Summary of Study ST001772

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 PR001127. The data can be accessed directly via it's Project DOI: 10.21228/M81D6M 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	ST001772
Study Title	Optimization of redox metabolite detection in mammalian cells (part II)
Study Summary	Conditions were tested to optimize number of cells and extraction buffer for the detection of redox reactive metabolites from mammalian cells. Four different extraction buffers were compared. Derivatization of glutathion was explored as a condition as well.
Institute	Boston Children's Hospital, Harvard Medical School
Department	Pathology
Laboratory	Naama Kanarek
Last Name	Petrova
First Name	Boryana
Address	300 Longwood Av, Boston, MA, 2115, USA
Email	boryana.petrova@childrens.harvard.edu
Phone	6173557433
Submit Date	2021-04-22
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2021-05-17
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001127
Project DOI:	doi: 10.21228/M81D6M
Project Title:	Redox metabolism measurement in mammalian cells and tissues by quantitative LC/MS method (part I)
Project Summary:	This study aimed to optimize the detection of several key redox-reactive metabolites from mammalian cells and tissues. We explored three different chromatographic methods and optimized sample preparation, extraction buffer and conditions as well as mass spectrometry detection parameters. The established method was tested and validated using biologically relevant ROS-inducing conditions. This study can be a valuable resource for the metabolomics community.
Institute:	Boston Childrens Hospital
Department:	Pathology
Laboratory:	Naama Kanarek
Last Name:	Petrova
First Name:	Boryana
Address:	300 Longwood Av, Boston, MA, 2115, USA
Email:	boryana.petrova@childrens.harvard.edu
Phone:	6173557433

Subject:

Subject ID:	SU001849
Subject Type:	Mammal
Subject Species:	Homo sapiens
Taxonomy ID:	9606

Factors:

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

mb_sample_id	local_sample_id	Factor
SA164462	pooled sample QC 1/10 dilution a	-
SA164463	pooled sample QC 1/3 dilution	-
SA164464	pooled sample QC5	-
SA164465	pooled sample QC2	-
SA164466	pooled sample QC3	-
SA164467	pooled sample QC1	-
SA164468	blank1	-
SA164469	blank3	-
SA164470	blank2	-
SA164471	blank4	-
SA164472	blank5	-
SA164473	pooled sample QC 1/10 dilution b	-
SA164474	pooled sample QC4	-
SA164475	1M K562 cell buffer A_5_1	buffer A
SA164476	1M K562 cell buffer A_1_1	buffer A
SA164477	1M K562 cell buffer A_1_2	buffer A
SA164478	1M K562 cell buffer A_2_1	buffer A
SA164479	1M K562 cell buffer A_2_2	buffer A
SA164480	1M K562 cell buffer A_5_2	buffer A
SA164481	1M K562 cell buffer B_1_2a	buffer B
SA164482	1M K562 cell buffer B_1_2	buffer B
SA164483	1M K562 cell buffer B_2_1	buffer B
SA164484	1M K562 cell buffer B_2_2	buffer B
SA164485	1M K562 cell buffer B_5_1	buffer B
SA164486	1M K562 cell buffer B_5_2	buffer B
SA164487	1M K562 cell buffer C_1_2	buffer C buffer
SA164488	1M K562 cell buffer C_5_1	buffer C buffer
SA164489	1M K562 cell buffer C_2_2	buffer C buffer
SA164490	1M K562 cell buffer C_2_1	buffer C buffer
SA164491	1M K562 cell buffer C_1_1	buffer C buffer
SA164492	1M K562 cell buffer C_5_2	buffer C buffer
SA164493	1M K562 cell buffer C_Ell_1_1	buffer C_Ell
SA164494	1M K562 cell buffer C_Ell_5_2	buffer C_Ell
SA164495	1M K562 cell buffer C_Ell_2_2	buffer C_Ell
SA164496	1M K562 cell buffer C_Ell_2_1	buffer C_Ell
SA164497	1M K562 cell buffer C_Ell_1_2	buffer C_Ell
SA164498	1M K562 cell buffer C_Ell_5_1	buffer C_Ell

Showing results 1 to 37 of 37

Showing results 1 to 37 of 37

Collection:

