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 IDST002238
Study TitleLC-HRMS based plasma metabolomics analysis for biomarker discovery of neuroblastoma: 3-O-methyldopa is a new biomarker of poor prognosis of metastatic disease
Study TypeBiomarker Discovery
Study SummaryIn 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 NameLavarello
First NameChiara
AddressVia Gaslini 5, Genoa, GE, 16147, Italy
Emailchiaralavarello@gaslini.org
Phone+3901056362911
Submit Date2021-10-15
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2022-08-17
Release Version1
Chiara Lavarello Chiara Lavarello
https://dx.doi.org/10.21228/M84Q4W
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001428
Project DOI:doi: 10.21228/M84Q4W
Project 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
Project Type:Biomarker Discovery
Project Summary:Neuroblastoma (NB) is the most common extra-cranial malignant tumor in children. Although the survival rate of NB has improved over the years, the outcome of NB still remains unfavorable in a high percentage of cases. Prognosis is currently based on a combination of clinical, histo-pathological and biological features, on which patients are classified in different risk groups and addressed to different treatment protocols. A more accurate risk stratification remains a key point in the study of NB: in particular, the availability of novel prognostic biomarkers of metastatic “high risk” NB at diagnosis could help in improving patient stratification, accurately predicting outcome, relapse or response to treatments and also reducing unnecessary therapies and related toxicities. In this study an HRMS-based approach was applied for the first time to study NB with a goal of developing prognostic biomarkers that could help in improving patient stratification and providing novel therapeutic targets. Starting from an untargeted approach the differences in the metabolomic profiles of localized and metastatic patients were investigated. Key metabolites of metastatic NB were identified through differential expression analysis. Among the metabolites of L-DOPA degradation pathway 3-o-methyldopa (3-O-MD) was selected and analysed in a second cohort of patients using a targeted approach based on liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS).
Institute:IRCCS Gaslini
Last Name:Lavarello
First Name:Chiara
Address:Via Gaslini 5, Genoa, GE, 16147, Italy
Email:chiaralavarello@gaslini.org
Phone:+3901056362911

Subject:

