Summary of Study ST003413

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 PR002112. The data can be accessed directly via it's Project DOI: 10.21228/M8MN9F 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	ST003413
Study Title	LampreyDB: a spatial metabolomics dataset for lampreys
Study Summary	Lampreys are blood-sucking vampires in marine environments. However, the lamprey-specific metabolomics database is still missing. As such, we have established LampreyDB (https://www.lampreydb.com), a tissue-wide spatial lamprey metabolomics database that contains all the identified and annotated metabolites from our experiment. LampreyDB allows users to explore lamprey-specific metabolites with text-based searches, i.e., chemical formula, m/z value, or a list of MS/MS fragments.
Institute	Liaoning Normal university
Last Name	Gou
First Name	Meng
Address	Liaoning Normal University
Email	gouer602@lnnu.edu.cn
Phone	+8613942673656
Submit Date	2024-08-14
Raw Data Available	Yes
Raw Data File Type(s)	mzML, raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2024-08-21
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR002112
Project DOI:	doi: 10.21228/M8MN9F
Project Title:	LampreyDB: a spatial metabolomics dataset for lampreys
Project Type:	Database
Project Summary:	Lampreys are blood-sucking vampires in marine environments. However, the lamprey-specific metabolomics database is still missing. As such, we have established LampreyDB (https://www.lampreydb.com), a tissue-wide spatial lamprey metabolomics database that contains all the identified and annotated metabolites from our experiment. LampreyDB allows users to explore lamprey-specific metabolites with text-based searches, i.e., chemical formula, m/z value, or a list of MS/MS fragments.
Institute:	Liaoning Normal University
Department:	College of Life Science
Laboratory:	Lamprey research center
Last Name:	Meng
First Name:	Gou
Address:	No. 850, Huanghe Road, Shahekou District
Email:	gouer602@lnnu.edu.cn
Phone:	+8613942673656
Funding Source:	Chinese National Natural Science Foundation Grant
Publications:	Spatial Metabolomics Reveals the Multifaceted Nature of Lamprey Buccal Gland and Its Diverse Mechanisms for Blood-Feeding
Contributors:	Meng Gou , Xuyuan Duan , Jun Li , Yaocen Wang , Qingwei Li , Yue Pang , Yonghui Dong

Subject:

Subject ID:	SU003539
Subject Type:	Fish
Subject Species:	Lethenteron camtschaticum
Taxonomy ID:	980415

Factors:

Subject type: Fish; Subject species: Lethenteron camtschaticum (Factor headings shown in green)

mb_sample_id	local_sample_id	Sample source	Tissue
SA376413	X3	Blood	Blood
SA376414	X2	Blood	Blood
SA376415	X1	Blood	Blood
SA376416	B2	Brain	Brain
SA376417	B1	Brain	Brain
SA376418	B3	Brain	Brain
SA376419	Bu1	Buccal	Buccal
SA376420	Bu2	Buccal	Buccal
SA376421	Bu3	Buccal	Buccal
SA376422	E1	Eye	Eye
SA376423	E2	Eye	Eye
SA376424	E3	Eye	Eye
SA376425	G2	Gill	Gill
SA376426	G3	Gill	Gill
SA376427	G1	Gill	Gill
SA376428	H1	Heart	Heart
SA376429	H2	Heart	Heart
SA376430	H3	Heart	Heart
SA376431	I1	Intestine	Intestine
SA376432	I2	Intestine	Intestine
SA376433	I3	Intestine	Intestine
SA376434	K1	Kidney	Kidney
SA376435	K2	Kidney	Kidney
SA376436	K3	Kidney	Kidney
SA376437	L1	Liver	Liver
SA376438	L2	Liver	Liver
SA376439	L3	Liver	Liver
SA376440	M1	Muscle	Muscle
SA376441	M2	Muscle	Muscle
SA376442	M3	Muscle	Muscle
SA376443	N3	Notochord	Notochord
SA376444	N2	Notochord	Notochord
SA376445	N1	Notochord	Notochord
SA376446	O3	Ovary	Ovary
SA376447	O1	Ovary	Ovary
SA376448	O2	Ovary	Ovary
SA376449	QC1	QC	QC
SA376450	QC2	QC	QC
SA376451	QC3	QC	QC
SA376452	QC4	QC	QC
SA376453	QC5	QC	QC
SA376454	S2	Supraneuralbody	Supraneuralbody
SA376455	S3	Supraneuralbody	Supraneuralbody
SA376456	S1	Supraneuralbody	Supraneuralbody
SA376457	T1	Testis	Testis
SA376458	T2	Testis	Testis
SA376459	T3	Testis	Testis

