Summary of Study ST003594

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 PR002222. The data can be accessed directly via it's Project DOI: 10.21228/M8DF9H This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study ID	ST003594
Study Title	Metabolomics of Drosophila melanogaster with a-Synuclein expression (body)
Study Type	untargeted metabolomics
Study Summary	High-coverage LC-HRMS metabolomics were applied to profiling αSyn-expressing flies vs. wild-type flies. Fly heads and bodies were extracted and analyzed using liquid chromatography–quadrupole-orbitrap mass spectrometry, following informatics approaches for compound identification and pathway analysis. The uploaded is the untargeted metabolomics component which contains raw data, alignment tables, and associated method details. This study provides comparative data for fly body.
Institute	Columbia University
Department	Department of Environmental Health Sciences
Last Name	Lai
First Name	Yunjia
Address	630 West 168th Street, P&S 16-421, New York, NY 10032
Email	yunjia.lai@outlook.com
Phone	9194805489
Submit Date	2024-11-24
Num Groups	2
Total Subjects	100; five samples per group; 10 subjects per sample
Num Males	100; five samples per group; 10 subjects per sample
Raw Data Available	Yes
Raw Data File Type(s)	mzXML
Analysis Type Detail	LC-MS
Release Date	2026-01-02
Release Version	1

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Project:

Project ID:	PR002222
Project DOI:	doi: 10.21228/M8DF9H
Project Title:	Comparative metabolomics of a-Synuclein expression in Drosophila melanogaster
Project Type:	untargeted metabolomics
Project Summary:	Drosophila melanogaster, or the fruit fly, is a great model system for motor disorders such as Parkinson’s disease (PD). However, Drosophila does not express in vivo the α-Synuclein (αSyn) protein, the chief molecular hallmark of PD. Therefore, αSyn-expression in Drosophila and profiling the associated metabolomic changes are crucial in elucidating molecular mechanism of PD using Drosophila models. Using comparative global metabolomics and integrated cheminformatics for high coverage, this study aims to provide fundamental metabolomics data specific to αSyn expression in Drosophila melanogaster. Fly heads and body compartments were analyzed separately, with an interest to probe the gut-brain axis potentially involved.
Institute:	Columbia University
Department:	Department of Environmental Health Sciences
Laboratory:	The Miller Lab
Last Name:	Lai
First Name:	Yunjia
Address:	630 West 168th Street, P&S 16-421, New York, NY 10032
Email:	yunjia.lai@outlook.com
Phone:	9194805489
Funding Source:	National Institutes of Health

Subject:

Subject ID:	SU003723
Subject Type:	Insect
Subject Species:	Drosophila melanogaster
Taxonomy ID:	7227
Genotype Strain:	alpha-synuclein; wild-type
Age Or Age Range:	adult
Gender:	Male
Species Group:	Insects

Factors:

Subject type: Insect; Subject species: Drosophila melanogaster (Factor headings shown in green)

mb_sample_id	local_sample_id	Genotype
SA391869	body_Pos_xSB2	aSyn expression, red eye
SA391870	body_Pos_xSB1	aSyn expression, red eye
SA391871	body_Pos_xSB5	aSyn expression, red eye
SA391872	body_Pos_xSB4	aSyn expression, red eye
SA391873	body_Neg_xSB1	aSyn expression, red eye
SA391874	body_Neg_xSB2	aSyn expression, red eye
SA391875	body_Neg_xSB3	aSyn expression, red eye
SA391876	body_Neg_xSB4	aSyn expression, red eye
SA391877	body_Neg_xSB5	aSyn expression, red eye
SA391878	body_Pos_xSB3	aSyn expression, red eye
SA391879	body_Pos_bQCinj2	n/a
SA391880	body_Pos_bQCinj3	n/a
SA391881	body_Pos_bQCinj1	n/a
SA391882	body_Neg_bQCinj1	n/a
SA391883	body_Neg_bQCinj2	n/a
SA391884	body_Neg_bQCinj3	n/a
SA391859	body_Pos_xCB2	Wild-type, red eye
SA391860	body_Neg_xCB5	Wild-type, red eye
SA391861	body_Neg_xCB4	Wild-type, red eye
SA391862	body_Neg_xCB3	Wild-type, red eye
SA391863	body_Neg_xCB2	Wild-type, red eye
SA391864	body_Pos_xCB1	Wild-type, red eye
SA391865	body_Neg_xCB1	Wild-type, red eye
SA391866	body_Pos_xCB5	Wild-type, red eye
SA391867	body_Pos_xCB4	Wild-type, red eye
SA391868	body_Pos_xCB3	Wild-type, red eye

Showing results 1 to 26 of 26

Showing results 1 to 26 of 26

Collection:

Collection ID:	CO003716
Collection Summary:	age-matched adult fruit fly with heads and bodies separated for comparative metabolomics of alpha-synuclein vs. wild-type control
Sample Type:	fly body

Treatment:

Treatment ID:	TR003732
Treatment Summary:	This is a baseline profiling for genotypes αSyn-expression vs. wild-type in Drosophila melanogaster. No treatment was involved.