Collection ID:	CO001842
Collection Summary:	All animal care and experimental procedures were approved by the Institutional Animal Care and Use Committees of Boston Children’s Hospital. Mouse strain used was C57BL/6. Pure CSF samples were collected from the cisterna magna [39]. Blood samples were collected from the retromandibular vein. The samples were coagulated and centrifuged. Liver and kidney were collected and flash frozen. Tissue chunks were cut on a glass plate while kept chilled on top of dry ice. K562 cells used in this manuscript were authenticated by short tandem repeat analysis and tested negative for mycoplasma. Cells were cultured in RPMI (Genesee Scientific) up to a density of 2 Million cells per ml. For redox chemical treatment experiments, cells were seeded at 1 Million cells per ml cell density in 6-well plates and drugs were added for 4h at the following concentrations: methotrexate: 5 µM; oligomycin: 80 µg/ml; H2O2: 1 mM; diamide: 0.5 mM; DMSO, which served as control: 0.6 µl per 1 mL of cell culture media (equivalent to volume used for oligomycin).
Sample Type:	K562 Cells

Treatment:

Treatment ID:	TR001862
Treatment Summary:	1M K562 cells + Buffers from Study Design

Sample Preparation:

Sampleprep ID:	SP001855
Sampleprep Summary:	Metabolites were quenched as quickly as possible while working with the samples at low temperatures. Cells were handled at 4ºC or on dry ice, extraction buffer was pre-chilled at -20ºC. Samples were analyzed by LC-MS on the same day of extraction (if impractical, best alternative is to store dried samples at -80ºC). Unless indicated otherwise, 1 million cells or about 2 mg of tissue was extracted per condition and a minimum of three replicates per condition was used in each experiment. K562 cells that are non-adherent, were collected by brief centrifugation at 4ºC using a table-top centrifuge (4,500 rpm, 1.5 min) and washed briefly in 0.9% NaCl (high grade salt and LC-MS-grade water Fisher Scientific W6500 or Sigma Aldrich 1.15333). 300 µl of prechilled extraction buffer were added per sample. For tissues – chunks were crushed using a hand-held homogenizer (VWR 47747-370) with several pulses while keeping the samples on ice. 300 µl of prechilled extraction buffer was used per 2 mg of tissue. Extraction buffer “A”: 40:40:20 of acetonitrile:methanol:water, supplemented with 0.1M formic acid and isotopically-labeled internal standards (17 amino acids and reduced glutathione, Cambridge Isotope Laboratories, MSK-A2-1.2 and CNLM-6245-10). Extraction buffer “B”: 80% LC-MS-grade methanol, 20% 25 mM Ammonium Acetate and 2.5 mM Na-Ascorbate prepared in LC-MS water and supplemented with isotopically labeled internal standards (17 amino acids and isotopically labelled reduced glutathione, Cambridge Isotope Laboratories, MSK-A2-1.2 and CNLM-6245-10). Extraction buffer “C” and “C + Ellman’s”: Solution 1: 100% LC-MS Methanol Solution 2: 25mM Ammonium Acetate and 2.5mM Na-Ascorbate in LC-MS water supplemented with isotopically labelled reduced glutathione and isotopically labeled internal standards (17 amino acids and reduced glutathione, Cambridge Isotope Laboratories, MSK-A2-1.2 and CNLM-6245-10). Ellman’s reagent (5,5′-Dithiobis(2-nitrobenzoic acid),D8130, Sigma Aldrich): 20 mM in “Solution 2”. Final composition is 80% solution 1 and 20% solution 2. Samples were vortexed briefly (10 sec) and sonicated for 3 min in a 4ºC water bath. Samples were then centrifuged for 10 min, 4ºC, at maximum speed on a benchtop centrifuge (Eppendorf) and the cleared supernatant was transferred to a new tube. Samples were dried using a nitrogen dryer while on ice, and special attention was given to minimize the time of drying and to not let samples idle in the dryer (Reacti-Vap™ Evaporator, Thermo Fisher Scientific, TS-18826) once the drying process was completed. Needles were continuously adjusted to the surface of the liquid as the samples evaporated to expedite the drying process. Samples were reconstituted in 30 µl LC-MS-grade water by brief sonication in a 4ºC water bath. Extracted metabolites were spun for 2 min at maximum speed on a bench-top centrifuge and cleared supernatant was transferred to LC-MS micro vials (National Scientific, C5000-45B). A small amount of each sample was pooled and serially diluted 3- and 10-fold to be used as quality controls throughout the run of each batch.

