Summary of Study ST002536

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 PR001632. The data can be accessed directly via it's Project DOI: 10.21228/M8RB05 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	ST002536
Study Title	Effectors enabling adaptation to mitochondrial complex I loss in Hürthle cell carcinoma
Study Type	comparison of tumor versus normal tissue
Study Summary	With the goal of performing RNA-seq and metabolomic profiling, a cohort of fresh frozen oncocytic (Hürthle cell) thyroid carcinoma (HCC) samples was established with confirmation of mtDNA mutation status and chromosomal copy number. This cohort contained 24 oncocytic (Hürthle cell) tumors with 18 cases having matched normal thyroid tissue. Tumor samples included 21 primary tumors comprised of 19 HCC (8 widely invasive, 11 minimally invasive) and 2 oncocytic (Hürthle cell) adenomas as well as 2 locoregional recurrences (LR) and 1 distant metastasis (DM). HCC samples were collected and stored as part of the Mass General Brigham Institutional Review Board (protocol number 2008P001466). Frozen tissue was accessed to create the cohort used in the study.
Institute	Broad Institute of MIT and Harvard
Department	Metabolomics Platform
Last Name	Clish
First Name	Clary
Address	415 Main Street, Cambridge, MA, 02142, USA
Email	clary@broadinstitute.org
Phone	617-714-7654
Submit Date	2023-03-30
Num Groups	2
Total Subjects	tumors from 24 subjects and matched normal tissue from a subset of 18 subjects
Num Males	N/A
Num Females	N/A
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2023-04-17
Release Version	1

Select appropriate tab below to view additional metadata details:

Combined analysis:

Analysis ID	AN004171	AN004172	AN004173	AN004174
Analysis type	MS	MS	MS	MS
Chromatography type	HILIC	HILIC	Reversed phase	Reversed phase
Chromatography system	Shimadzu Nexera X2	Shimadzu Nexera X2	Shimadzu Nexera X2	Shimadzu Nexera X2
Column	Waters Atlantis HILIC (150 x 2.1mm,3um,100Å	Phenomenex Luna NH2 (150 x 2 mm,5um;100Å)	Waters ACQUITY UPLC BEH C8 Column (2.1 mm X 100 mm,1.7 µm,130Å)	Waters ACQUITY UPLC BEH C18 Column (2.1 mm X 150 mm,1.7 µm,130Å)
MS Type	ESI	ESI	ESI	ESI
MS instrument type	Orbitrap	Orbitrap	Orbitrap	Orbitrap
MS instrument name	Thermo Q Exactive Orbitrap	Thermo Q Exactive Plus Orbitrap	Thermo Exactive Plus Orbitrap	Thermo Q Exactive Orbitrap
Ion Mode	POSITIVE	NEGATIVE	POSITIVE	NEGATIVE
Units	peak area	peak area	peak area	peak area

MS:

MS ID:	MS003918
Analysis ID:	AN004171
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	MS analyses were carried out using electrospray ionization in the positive ion mode using full scan analysis over 70-800 m/z at 70,000 resolution and 3 Hz data acquisition rate. Other MS settings were: sheath gas 40, sweep gas 2, spray voltage 3.5 kV, capillary temperature 350°C, S-lens RF 40, heater temperature 300°C, microscans 1, automatic gain control target 1e6, and maximum ion time 250 ms. Raw data were processed using TraceFinder 3.3 software (Thermo Fisher Scientific; Waltham, MA) and Progenesis QI (Nonlinear Dynamics; Newcastle upon Tyne, UK). Metabolite identities were confirmed using authentic reference standards.
Ion Mode:	POSITIVE

MS ID:	MS003919
Analysis ID:	AN004172
Instrument Name:	Thermo Q Exactive Plus Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	MS analyses were carried out using electrospray ionization in the negative ion mode using full scan analysis over m/z 70-750 at 70,000 resolution and 3 Hz data acquisition rate. Additional MS settings were: ion spray voltage, -3.0 kV; capillary temperature, 350°C; probe heater temperature, 325 °C; sheath gas, 55; auxiliary gas, 10; and S-lens RF level 50. Raw data were processed using TraceFinder 3.3 software (Thermo Fisher Scientific; Waltham, MA) and Progenesis QI (Nonlinear Dynamics; Newcastle upon Tyne, UK). Metabolite identities were confirmed using authentic reference standards.
Ion Mode:	NEGATIVE

MS ID:	MS003920
Analysis ID:	AN004173
Instrument Name:	Thermo Exactive Plus Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	MS analyses were carried out using electrospray ionization in the positive ion mode using full scan analysis over 200–1100 m/z at 70,000 resolution and 3 Hz data acquisition rate. Other MS settings were: sheath gas 50, in source CID 5 eV, sweep gas 5, spray voltage 3 kV, capillary temperature 300°C, S-lens RF 60, heater temperature 300°C, microscans 1, automatic gain control target 1e6, and maximum ion time 100 ms. Representative standards from each lipid class were used to identify lipids based on RT and m/z patterns, and characteristic product ion spectra. Lipid identities were denoted by total acyl carbon number and total number of double bond number.
Ion Mode:	POSITIVE

MS ID:	MS003921
Analysis ID:	AN004174
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	MS analyses were carried out using electrospray ionization in the negative ion mode using full scan analysis over m/z 70-850 at 70,000 resolution and 3 Hz data acquisition rate. Additional MS settings were: ion spray voltage, -3.5 kV; capillary temperature, 320°C; probe heater temperature, 300 °C; sheath gas, 45; auxiliary gas, 10; and S-lens RF level 60. Raw data were processed using TraceFinder 3.3 software (Thermo Fisher Scientific; Waltham, MA) and Progenesis QI (Nonlinear Dynamics; Newcastle upon Tyne, UK). Metabolite identities were confirmed using authentic reference standards.
Ion Mode:	NEGATIVE