyte culture supernatant from uninfected RBC
SA453248uS5_GC-QTOF-MSerythrocyte culture supernatant from uninfected RBC
SA453249uS4_LC-QTOF-MSposerythrocyte culture supernatant from uninfected RBC
SA453250uS4_CE-TOF-MSerythrocyte culture supernatant from uninfected RBC
SA453251uS5_LC-QqQ-MS Berythrocyte culture supernatant from uninfected RBC
SA453252uS3_CE-TOF-MSerythrocyte culture supernatant from uninfected RBC
SA453253uS4_LC-QqQ-MS Berythrocyte culture supernatant from uninfected RBC
SA453254uS3_LC-QqQ-MS Berythrocyte culture supernatant from uninfected RBC
SA453255uS1_CE-TOF-MSerythrocyte culture supernatant from uninfected RBC
SA453256uS1_LC-QTOF-MSposerythrocyte culture supernatant from uninfected RBC
SA453257uS2_LC-QTOF-MSposerythrocyte culture supernatant from uninfected RBC
SA453258uS3_LC-QTOF-MSposerythrocyte culture supernatant from uninfected RBC
SA453259uS5_CE-TOF-MSerythrocyte culture supernatant from uninfected RBC
SA453260uS2_CE-TOF-MSerythrocyte culture supernatant from uninfected RBC
SA453261uS5_LC-QTOF-MSposerythrocyte culture supernatant from uninfected RBC
SA453262uRBC2_LC-QqQ-MS Berythrocyte culture uninfected RBC
SA453263uRBC3_LC-QqQ-MS Berythrocyte culture uninfected RBC
SA453264uRBC4_LC-QqQ-MS Berythrocyte culture uninfected RBC
SA453265uRBC5_LC-QqQ-MS Berythrocyte culture uninfected RBC
SA453266uRBC5_GC-QTOF-MSerythrocyte culture uninfected RBC
SA453267uRBC4_GC-QTOF-MSerythrocyte culture uninfected RBC
SA453268uRBC3_GC-QTOF-MSerythrocyte culture uninfected RBC
SA453269uRBC1_GC-QTOF-MSerythrocyte culture uninfected RBC
SA453270uRBC2_GC-QTOF-MSerythrocyte culture uninfected RBC
SA453271uRBC5_LC-QTOF-MSposerythrocyte culture uninfected RBC
SA453272uRBC1_CE-TOF-MSerythrocyte culture uninfected RBC
SA453273uRBC5_LC-QTOF-MSnegerythrocyte culture uninfected RBC
SA453274uRBC3_LC-QTOF-MSposerythrocyte culture uninfected RBC
SA453275uRBC2_LC-QTOF-MSposerythrocyte culture uninfected RBC
SA453276uRBC1_LC-QTOF-MSposerythrocyte culture uninfected RBC
SA453277uRBC1_LC-QTOF-MSnegerythrocyte culture uninfected RBC
SA453278uRBC3_LC-QTOF-MSnegerythrocyte culture uninfected RBC
SA453279uRBC4_LC-QTOF-MSnegerythrocyte culture uninfected RBC
SA453280uRBC4_CE-TOF-MSerythrocyte culture uninfected RBC
SA453281uRBC4_LC-QTOF-MSposerythrocyte culture uninfected RBC
SA453282uRBC3_CE-TOF-MSerythrocyte culture uninfected RBC
SA453283uRBC2_CE-TOF-MSerythrocyte culture uninfected RBC
SA453284uRBC2_LC-QqQ-MS Aerythrocyte culture uninfected RBC
SA453285uRBC3_LC-QqQ-MS Aerythrocyte culture uninfected RBC
Showing page 1 of 2     Results:    1  2  Next     Showing results 1 to 100 of 103

Collection:

