#METABOLOMICS WORKBENCH Gouer_20240814_200121 DATATRACK_ID:5108 STUDY_ID:ST003413 ANALYSIS_ID:AN005607 PROJECT_ID:PR002112 VERSION 1 CREATED_ON August 19, 2024, 3:03 pm #PROJECT PR:PROJECT_TITLE LampreyDB: a spatial metabolomics dataset for lampreys PR:PROJECT_TYPE Database PR:PROJECT_SUMMARY Lampreys are blood-sucking vampires in marine environments. However, the PR:PROJECT_SUMMARY lamprey-specific metabolomics database is still missing. As such, we have PR:PROJECT_SUMMARY established LampreyDB (https://www.lampreydb.com), a tissue-wide spatial lamprey PR:PROJECT_SUMMARY metabolomics database that contains all the identified and annotated metabolites PR:PROJECT_SUMMARY from our experiment. LampreyDB allows users to explore lamprey-specific PR:PROJECT_SUMMARY metabolites with text-based searches, i.e., chemical formula, m/z value, or a PR:PROJECT_SUMMARY list of MS/MS fragments. PR:INSTITUTE Liaoning Normal University PR:DEPARTMENT College of Life Science PR:LABORATORY Lamprey research center PR:LAST_NAME Meng PR:FIRST_NAME Gou PR:ADDRESS No. 850, Huanghe Road, Shahekou District PR:EMAIL gouer602@lnnu.edu.cn PR:PHONE +8613942673656 PR:FUNDING_SOURCE Chinese National Natural Science Foundation Grant PR:PUBLICATIONS Spatial Metabolomics Reveals the Multifaceted Nature of Lamprey Buccal Gland and PR:PUBLICATIONS Its Diverse Mechanisms for Blood-Feeding PR:CONTRIBUTORS Meng Gou , Xuyuan Duan , Jun Li , Yaocen Wang , Qingwei Li , Yue Pang , Yonghui PR:CONTRIBUTORS Dong #STUDY ST:STUDY_TITLE LampreyDB: a spatial metabolomics dataset for lampreys ST:STUDY_SUMMARY Lampreys are blood-sucking vampires in marine environments. However, the ST:STUDY_SUMMARY lamprey-specific metabolomics database is still missing. As such, we have ST:STUDY_SUMMARY established LampreyDB (https://www.lampreydb.com), a tissue-wide spatial lamprey ST:STUDY_SUMMARY metabolomics database that contains all the identified and annotated metabolites ST:STUDY_SUMMARY from our experiment. LampreyDB allows users to explore lamprey-specific ST:STUDY_SUMMARY metabolites with text-based searches, i.e., chemical formula, m/z value, or a ST:STUDY_SUMMARY list of MS/MS fragments. ST:INSTITUTE Liaoning Normal university ST:LAST_NAME Gou ST:FIRST_NAME Meng ST:ADDRESS Liaoning Normal University ST:EMAIL gouer602@lnnu.edu.cn ST:PHONE +8613942673656 #SUBJECT SU:SUBJECT_TYPE Fish SU:SUBJECT_SPECIES Lethenteron camtschaticum SU:TAXONOMY_ID 980415 #FACTORS #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data SUBJECT_SAMPLE_FACTORS - B1 Sample source:Brain | Tissue:Brain RAW_FILE_NAME=B1.mzML SUBJECT_SAMPLE_FACTORS - B2 Sample source:Brain | Tissue:Brain RAW_FILE_NAME=B2.mzML SUBJECT_SAMPLE_FACTORS - B3 Sample source:Brain | Tissue:Brain RAW_FILE_NAME=B3.mzML SUBJECT_SAMPLE_FACTORS - Bu1 Sample source:Buccal | Tissue:Buccal RAW_FILE_NAME=Bu1.mzML SUBJECT_SAMPLE_FACTORS - Bu2 