Summary of Study ST002238

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 PR001428. The data can be accessed directly via it's Project DOI: 10.21228/M84Q4W 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.

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Study ID	ST002238
Study Title	LC-HRMS based plasma metabolomics analysis for biomarker discovery of neuroblastoma: 3-O-methyldopa is a new biomarker of poor prognosis of metastatic disease
Study Type	Biomarker Discovery
Study Summary	In this paper we show for the first time a metabolomic-based biomarker discovery using HRMS applied to plasma of NB patients and its validation on a second independent cohort of patients using a different analytical method.
Institute	Istituto Giannina Gaslini
Last Name	Lavarello
First Name	Chiara
Address	Via Gaslini 5, Genoa, GE, 16147, Italy
Email	chiaralavarello@gaslini.org
Phone	+3901056362911
Submit Date	2021-10-15
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	LC-MS
Release Date	2022-08-17
Release Version	1

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Combined analysis:

Analysis ID	AN003651	AN003652	AN003653	AN003654
Analysis type	MS	MS	MS	MS
Chromatography type	Reversed phase	Reversed phase	HILIC	HILIC
Chromatography system	Thermo Vanquish	Thermo Vanquish	Thermo Vanquish	Thermo Vanquish
Column	Waters Acquity BEH C18 (150 x 2mm,1.7um)	Waters Acquity BEH C18 (100 x 2mm,1.7um)	Waters Acquity BEH Amide (150 x 2.1mm,1.7um)	Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
MS Type	ESI	ESI	ESI	ESI
MS instrument type	Orbitrap	Orbitrap	Orbitrap	Orbitrap
MS instrument name	Thermo Q Exactive Plus Orbitrap	Thermo Q Exactive Plus Orbitrap	Thermo Q Exactive Plus Orbitrap	Thermo Q Exactive Plus Orbitrap
Ion Mode	POSITIVE	NEGATIVE	POSITIVE	NEGATIVE
Units	Peak area	Peak area	Peak area	Peak area

MS:

MS ID:	MS003402
Analysis ID:	AN003651
Instrument Name:	Thermo Q Exactive Plus Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Data processing was performed using MS-DIAL for peak picking, alignment, and identification. For metabolite analysis, in house m/z and retention time libraries were used in addition to MS/MS spectra databases in msp format. MS-DIAL parameters were set as follows: MS1 tolerance, 0.05Da; MS2 tolerance, 0.025 Da; retention time begin, 0 min; retention time end, 100 min; minimum peak height, 10000; mass slice width, 0.1 Da; smoothing level, 3 scans; minimum peak width, 5 scans; sigma window value, 0.5. We considered M−H, M–H2O−H, M+Na-2H, M+Cl, M+FA-H, 2M−H, 2M+FA-H, M−2H, 3M-H adduct in negative ionization mode and M+H, M+Na, M+ACN+H, M+H–H2O, M+H–2H2O, M+2Na-H, M+ACN+Na, M+2ACN+H, 2M+H, M+2H, 2M+ACN+Na in positive ionization mode. Execute retention time correction on IS and IS kit with a RT tolerance of 0.1 min and a mass tolerance of 0.015 Da were performed. In supplementary table X all parameter settings for MS-Dial were reported. For in silico compound annotation of ion features with an acquired tandem mass spectrum MS-FINDER The MS1 and MS2 tolerances were set to 5 and 15 ppm, respectively. Formula finder were exclusively processed with C, H, O, N, P and S atoms.
Ion Mode:	POSITIVE