Collection ID:CO004100
Collection Summary:Human A+ erythrocytes were obtained from healthy volunteer donors at the Blood Transfusion Center in Madrid, Spain. Donors provided written informed consent for the use of their blood in research. All procedures were approved by the center and carried out in accordance with institutional and regulatory guidelines. Asynchronous cultures of Babesia divergens (Bd Rouen 1986 strain) were maintained using human A+ erythrocytes at 5% hematocrit in RPMI 1640 medium (Gibco, Grand Island, NY, USA), supplemented with 10% human serum (The Interstate Companies, Memphis, TN, USA), 7.5% (w/v) sodium bicarbonate (Lonza Group Ltd., Basel, Switzerland), and 50 μg/mL hypoxanthine (Sigma-Aldrich, St. Louis, MO, USA). Control flasks containing uninfected erythrocytes were incubated under the same conditions using identical medium. All cultures were maintained at 37 °C in a humidified atmosphere with 5% CO₂. Samples were collected from independent asynchronous cultures of B. divergens at approximately 40% parasitemia. Infected cultures were centrifuged at 600 × g for 5 minutes at 4 °C using fixed-angle rotors to pellet the cells (iRBC). The pellets, containing a mixture of infected and uninfected erythrocytes, were washed and centrifuged three times (2,000 × g, 5 minutes, 4 °C), resuspended in RPMI, and kept on ice. Supernatants (iS) were obtained from infected cultures by sequential centrifugation at 2,000 × g and 8,000 × g (5 minutes each, 4 °C), and stored at –80 °C. Control samples (uRBC and uS) from uninfected cultures were processed in parallel using the same protocol. Detailed description of sample collection can be found at DOI: 10.1007/978-1-0716-1681-9_13
Sample Type:Red blood cells and culture media

Treatment:

Treatment ID:TR004116
Treatment Summary:Since the study was aimed to describe changes ocurring upon an in vitro model of a natural disease, no treatment was performed.

Sample Preparation:

Sampleprep ID:SP004113
Sampleprep Summary:Metabolite extraction was carried out using a multi-step procedure designed to rapidly quench metabolism, promote cell lysis, and enhance metabolite recovery. For intracellular extraction, 800 μL of cold (–20 °C) methanol (Thermo Fisher Scientific, Loughborough, UK) was added to 200 μL of either infected (iRBC) or uninfected (uRBC) red blood cells. Samples underwent two freeze–thaw cycles by immersion in liquid nitrogen for 10 minutes, followed by thawing on ice and light vortexing. After centrifugation at 5,725 × g for 5 minutes at 4 °C, the supernatants were collected. The residual pellets were re-extracted twice with 400 μL of cold methanol per step, using the same freeze–thaw and centrifugation conditions. All supernatants from the same sample were pooled and stored at –80 °C until analysis. Extracellular samples (iS and uS) were processed based on the analytical platform. For untargeted CE-TOF/MS, GC-QTOF/MS, and LC-QTOF/MS analyses, cold acetonitrile (Thermo Fisher Scientific, Loughborough, UK) was used in a 1:4 (v/v) sample-to-solvent ratio. For targeted LC-QqQ/MS profiling, cold methanol was used in a 1:3 (v/v) ratio. Following quenching and extraction, supernatants were filtered through 0.22 μm MS® Nylon syringe filters (Membrane Solutions, Plano, USA) and stored at –80 °C. For CE-TOF/MS analysis, 250 μL of each extract (iRBC, uRBC, iS, and uS) was dried under vacuum and reconstituted in 50 μL of CE/MS sample solution prepared by dissolving methionine sulfone (internal standard; Sigma-Aldrich, Steinheim, Germany) at 0.2 mM in Milli-Q water with 0.1 M formic acid (Sigma-Aldrich). After vortexing for 1 minute and centrifugation at 12,600 × g for 15 minutes at 4 °C, the supernatants were used for analysis. GC-QTOF/MS samples were prepared by adding 10 μL of ethoxymation solution and 12 μL of internal standard to 240 μL of each sample. The ethoxymation reagent was anhydrous pyridine containing 19 mg·mL⁻¹ O-ethoxyamine (Sigma-Aldrich, Steinheim, Germany), and the internal standard solution contained 10 mg·L⁻¹ meso-erythritol in Milli-Q water. After vacuum drying, derivatization was performed automatically using an MPS autosampler. O-ethyloxime derivatives were formed by incubating the extracts for 90 minutes at 40 °C, followed by silylation of acidic compounds using 42 μL of N-methyl-N-(trimethylsilyl)trifluoroacetamide (MSTFA) with 1% trimethylchlorosilane (TCMS; Sigma-Aldrich, Germany) for 50 minutes at 40 °C. For LC-QTOF/MS analysis, 100 μL of each processed extract (iRBC, uRBC, iS, and uS) was transferred to LC vials after brief vortexing. For LC-QqQ/MS analysis of polar metabolites, 12 μL of internal standard solution (50.09 µM p-chlorophenylalanine in Milli-Q water; Sigma-Aldrich, Steinheim, Germany) were added to 300 μL of each extract — methanol for iRBC/uRBC and methanol:water (3:1, v/v) for iS/uS. Samples were then evaporated under vacuum, reconstituted in 60 μL of Milli-Q water with the aid of a 5-minute sonication bath, and centrifuged at 3,000 × g for 10 minutes at 4 °C before injection. Detailed protocols of the conditions followed sample preparation can be found at DOI: 10.1007/978-1-0716-1681-9_13