Subject ID:SU002324
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 Type
SA213147BLK_C18_Pos_002_146Blank
SA213148BLK_C18_Neg_002_145Blank
SA213149BLK_HILIC_Pos_003_144Blank
SA213150BLK_C18_Pos_001_145Blank
SA213151BLK_C18_Neg_001_144Blank
SA213152BLK_C18_Pos_003_147Blank
SA213153BLK_HILIC_Neg_001_144Blank
SA213154BLK_C18_Neg_003_146Blank
SA213155BLK_HILIC_Neg_003_146Blank
SA213156BLK_HILIC_Neg_002_145Blank
SA213157NB_Plasma_EXT_C18_Neg_001QC
SA213158NB_Plasma_QC_C18_Neg_109QC
SA213159NB_Plasma_QC_C18_Neg_117QC
SA213160NB_Plasma_QC_C18_Neg_102QC
SA213161NB_Plasma_QC_C18_Neg_142QC
SA213162NB_Plasma_QC_C18_Neg_094QC
SA213163NB_Plasma_QC_C18_Neg_132QC
SA213164NB_Plasma_QC_C18_Neg_124QC
SA213165NB_Plasma_QC_C18_Neg_072QC
SA213166NB_Plasma_EXT_HILIC_Pos_128QC
SA213167NB_Plasma_EXT_HILIC_Pos_129QC
SA213168NB_Plasma_EXT_HILIC_Pos_130QC
SA213169NB_Plasma_QC_HILIC_Pos_184QC
SA213170NB_Plasma_QC_HILIC_Pos_175QC
SA213171NB_Plasma_QC_HILIC_Pos_157QC
SA213172NB_Plasma_QC_HILIC_Pos_166QC
SA213173NB_Plasma_EXT_HILIC_Pos_149QC
SA213174NB_Plasma_EXT_HILIC_Pos_167QC
SA213175NB_Plasma_QC_C18_Neg_064QC
SA213176NB_Plasma_EXT_C18_Neg_002QC
SA213177NB_Plasma_QC_C18_Neg_057QC
SA213178NB_Plasma_QC_C18_Neg_049QC
SA213179NB_Plasma_QC_C18_Neg_034QC
SA213180NB_Plasma_QC_C18_Neg_042QC
SA213181NB_Plasma_QC_C18_Neg_079QC
SA213182NB_Plasma_EXT_C18_Neg_003QC
SA213183NB_Plasma_QC_C18_Pos_050QC
SA213184NB_Plasma_QC_C18_Pos_058QC
SA213185NB_Plasma_QC_C18_Pos_065QC
SA213186NB_Plasma_QC_C18_Pos_043QC
SA213187NB_Plasma_QC_C18_Pos_035QC
SA213188NB_Plasma_EXT_C18_Neg_108QC
SA213189NB_Plasma_QC_C18_Pos_028QC
SA213190NB_Plasma_QC_C18_Pos_073QC
SA213191NB_Plasma_QC_C18_Pos_080QC
SA213192NB_Plasma_QC_C18_Pos_118QC
SA213193NB_Plasma_QC_C18_Pos_125QC
SA213194NB_Plasma_QC_C18_Pos_133QC
SA213195NB_Plasma_QC_C18_Pos_110QC
SA213196NB_Plasma_QC_C18_Pos_103QC
SA213197NB_Plasma_QC_C18_Pos_088QC
SA213198NB_Plasma_QC_C18_Pos_095QC
SA213199NB_Plasma_EXT_C18_Neg_088QC
SA213200NB_Plasma_EXT_C18_Neg_067QC
SA213201NB_Plasma_EXT_C18_Neg_095QC
SA213202NB_Plasma_EXT_C18_Neg_110QC
SA213203NB_Plasma_EXT_C18_Neg_125QC
SA213204NB_Plasma_EXT_C18_Neg_080QC
SA213205NB_Plasma_EXT_C18_Neg_065QC
SA213206NB_Plasma_EXT_C18_Neg_035QC
SA213207NB_Plasma_EXT_C18_Neg_050QC
SA213208NB_Plasma_EXT_C18_Neg_143QC
SA213209NB_Plasma_QC_C18_Neg_068QC
SA213210NB_Plasma_QC_C18_Neg_ID_117QC
SA213211NB_Plasma_QC_C18_Neg_127QC
SA213212NB_Plasma_QC_C18_Neg_107QC
SA213213NB_Plasma_QC_C18_Neg_097QC
SA213214NB_Plasma_QC_C18_Neg_077QC
SA213215NB_Plasma_QC_C18_Neg_ID_087QC
SA213216NB_Plasma_QC_HILIC_Pos_148QC
SA213217NB_Plasma_QC_HILIC_Pos_025QC
SA213218NB_Plasma_QC_HILIC_Neg_57QC
SA213219NB_Plasma_QC_HILIC_Neg_49QC
SA213220NB_Plasma_QC_HILIC_Neg_42QC
SA213221NB_Plasma_QC_HILIC_Neg_64QC
SA213222NB_Plasma_QC_HILIC_Neg_72QC
SA213223NB_Plasma_QC_HILIC_Neg_87QC
SA213224NB_Plasma_QC_HILIC_Neg_79QC
SA213225NB_Plasma_QC_HILIC_Neg_34QC
SA213226NB_Plasma_QC_HILIC_Neg_27QC
SA213227NB_Plasma_EXT_HILIC_Neg_80QC
SA213228NB_Plasma_EXT_HILIC_Neg_65QC
SA213229NB_Plasma_EXT_HILIC_Neg_95QC
SA213230NB_Plasma_EXT_HILIC_Neg_110QC
SA213231NB_Plasma_EXT_HILIC_Neg_143QC
SA213232NB_Plasma_EXT_HILIC_Neg_125QC
SA213233NB_Plasma_QC_HILIC_Neg_94QC
SA213234NB_Plasma_QC_HILIC_Neg_102QC
SA213235NB_Plasma_QC_HILIC_Neg235QC
SA213236NB_Plasma_QC_HILIC_Neg225QC
SA213237NB_Plasma_QC_HILIC_Neg215QC
SA213238NB_Plasma_QC_HILIC_Neg245QC
SA213239NB_Plasma_EXT_HILIC_Neg_185QC
SA213240NB_Plasma_EXT_HILIC_Neg_226QC
SA213241NB_Plasma_EXT_HILIC_Neg_206QC
SA213242NB_Plasma_QC_HILIC_Neg205QC
SA213243NB_Plasma_QC_HILIC_Neg195QC
SA213244NB_Plasma_QC_HILIC_Neg_117QC
SA213245NB_Plasma_QC_HILIC_Neg_109QC
SA213246NB_Plasma_QC_HILIC_Neg_124QC
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Collection:

Collection ID:CO002317
Collection Summary:Plasma samples were obtained from patients with NB at the diagnosis from peripheral venous blood collected in 3 mL EDTA K3-containing tubes, centrifuged at 4000 g for 5 min at 4 °C and stored at -80°C until analysed.
Sample Type:Blood (plasma)
Storage Conditions:-80℃

Treatment:

Treatment ID:TR002336
Treatment Summary:-

Sample Preparation:

Sampleprep ID:SP002330
Sampleprep Summary:A 50 µL aliquot of plasma was extracted adding 150 µL cold (-20 C) methanol containing as internal standard mixture of creatine (methyl-D3, 98%), vitamin B3 (D4, 98%), uracil (1,3-15N2, 98%), chenodeoxycholic acid (2,2,4,4-D4, 98%). After over-night protein precipitation, proteins were removed by centrifugation for 10 minutes at 14,000 x g and 4 °C. The supernatant was collected and stored at -80 °C until analysis when was adding to the samples a second internal standard mixture of L-alanine (13C3, 99%), chenodeoxycholic acid (2,2,4,4-D4, 98%), L-leucine (13C6, 99%), L-phenylalanine (13C6, 99%), L-tryptophan (13C11, 99%), L-tyrosine (13C6, 99%), caffeine (13C3, 99%). stearic acid, sodium salt (13C18, 98%), sodium benzoate (13C6, 99%). Quality control (QC) samples were prepared by mixing equal volumes of all the NB plasma samples. In addition, a procedural blank, used to monitor contamination acquired during all stages of sample preparation, and external quality control (EQC) samples were included in the study and were prepared in the same way as the study samples. To avoid bias due to instrument drift, the analytical study design involves analyzing the 99 samples in a randomized way, with 16 QC and 9 EQC inserted every 6 and 12 runs respectively to assess analytical precision. Subsequently, 18 identification runs and a procedural blank were analyzed.
Extract Storage:-20℃

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

Chromatography:

Chromatography ID:CH002705
Chromatography Summary:Reverse phase column was eluted with 99% of mobile phase A (0.1% formic acid in water) for 0.1 min followed by a linear gradient to 100% of mobile phase B (0.1% formic acid in acetonitrile) over 15 min, then kept constant for 5 min, brought back to the initial conditions in 0.5 min, and maintained for 5 min.
Instrument Name:Thermo Vanquish
Column Name:Waters Acquity BEH C18 (150 x 2mm,1.7um)
Flow Gradient:99% of A for 0.1 min followed by a linear gradient to 100% of B over 15 min, then kept constant for 5 min, brought back to the initial conditions in 0.5 min, and maintained for 5 min.
Flow Rate:250 µl/min
Injection Temperature:40
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Randomization Order:yes
Chromatography Type:Reversed phase
  
Chromatography ID:CH002706
Chromatography Summary:Reverse phase column was eluted with 99% of mobile phase A (0.1% formic acid in water) for 0.1 min followed by a linear gradient to 100% of mobile phase B (0.1% formic acid in acetonitrile) over 15 min, then kept constant for 5 min, brought back to the initial conditions in 0.5 min, and maintained for 5 min.
Instrument Name:Thermo Vanquish
Column Name:Waters Acquity BEH C18 (100 x 2mm,1.7um)
Flow Gradient:99% of A for 0.1 min followed by a linear gradient to 100% of B over 15 min, then kept constant for 5 min, brought back to the initial conditions in 0.5 min, and maintained for 5 min.
Flow Rate:250 µl/min
Injection Temperature:40
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Randomization Order:yes
Chromatography Type:Reversed phase
  
Chromatography ID:CH002707
Chromatography Summary:HILIC column was eluted at a flow rate of 200 µl/min with 90% of mobile phase B (acetonitrile) for 0.1 min followed by a linear gradient to 70% of mobile phase A ( H2O 5 mM ammonium formate, pH 3) over 15 min, then kept constant for 5 min, brought back to the initial conditions in 0.5 min, and maintained for 9 min.
Instrument Name:Thermo Vanquish
Column Name:Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
Flow Gradient:90% of mobile phase B for 0.1 min followed by a linear gradient to 70% of mobile phase A over 15 min, then kept constant for 5 min, brought back to the initial conditions in 0.5 min, and maintained for 9 min.
Flow Rate:200 µl/min
Injection Temperature:25
Solvent A:100% water; 5 mM ammonium formate, pH 3
Solvent B:100% acetonitrile
Randomization Order:yes
Chromatography Type:HILIC
  
Chromatography ID:CH002708
Chromatography Summary:HILIC column was eluted at a flow rate of 200 µl/min with 90% of mobile phase B (acetonitrile) for 0.1 min followed by a linear gradient to 70% of mobile phase A ( H2O 5 mM ammonium formate, pH 3) over 15 min, then kept constant for 5 min, brought back to the initial conditions in 0.5 min, and maintained for 9 min.
Instrument Name:Thermo Vanquish
Column Name:Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
Flow Gradient:90% of mobile phase B for 0.1 min followed by a linear gradient to 70% of mobile phase A over 15 min, then kept constant for 5 min, brought back to the initial conditions in 0.5 min, and maintained for 9 min.
Flow Rate:200 µl/min
Injection Temperature:25
Solvent A:100% water; 5 mM ammonium formate, pH 3
Solvent B:100% acetonitrile
Randomization Order:yes
Chromatography Type:HILIC

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
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