MS ID:	MS003403
Analysis ID:	AN003652
Instrument Name:	Thermo Q Exactive Plus Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Data processing was performed using MS-DIAL for peak picking, alignment, and identification. For metabolite analysis, in house m/z and retention time libraries were used in addition to MS/MS spectra databases in msp format. MS-DIAL parameters were set as follows: MS1 tolerance, 0.05Da; MS2 tolerance, 0.025 Da; retention time begin, 0 min; retention time end, 100 min; minimum peak height, 10000; mass slice width, 0.1 Da; smoothing level, 3 scans; minimum peak width, 5 scans; sigma window value, 0.5. We considered M−H, M–H2O−H, M+Na-2H, M+Cl, M+FA-H, 2M−H, 2M+FA-H, M−2H, 3M-H adduct in negative ionization mode and M+H, M+Na, M+ACN+H, M+H–H2O, M+H–2H2O, M+2Na-H, M+ACN+Na, M+2ACN+H, 2M+H, M+2H, 2M+ACN+Na in positive ionization mode. Execute retention time correction on IS and IS kit with a RT tolerance of 0.1 min and a mass tolerance of 0.015 Da were performed. In supplementary table X all parameter settings for MS-Dial were reported. For in silico compound annotation of ion features with an acquired tandem mass spectrum MS-FINDER The MS1 and MS2 tolerances were set to 5 and 15 ppm, respectively. Formula finder were exclusively processed with C, H, O, N, P and S atoms.
Ion Mode:	NEGATIVE

MS ID:	MS003404
Analysis ID:	AN003653
Instrument Name:	Thermo Q Exactive Plus Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Data processing was performed using MS-DIAL for peak picking, alignment, and identification. For metabolite analysis, in house m/z and retention time libraries were used in addition to MS/MS spectra databases in msp format. MS-DIAL parameters were set as follows: MS1 tolerance, 0.05Da; MS2 tolerance, 0.025 Da; retention time begin, 0 min; retention time end, 100 min; minimum peak height, 10000; mass slice width, 0.1 Da; smoothing level, 3 scans; minimum peak width, 5 scans; sigma window value, 0.5. We considered M−H, M–H2O−H, M+Na-2H, M+Cl, M+FA-H, 2M−H, 2M+FA-H, M−2H, 3M-H adduct in negative ionization mode and M+H, M+Na, M+ACN+H, M+H–H2O, M+H–2H2O, M+2Na-H, M+ACN+Na, M+2ACN+H, 2M+H, M+2H, 2M+ACN+Na in positive ionization mode. Execute retention time correction on IS and IS kit with a RT tolerance of 0.1 min and a mass tolerance of 0.015 Da were performed. In supplementary table X all parameter settings for MS-Dial were reported. For in silico compound annotation of ion features with an acquired tandem mass spectrum MS-FINDER The MS1 and MS2 tolerances were set to 5 and 15 ppm, respectively. Formula finder were exclusively processed with C, H, O, N, P and S atoms.
Ion Mode:	POSITIVE

MS ID:	MS003405
Analysis ID:	AN003654
Instrument Name:	Thermo Q Exactive Plus Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Data processing was performed using MS-DIAL for peak picking, alignment, and identification. For metabolite analysis, in house m/z and retention time libraries were used in addition to MS/MS spectra databases in msp format. MS-DIAL parameters were set as follows: MS1 tolerance, 0.05Da; MS2 tolerance, 0.025 Da; retention time begin, 0 min; retention time end, 100 min; minimum peak height, 10000; mass slice width, 0.1 Da; smoothing level, 3 scans; minimum peak width, 5 scans; sigma window value, 0.5. We considered M−H, M–H2O−H, M+Na-2H, M+Cl, M+FA-H, 2M−H, 2M+FA-H, M−2H, 3M-H adduct in negative ionization mode and M+H, M+Na, M+ACN+H, M+H–H2O, M+H–2H2O, M+2Na-H, M+ACN+Na, M+2ACN+H, 2M+H, M+2H, 2M+ACN+Na in positive ionization mode. Execute retention time correction on IS and IS kit with a RT tolerance of 0.1 min and a mass tolerance of 0.015 Da were performed. In supplementary table X all parameter settings for MS-Dial were reported. For in silico compound annotation of ion features with an acquired tandem mass spectrum MS-FINDER The MS1 and MS2 tolerances were set to 5 and 15 ppm, respectively. Formula finder were exclusively processed with C, H, O, N, P and S atoms.
Ion Mode:	NEGATIVE