Chromatography:

Chromatography ID:CH004958
Chromatography Summary:Cromatography summary. Non-targeted GC-MS method adapted for the determination of metabolites with acidic hydrogens through two-step derivatization (ethoxymation and trimethylsilylation).
Instrument Name:Agilent 7890B
Column Name:Macherey Nagel Optima 726 (60 m x 0.25 mm, 0.25 um)
Column Temperature:80º C for 1 min. Then, increase at 20 ºC/min until 200 ºC. Then, increase at 5 ºC/min until 235 ºC. Then, increase at 3 ºC/min until 270 ºC. Finally, increase at 20 ºC/min until 320 ºC, which was held for 1 min.
Flow Gradient:-
Flow Rate:1.3 mL/min
Solvent A:-
Solvent B:-
Chromatography Type:GC
  
Chromatography ID:CH004959
Chromatography Summary:Cromatography summary. Non-targeted, CE-ESI-MS, method applied for the determination of positively-charged metabolites under acidic conditions.
Instrument Name:Agilent 7100 CE
Column Name:Agilent bare fused silica capillary, (96 cm x 50 um)
Column Temperature:-
Flow Gradient:-
Flow Rate:-
Solvent A:-
Solvent B:-
Chromatography Type:CE
  
Chromatography ID:CH004960
Chromatography Summary:non-targeted, LC-MS method for the determination of compounds with intermediate polarity
Instrument Name:Agilent 1200
Column Name:Supelco Discovery HS C18 (150 × 2.1 mm, 3 um)
Column Temperature:40 ºC
Flow Gradient:25 %B at 0 min, increased until 95% B at 35 min. Return to 25 %B at 36 min, which was held until 45 min
Flow Rate:0.6 mL/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase
  
Chromatography ID:CH004961
Chromatography Summary:targeted, LC-MS method for the determination of polar compounds. Ion pair with tributylamine
Instrument Name:Agilent 1200
Column Name:Agilent RRHD Zorbax Extend C18 column (150 x 2.1mm, 1.8 um)
Column Temperature:35 ºC
Flow Gradient:0%B at 0-2.5 min; increased up to 20%B at 7.5 min; increased up to 45%B at 13 min; increased up to 99%B at 20 min; held at 24 min; washing step with quaternary pump until 59 min; then 0%B at 59 min
Flow Rate:0.25 mL/min (until 24 min); 0.2 mL/min at 59 min, gradually increased up to 0.25 mL/min at 60 min
Solvent A:97% water/3% methanol; 15 mM acetic acid; 10 mM tributylamine
Solvent B:100% methanol; 15 mM acetic acid; 10 mM tributylamine
Chromatography Type:Ion pair

Analysis:

Analysis ID:AN006531
Analysis Type:MS
Chromatography ID:CH004958
Num Factors:4
Num Metabolites:52
Units:normalized (total useful signal) abundances
  
Analysis ID:AN006532
Analysis Type:MS
Chromatography ID:CH004959
Num Factors:4
Num Metabolites:81
Units:normalized (total useful signal) abundances
  
Analysis ID:AN006533
Analysis Type:MS
Chromatography ID:CH004960
Num Factors:4
Num Metabolites:29
Units:normalized (total useful signal) abundances
  
Analysis ID:AN006534
Analysis Type:MS
Chromatography ID:CH004960
Num Factors:4
Num Metabolites:16
Units:Internal standard normalized abundances
  
Analysis ID:AN006535
Analysis Type:MS
Chromatography ID:CH004961
Num Factors:4
Num Metabolites:62
Units:Internal standard normalized abundances
  
Analysis ID:AN006536
Analysis Type:MS
Chromatography ID:CH004961
Num Factors:4
Num Metabolites:31
Units:normalized (total useful signal) abundances
  logo