Sample source:Buccal | Tissue:Buccal RAW_FILE_NAME=Bu2.mzML SUBJECT_SAMPLE_FACTORS - Bu3 Sample source:Buccal | Tissue:Buccal RAW_FILE_NAME=Bu3.mzML SUBJECT_SAMPLE_FACTORS - E1 Sample source:Eye | Tissue:Eye RAW_FILE_NAME=E1.mzML SUBJECT_SAMPLE_FACTORS - E2 Sample source:Eye | Tissue:Eye RAW_FILE_NAME=E2.mzML SUBJECT_SAMPLE_FACTORS - E3 Sample source:Eye | Tissue:Eye RAW_FILE_NAME=E3.mzML SUBJECT_SAMPLE_FACTORS - G1 Sample source:Gill | Tissue:Gill RAW_FILE_NAME=G1.mzML SUBJECT_SAMPLE_FACTORS - G2 Sample source:Gill | Tissue:Gill RAW_FILE_NAME=G2.mzML SUBJECT_SAMPLE_FACTORS - G3 Sample source:Gill | Tissue:Gill RAW_FILE_NAME=G3.mzML SUBJECT_SAMPLE_FACTORS - H1 Sample source:Heart | Tissue:Heart RAW_FILE_NAME=H1.mzML SUBJECT_SAMPLE_FACTORS - H2 Sample source:Heart | Tissue:Heart RAW_FILE_NAME=H2.mzML SUBJECT_SAMPLE_FACTORS - H3 Sample source:Heart | Tissue:Heart RAW_FILE_NAME=H3.mzML SUBJECT_SAMPLE_FACTORS - I1 Sample source:Intestine | Tissue:Intestine RAW_FILE_NAME=I1.mzML SUBJECT_SAMPLE_FACTORS - I2 Sample source:Intestine | Tissue:Intestine RAW_FILE_NAME=I2.mzML SUBJECT_SAMPLE_FACTORS - I3 Sample source:Intestine | Tissue:Intestine RAW_FILE_NAME=I3.mzML SUBJECT_SAMPLE_FACTORS - K1 Sample source:Kidney | Tissue:Kidney RAW_FILE_NAME=K1.mzML SUBJECT_SAMPLE_FACTORS - K2 Sample source:Kidney | Tissue:Kidney RAW_FILE_NAME=K2.mzML SUBJECT_SAMPLE_FACTORS - K3 Sample source:Kidney | Tissue:Kidney RAW_FILE_NAME=K3.mzML SUBJECT_SAMPLE_FACTORS - L1 Sample source:Liver | Tissue:Liver RAW_FILE_NAME=L1.mzML SUBJECT_SAMPLE_FACTORS - L2 Sample source:Liver | Tissue:Liver RAW_FILE_NAME=L2.mzML SUBJECT_SAMPLE_FACTORS - L3 Sample source:Liver | Tissue:Liver RAW_FILE_NAME=L3.mzML SUBJECT_SAMPLE_FACTORS - M1 Sample source:Muscle | Tissue:Muscle RAW_FILE_NAME=M1.mzML SUBJECT_SAMPLE_FACTORS - M2 Sample source:Muscle | Tissue:Muscle RAW_FILE_NAME=M2.mzML SUBJECT_SAMPLE_FACTORS - M3 Sample source:Muscle | Tissue:Muscle RAW_FILE_NAME=M3.mzML SUBJECT_SAMPLE_FACTORS - N1 Sample source:Notochord | Tissue:Notochord RAW_FILE_NAME=N1.mzML SUBJECT_SAMPLE_FACTORS - N2 Sample source:Notochord | Tissue:Notochord RAW_FILE_NAME=N2.mzML SUBJECT_SAMPLE_FACTORS - N3 Sample source:Notochord | Tissue:Notochord RAW_FILE_NAME=N3.mzML SUBJECT_SAMPLE_FACTORS - O1 Sample source:Ovary | Tissue:Ovary RAW_FILE_NAME=O1.mzML SUBJECT_SAMPLE_FACTORS - O2 Sample source:Ovary | Tissue:Ovary RAW_FILE_NAME=O2.mzML SUBJECT_SAMPLE_FACTORS - O3 Sample source:Ovary | Tissue:Ovary RAW_FILE_NAME=O3.mzML SUBJECT_SAMPLE_FACTORS - S1 Sample source:Supraneuralbody | Tissue:Supraneuralbody RAW_FILE_NAME=S1.mzML SUBJECT_SAMPLE_FACTORS - S2 Sample source:Supraneuralbody | Tissue:Supraneuralbody RAW_FILE_NAME=S2.mzML SUBJECT_SAMPLE_FACTORS - S3 Sample source:Supraneuralbody | Tissue:Supraneuralbody RAW_FILE_NAME=S3.mzML SUBJECT_SAMPLE_FACTORS - T1 Sample source:Testis | Tissue:Testis