Sampleprep ID:

SP001855

Sampleprep Summary:

Metabolites were quenched as quickly as possible while working with the samples at low temperatures. Cells were handled at 4ºC or on dry ice, extraction buffer was pre-chilled at -20ºC. Samples were analyzed by LC-MS on the same day of extraction (if impractical, best alternative is to store dried samples at -80ºC). Unless indicated otherwise, 1 million cells or about 2 mg of tissue was extracted per condition and a minimum of three replicates per condition was used in each experiment. K562 cells that are non-adherent, were collected by brief centrifugation at 4ºC using a table-top centrifuge (4,500 rpm, 1.5 min) and washed briefly in 0.9% NaCl (high grade salt and LC-MS-grade water Fisher Scientific W6500 or Sigma Aldrich 1.15333). 300 µl of prechilled extraction buffer were added per sample. For tissues – chunks were crushed using a hand-held homogenizer (VWR 47747-370) with several pulses while keeping the samples on ice. 300 µl of prechilled extraction buffer was used per 2 mg of tissue. Extraction buffer “A”: 40:40:20 of acetonitrile:methanol:water, supplemented with 0.1M formic acid and isotopically-labeled internal standards (17 amino acids and reduced glutathione, Cambridge Isotope Laboratories, MSK-A2-1.2 and CNLM-6245-10). Extraction buffer “B”: 80% LC-MS-grade methanol, 20% 25 mM Ammonium Acetate and 2.5 mM Na-Ascorbate prepared in LC-MS water and supplemented with isotopically labeled internal standards (17 amino acids and isotopically labelled reduced glutathione, Cambridge Isotope Laboratories, MSK-A2-1.2 and CNLM-6245-10). Extraction buffer “C” and “C + Ellman’s”: Solution 1: 100% LC-MS Methanol Solution 2: 25mM Ammonium Acetate and 2.5mM Na-Ascorbate in LC-MS water supplemented with isotopically labelled reduced glutathione and isotopically labeled internal standards (17 amino acids and reduced glutathione, Cambridge Isotope Laboratories, MSK-A2-1.2 and CNLM-6245-10). Ellman’s reagent (5,5′-Dithiobis(2-nitrobenzoic acid),D8130, Sigma Aldrich): 20 mM in “Solution 2”. Final composition is 80% solution 1 and 20% solution 2. Samples were vortexed briefly (10 sec) and sonicated for 3 min in a 4ºC water bath. Samples were then centrifuged for 10 min, 4ºC, at maximum speed on a benchtop centrifuge (Eppendorf) and the cleared supernatant was transferred to a new tube. Samples were dried using a nitrogen dryer while on ice, and special attention was given to minimize the time of drying and to not let samples idle in the dryer (Reacti-Vap™ Evaporator, Thermo Fisher Scientific, TS-18826) once the drying process was completed. Needles were continuously adjusted to the surface of the liquid as the samples evaporated to expedite the drying process. Samples were reconstituted in 30 µl LC-MS-grade water by brief sonication in a 4ºC water bath. Extracted metabolites were spun for 2 min at maximum speed on a bench-top centrifuge and cleared supernatant was transferred to LC-MS micro vials (National Scientific, C5000-45B). A small amount of each sample was pooled and serially diluted 3- and 10-fold to be used as quality controls throughout the run of each batch.

Combined analysis:

Analysis ID	AN002879
Analysis type	MS
Chromatography type	HILIC
Chromatography system	Thermo Vanquish
Column	EMD Millipore ZIC HILIC (150 x 2.1mm,5um)
MS Type	ESI
MS instrument type	Orbitrap
MS instrument name	Thermo Q Exactive Orbitrap
Ion Mode	UNSPECIFIED
Units	ppm

Chromatography:

Chromatography ID:	CH002134
Chromatography Summary:	ZIC-pHILIC chromatography: One ml of reconstituted sample was injected into a ZIC-pHILIC 150 × 2.1 mm (5 µm particle size) column (EMD Millipore) operated on a Vanquish™ Flex UHPLC Systems (Thermo Fisher Scientific, San Jose, CA). Chromatographic separation was achieved using the following conditions: buffer A was acetonitrile; buffer B was 20 mM ammonium carbonate, 0.1% ammonium hydroxide. Gradient conditions were: linear gradient from 20% to 80% B; 20–20.5 min: from 80% to 20% B; 20.5–28 min: hold at 20% B. The column oven and autosampler tray were held at 25 °C and 4 °C, respectively.
Instrument Name:	Thermo Vanquish
Column Name:	EMD Millipore ZIC HILIC (150 x 2.1mm,5um)
Column Temperature:	25
Flow Gradient:	linear gradient from 20% to 80% B; 20-20.5 min: from 80% to 20% B; 20.5-28 min: hold at 20% B.
Solvent A:	100% acetonitrile
Solvent B:	100% water; 20 mM ammonium carbonate; 0.1% ammonium hydroxide
Chromatography Type:	HILIC

MS:

MS ID:	MS002672
Analysis ID:	AN002879
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	HESI
Ion Mode:	UNSPECIFIED