Showing results 1 to 47 of 47

Showing results 1 to 47 of 47

Collection:

Collection ID:	CO003532
Collection Summary:	The adult Arctic lamprey (Lethenteron camtschaticum) at spawning migration stage were obtained in December 2020 in Songhua River in Heilongjiang province of China. Fourteen lamprey tissues, i.e., heart, liver, kidney, brain, supraneural body, muscle, intestine, gill, eye, testis, ovary, buccal gland, blood, and notochord, were carefully dissected, and subjected to untargeted metabolomics using liquid chromatography mass spectrometry (LCMS).
Sample Type:	heart, liver, kidney, brain, supraneural body, muscle, intestine, gill, eye, testis, ovary, buccal gland, blood, and notochord

Treatment:

Treatment ID:	TR003548
Treatment Summary:	Fourteen different lamprey tissues, i.e., heart, liver, kidney, brain, supraneural body, muscle, intestine, gill, eye, testis, ovary, buccal gland, blood, and notochord, were carefully dissected and washed in sterile phosphate buffered saline (PBS: 10 mM phosphate buffer, 2.7 mM potassium chloride, 137 mM sodium chloride, pH 7.4). The secretion of lamprey buccal gland was collected through a syringe. All the samples were snap frozen in liquid N2 and stored at −80 °C before LCMS analysis.

Treatment ID:

TR003548

Treatment Summary:

Fourteen different lamprey tissues, i.e., heart, liver, kidney, brain, supraneural body, muscle, intestine, gill, eye, testis, ovary, buccal gland, blood, and notochord, were carefully dissected and washed in sterile phosphate buffered saline (PBS: 10 mM phosphate buffer, 2.7 mM potassium chloride, 137 mM sodium chloride, pH 7.4). The secretion of lamprey buccal gland was collected through a syringe. All the samples were snap frozen in liquid N2 and stored at −80 °C before LCMS analysis.

Sample Preparation:

Sampleprep ID:	SP003546
Sampleprep Summary:	To extract the samples, 30 mg of each sample, 20 μL IS (L-2-chlorophenylalanine, 0.3 mg/mL) and 400 μL extraction solution (80% methanol/water, v/v) were added into a 2 mL Eppendorf tube, followed by adding two small steel balls. After precooling the tube at −20 °C for 2 min, each sample was ground at 60 Hz for 2 min using a Tissuelyser-48 grinding miller (Jingxing Limited Company, Shanghai, China). The resulting extract was briefly vortexed and sonicated at ambient temperature (25–28 °C) for 10 min. Subsequently, the extracts were centrifuged at 13,000 rpm and 4 °C for 10 min. Next, 300 μL of the supernatant was transferred into a brown glass vial and dried using a freeze concentration centrifugal dryer. To each sample, 300 μL of a methanol and water mixture (1/4, v/v) was added. The mixture was vortexed for 30 s and then placed at −20 °C for 2 h. Afterward, the samples were centrifuged at 13,000 rpm and 4 °C for 5 min. The resulting supernatants (150 μL) from each tube were collected using crystal syringes, filtered through a 0.22 μm PTFE filter (Acrodisc® CR 13 mm; PALL), and transferred to LC vials for LCMS analysis. Pooled QC samples were prepared by combining aliquots of 20 μL from each extracted sample.