RAW_FILE_NAME=T1.mzML SUBJECT_SAMPLE_FACTORS - T2 Sample source:Testis | Tissue:Testis RAW_FILE_NAME=T2.mzML SUBJECT_SAMPLE_FACTORS - T3 Sample source:Testis | Tissue:Testis RAW_FILE_NAME=T3.mzML SUBJECT_SAMPLE_FACTORS - X1 Sample source:Blood | Tissue:Blood RAW_FILE_NAME=X1.mzML SUBJECT_SAMPLE_FACTORS - X2 Sample source:Blood | Tissue:Blood RAW_FILE_NAME=X2.mzML SUBJECT_SAMPLE_FACTORS - X3 Sample source:Blood | Tissue:Blood RAW_FILE_NAME=X3.mzML SUBJECT_SAMPLE_FACTORS - QC1 Sample source:QC | Tissue:QC RAW_FILE_NAME=QC1.mzML SUBJECT_SAMPLE_FACTORS - QC2 Sample source:QC | Tissue:QC RAW_FILE_NAME=QC2.mzML SUBJECT_SAMPLE_FACTORS - QC3 Sample source:QC | Tissue:QC RAW_FILE_NAME=QC3.mzML SUBJECT_SAMPLE_FACTORS - QC4 Sample source:QC | Tissue:QC RAW_FILE_NAME=QC4.mzML SUBJECT_SAMPLE_FACTORS - QC5 Sample source:QC | Tissue:QC RAW_FILE_NAME=QC5.mzML #COLLECTION CO:COLLECTION_SUMMARY The adult Arctic lamprey (Lethenteron camtschaticum) at spawning migration stage CO:COLLECTION_SUMMARY were obtained in December 2020 in Songhua River in Heilongjiang province of CO:COLLECTION_SUMMARY China. Fourteen lamprey tissues, i.e., heart, liver, kidney, brain, supraneural CO:COLLECTION_SUMMARY body, muscle, intestine, gill, eye, testis, ovary, buccal gland, blood, and CO:COLLECTION_SUMMARY notochord, were carefully dissected, and subjected to untargeted metabolomics CO:COLLECTION_SUMMARY using liquid chromatography mass spectrometry (LCMS). CO:SAMPLE_TYPE heart, liver, kidney, brain, supraneural body, muscle, intestine, gill, eye, CO:SAMPLE_TYPE testis, ovary, buccal gland, blood, and notochord #TREATMENT TR:TREATMENT_SUMMARY Fourteen different lamprey tissues, i.e., heart, liver, kidney, brain, TR:TREATMENT_SUMMARY supraneural body, muscle, intestine, gill, eye, testis, ovary, buccal gland, TR:TREATMENT_SUMMARY blood, and notochord, were carefully dissected and washed in sterile phosphate TR:TREATMENT_SUMMARY buffered saline (PBS: 10 mM phosphate buffer, 2.7 mM potassium chloride, TR:TREATMENT_SUMMARY 137 mM sodium chloride, pH 7.4). The secretion of lamprey buccal gland was TR:TREATMENT_SUMMARY collected through a syringe. All the samples were snap frozen in liquid N2 and TR:TREATMENT_SUMMARY stored at −80 °C before LCMS analysis. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY To extract the samples, 30 mg of each sample, 20 μL IS SP:SAMPLEPREP_SUMMARY (L-2-chlorophenylalanine, 0.3 mg/mL) and 400 μL extraction solution (80% SP:SAMPLEPREP_SUMMARY methanol/water, v/v) were added into a 2 mL Eppendorf tube, followed by adding SP:SAMPLEPREP_SUMMARY two small steel balls. After precooling the tube at −20 °C for 2 min, SP:SAMPLEPREP_SUMMARY each sample was ground at 60 Hz for 2 min using a Tissuelyser-48 grinding SP:SAMPLEPREP_SUMMARY miller (Jingxing Limited Company, Shanghai, China). The resulting extract was SP:SAMPLEPREP_SUMMARY briefly vortexed