Sample Preparation:

Sampleprep ID:	SP003730
Sampleprep Summary:	Age-matched adult flies were used, with each genotypic group containing five sample replicates, and each replicate sample ten heads/bodies. To extract metabolites, thawed heads and bodies were added with ice-cold methanol:H2O (2:1, v/v) solution pre-spiked with isotope-labeled internal standards alongside zirconium oxide beads (0.5 mm i.d., Yittria stabilized) (Next Advance, Troy, NY). Samples were touch vortexed for 30 sec, manually ground using sterile, disposable pestles (DWK Life Sciences, Millville, NJ), placed on a bead beater (Next Advance, Troy, NY) in a cold room for 5 mins at the maximum speed, and finally centrifuged at 18,000 × g for 10 mins. The supernatant was SpeedVac-dried and reconstituted into acetonitrile:H2O (2:98, v/v) upon instrumental analysis.

Sampleprep ID:

SP003730

Sampleprep Summary:

Age-matched adult flies were used, with each genotypic group containing five sample replicates, and each replicate sample ten heads/bodies. To extract metabolites, thawed heads and bodies were added with ice-cold methanol:H2O (2:1, v/v) solution pre-spiked with isotope-labeled internal standards alongside zirconium oxide beads (0.5 mm i.d., Yittria stabilized) (Next Advance, Troy, NY). Samples were touch vortexed for 30 sec, manually ground using sterile, disposable pestles (DWK Life Sciences, Millville, NJ), placed on a bead beater (Next Advance, Troy, NY) in a cold room for 5 mins at the maximum speed, and finally centrifuged at 18,000 × g for 10 mins. The supernatant was SpeedVac-dried and reconstituted into acetonitrile:H2O (2:98, v/v) upon instrumental analysis.

Combined analysis:

Analysis ID	AN005901	AN005902
Chromatography ID	CH004481	CH004481
MS ID	MS005619	MS005620
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Thermo Vanquish	Thermo Vanquish
Column	Waters ACQUITY UPLC HSS C18 (100 x 2.1mm,1.8um)	Waters ACQUITY UPLC HSS C18 (100 x 2.1mm,1.8um)
MS Type	ESI	ESI
MS instrument type	Orbitrap	Orbitrap
MS instrument name	Thermo Orbitrap IQ-X Tribrid	Thermo Orbitrap IQ-X Tribrid
Ion Mode	POSITIVE	NEGATIVE
Units	Peak intensity (area)	Peak intensity (area)

Chromatography:

Chromatography ID:	CH004481
Instrument Name:	Thermo Vanquish
Column Name:	Waters ACQUITY UPLC HSS C18 (100 x 2.1mm,1.8um)
Column Temperature:	40°C
Flow Gradient:	a 15-min gradient: 2% B, 0–1 min; 2 to 15% B, 1–3 min; 15 to 50% B, 3–6 min; 50 to 98% B, 6–7.5 min; 98% B, 7.5–11.5 min; 98 to 2% B, 11.5–11.6 min; 2% B, 11.6–15 min.
Flow Rate:	0.4 mL/min
Solvent A:	100% Water; 0.1% formic acid
Solvent B:	100% Acetonitrile; 0.1% formic acid
Chromatography Type:	Reversed phase

MS:

MS ID:	MS005619
Analysis ID:	AN005901
Instrument Name:	Thermo Orbitrap IQ-X Tribrid
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Data in both heated ESI positive and negative modes were acquired. Quality assurance and quality control (QA/QC) procedures were implemented, spanning timely mass calibration, sample blindfolding, sample randomization, and internal standard-based monitoring.MS1 .raw data were converted to .abf, and processed in MS-DIAL 4.90 (Riken, Japan) to obtain peak alignment tables separately for the head (ESI+), head (ESI-), body (ESI+), and body (ESI-) modes of analysis; detailed settings for data processing can be found in the SI Appendix. Welch's t-test and one-way ANOVA were performed on each of the four datasets to screen for ion features of statistical significance; retrospectively, tandem MS/MS mass spectra were collected for these features correspondingly using pooled samples, separately for fly heads and bodies.
Ion Mode:	POSITIVE

MS ID:	MS005620
Analysis ID:	AN005902
Instrument Name:	Thermo Orbitrap IQ-X Tribrid
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Data in both heated ESI positive and negative modes were acquired. Quality assurance and quality control (QA/QC) procedures were implemented, spanning timely mass calibration, sample blindfolding, sample randomization, and internal standard-based monitoring.MS1 .raw data were converted to .abf, and processed in MS-DIAL 4.90 (Riken, Japan) to obtain peak alignment tables separately for the head (ESI+), head (ESI-), body (ESI+), and body (ESI-) modes of analysis; detailed settings for data processing can be found in the SI Appendix. Welch's t-test and one-way ANOVA were performed on each of the four datasets to screen for ion features of statistical significance; retrospectively, tandem MS/MS mass spectra were collected for these features correspondingly using pooled samples, separately for fly heads and bodies.
Ion Mode:	NEGATIVE