Sampleprep ID:

SP003546

Sampleprep Summary:

To extract the samples, 30 mg of each sample, 20 μL IS (L-2-chlorophenylalanine, 0.3 mg/mL) and 400 μL extraction solution (80% methanol/water, v/v) were added into a 2 mL Eppendorf tube, followed by adding two small steel balls. After precooling the tube at −20 °C for 2 min, each sample was ground at 60 Hz for 2 min using a Tissuelyser-48 grinding miller (Jingxing Limited Company, Shanghai, China). The resulting extract was briefly vortexed and sonicated at ambient temperature (25–28 °C) for 10 min. Subsequently, the extracts were centrifuged at 13,000 rpm and 4 °C for 10 min. Next, 300 μL of the supernatant was transferred into a brown glass vial and dried using a freeze concentration centrifugal dryer. To each sample, 300 μL of a methanol and water mixture (1/4, v/v) was added. The mixture was vortexed for 30 s and then placed at −20 °C for 2 h. Afterward, the samples were centrifuged at 13,000 rpm and 4 °C for 5 min. The resulting supernatants (150 μL) from each tube were collected using crystal syringes, filtered through a 0.22 μm PTFE filter (Acrodisc® CR 13 mm; PALL), and transferred to LC vials for LCMS analysis. Pooled QC samples were prepared by combining aliquots of 20 μL from each extracted sample.

Combined analysis:

Analysis ID	AN005606	AN005607
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Ultimate 3000	Ultimate 3000
Column	ACQUITY UPLC HSS T3 column (1.8 μm, 2.1 × 100 mm)	ACQUITY UPLC HSS T3 column (1.8 μm, 2.1 × 100 mm)
MS Type	ESI	ESI
MS instrument type	Orbitrap	Orbitrap
MS instrument name	Thermo Q Exactive Plus Orbitrap	Thermo Q Exactive Plus Orbitrap
Ion Mode	POSITIVE	NEGATIVE
Units	da	da

Chromatography:

Chromatography ID:	CH004259
Instrument Name:	Ultimate 3000
Column Name:	ACQUITY UPLC HSS T3 column (1.8 μm, 2.1 × 100 mm)
Column Temperature:	45 °C
Flow Gradient:	5% B over 0–2 min, 5–25% B over 2–4 min, 25–50 B over 4–8 min, 50–80% B over 8–10 min, 80–100% B over 10–14 min, the composition was held at 100% B for 1 min, then 15–15.1 min, 100% to 5% B, and 15.1–18 min holding at 5% B.
Flow Rate:	0.35 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:	MS005331
Analysis ID:	AN005606
Instrument Name:	Thermo Q Exactive Plus Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	The mass range was from m/z 66.7 to 1000.5. The resolution was set at 70,000 for the full MS scans and 35,000 for HCD MS/MS scans. The Collision energy was set at 10, 20 and 40 eV. The mass spectrometer operated as follows: spray voltage, 3800 V (+) and −3000 V (−); sheath gas flow rate, 35 arbitrary units; auxiliary gas flow rate, 8 arbitrary units; capillary temperature, 320 °C. The QCs were injected at regular intervals (every 10 samples) throughout the analytical run to provide a set of data from which repeatability can be assessed.Raw data quality was first checked using R package RawHummus on QC samples in both positive and negative ion modes. Data pre-processing and metabolite identification were performed using three different software tools, i.e., Compound Discoverer (v.3.3, Thermo Scientific), Progenesis QI (v.2.3, Waters), and MS-DIAL (v.4.0).
Ion Mode:	POSITIVE

MS ID:	MS005332
Analysis ID:	AN005607
Instrument Name:	Thermo Q Exactive Plus Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	The mass range was from m/z 66.7 to 1000.5. The resolution was set at 70,000 for the full MS scans and 35,000 for HCD MS/MS scans. The Collision energy was set at 10, 20 and 40 eV. The mass spectrometer operated as follows: spray voltage, 3800 V (+) and −3000 V (−); sheath gas flow rate, 35 arbitrary units; auxiliary gas flow rate, 8 arbitrary units; capillary temperature, 320 °C. The QCs were injected at regular intervals (every 10 samples) throughout the analytical run to provide a set of data from which repeatability can be assessed.Raw data quality was first checked using R package RawHummus on QC samples in both positive and negative ion modes. Data pre-processing and metabolite identification were performed using three different software tools, i.e., Compound Discoverer (v.3.3, Thermo Scientific), Progenesis QI (v.2.3, Waters), and MS-DIAL (v.4.0).
Ion Mode:	NEGATIVE