and sonicated at ambient temperature (25–28 °C) for SP:SAMPLEPREP_SUMMARY 10 min. Subsequently, the extracts were centrifuged at 13,000 rpm and SP:SAMPLEPREP_SUMMARY 4 °C for 10 min. Next, 300 μL of the supernatant was transferred into a SP:SAMPLEPREP_SUMMARY brown glass vial and dried using a freeze concentration centrifugal dryer. To SP:SAMPLEPREP_SUMMARY each sample, 300 μL of a methanol and water mixture (1/4, v/v) was added. The SP:SAMPLEPREP_SUMMARY mixture was vortexed for 30 s and then placed at −20 °C for 2 h. SP:SAMPLEPREP_SUMMARY Afterward, the samples were centrifuged at 13,000 rpm and 4 °C for 5 min. SP:SAMPLEPREP_SUMMARY The resulting supernatants (150 μL) from each tube were collected using SP:SAMPLEPREP_SUMMARY crystal syringes, filtered through a 0.22 μm PTFE filter (Acrodisc® CR SP:SAMPLEPREP_SUMMARY 13 mm; PALL), and transferred to LC vials for LCMS analysis. Pooled QC samples SP:SAMPLEPREP_SUMMARY were prepared by combining aliquots of 20 μL from each extracted sample. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Ultimate 3000 CH:COLUMN_NAME ACQUITY UPLC HSS T3 column (1.8 μm, 2.1 × 100 mm) CH:SOLVENT_A 100% water; 0.1% formic acid CH:SOLVENT_B 100% acetonitrile ; 0.1% formic acid CH:FLOW_GRADIENT 5% B over 0–2 min, 5–25% B over 2–4 min, 25–50 B over 4–8 min, CH:FLOW_GRADIENT 50–80% B over 8–10 min, 80–100% B over 10–14 min, the composition CH:FLOW_GRADIENT was held at 100% B for 1 min, then 15–15.1 min, 100% to 5% B, and CH:FLOW_GRADIENT 15.1–18 min holding at 5% B. CH:FLOW_RATE 0.35 mL/min CH:COLUMN_TEMPERATURE 45 °C #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo Q Exactive Plus Orbitrap MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:ION_MODE NEGATIVE MS:MS_COMMENTS The mass range was from m/z 66.7 to 1000.5. The resolution was set at 70,000 for MS:MS_COMMENTS the full MS scans and 35,000 for HCD MS/MS scans. The Collision energy was set MS:MS_COMMENTS at 10, 20 and 40 eV. The mass spectrometer operated as follows: spray voltage, MS:MS_COMMENTS 3800 V (+) and −3000 V (−); sheath gas flow rate, 35 arbitrary units; MS:MS_COMMENTS auxiliary gas flow rate, 8 arbitrary units; capillary temperature, 320 °C. MS:MS_COMMENTS The QCs were injected at regular intervals (every 10 samples) throughout the MS:MS_COMMENTS analytical run to provide a set of data from which repeatability can be MS:MS_COMMENTS assessed.Raw data quality was first checked using R package RawHummus on QC MS:MS_COMMENTS samples in both positive and negative ion modes. Data pre-processing and MS:MS_COMMENTS metabolite identification were performed using three different software tools, MS:MS_COMMENTS i.e., Compound Discoverer (v.3.3, Thermo Scientific), Progenesis QI (v.2.3, MS:MS_COMMENTS Waters), and MS-DIAL (v.4.0). MS:MS_RESULTS_FILE ST003413_AN005607_Results.txt UNITS:da Has m/z:Yes Has RT:Yes RT units:Minutes #END