{ "METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001028","ANALYSIS_ID":"AN001686","VERSION":"1","CREATED_ON":"July 30, 2018, 3:43 pm"}, "PROJECT":{"PROJECT_TITLE":"Trace: Machine Learning of Signal Images for Trace-Sensitive Mass Spectrometry – A Case Study from Single-Cell Metabolomics","PROJECT_TYPE":"Study from Single-Cell Metabolomics","PROJECT_SUMMARY":"The goal of this study was to validate the performance of a custom-written software tool, called Trace, for finding molecular features from ultrasensitive metabolomics experiments using high-resolution mass spectrometry. The software uses a trained neural network model to extract molecular features. As model for validation, we performed MS profiling of single identified cells from early developing embryos of the South African clawed frog (Xenopus laevis) using a custom-built capillary electrophoresis electrospray ionization platform coupled to a quadrupole time-of-flight mass spectrometer. The MS dataset from these measurements was manually curated for molecular features, and the resulting list of molecular features were used to test the robustness and accuracy of Trace at predicting molecular features that were detected from the single cells.","INSTITUTE":"University of Maryland","DEPARTMENT":"Department of Chemistry & Biochemistry","LABORATORY":"Nemes Laboratory","LAST_NAME":"Nemes","FIRST_NAME":"Peter","ADDRESS":"0107 Chemistry Building, 8051 Regents Dr, College Park, MD 20742","EMAIL":"nemes@umd.edu","PHONE":"301-405-0373","FUNDING_SOURCE":"National Cancer Institute award no. 7R03CA211635","PUBLICATIONS":"Trace: Machine Learning of Signal Images for Trace-Sensitive Mass Spectrometry – A Case Study from Single-Cell Metabolomics"}, "STUDY":{"STUDY_TITLE":"Metabolic profiling of identified single cells in Xenopus laevis embryos","STUDY_TYPE":"Metabolic profiling of single cells","STUDY_SUMMARY":"Single D11 cells were identified in 16-cell embryos of Xenopus laevis. Metabolites were extracted, and the extracts were analyzed using a custom-built capillary electrophoresis electrospray ionization platform coupled to a quadrupole time-of-flight mass spectrometer. The resulting metadata was analyzed by Trace, a custom-design software, designed to extract molecular feautres from trace-sensitive metabolomics experiments. The results were validated against molecular features that were extracted by manual curation of the same raw mass spectrometer files.","INSTITUTE":"University of Maryland","DEPARTMENT":"Department of Chemistry & Biochemistry","LABORATORY":"Nemes Laboratory","LAST_NAME":"Nemes","FIRST_NAME":"Peter","ADDRESS":"0107 Chemistry Building, 8051 Regents Dr, College Park, MD 20742","EMAIL":"nemes@umd.edu","PHONE":"3014050373","NUM_GROUPS":"5 biological replicates (different cells from different embryos) + 1-to-3 technical replicates (same extract analyzed multiple times)","TOTAL_SUBJECTS":"5 different D11 cells were analyzed, each from a different embryo","PUBLICATIONS":"Trace: Machine Learning of Signal Images for Trace-Sensitive Mass Spectrometry – A Case Study from Single-Cell Metabolomics"}, "SUBJECT":{"SUBJECT_TYPE":"Other","SUBJECT_SPECIES":"Xenopus laevis","TAXONOMY_ID":"8355","AGE_OR_AGE_RANGE":"Embryos were obtained from natural mating of frogs (Nasco)","WEIGHT_OR_WEIGHT_RANGE":"Sexually mature male and female frogs","GENDER":"Not applicable"}, "SUBJECT_SAMPLE_FACTORS":[ { "Subject ID":"2016-03-15_EP03 D11 cell-E2-2", "Sample ID":"D11cellE2T2", "Factors":{"Embryo Type":"WT"} }, { "Subject ID":"2016-03-15_EP03 D11 cell-E2-1", "Sample ID":"D11cellE2T1", "Factors":{"Embryo Type":"WT"} }, { "Subject ID":"2016-03-14_EP04 D11 cell-E1-1", "Sample ID":"D11cellE4T1", "Factors":{"Embryo Type":"WT"} }, { "Subject ID":"2016-02-17_RM02 v23 D11", "Sample ID":"D11cellE1T1", "Factors":{"Embryo Type":"WT"} }, { "Subject ID":"2016-06-01_EP05 u-cap E3-D11-1", "Sample ID":"D11cellE3T1", "Factors":{"Embryo Type":"WT"} }, { "Subject ID":"2016-06-01_EP09 u-cap E3-D11-2", "Sample ID":"D11cellE3T2", "Factors":{"Embryo Type":"WT"} }, { "Subject ID":"2016-06-01_EP11 u-cap E3-D11-3", "Sample ID":"D11cellE3T3", "Factors":{"Embryo Type":"WT"} }, { "Subject ID":"2016-06-02_EP04 u-cap E1-D11-1", "Sample ID":"D11cellE5T1", "Factors":{"Embryo Type":"WT"} } ], "COLLECTION":{"COLLECTION_SUMMARY":"Cells were identified based on morphology, pigmentation, and location in the embryo in comparision to established cell-fate maps for 16-cell Xenopus laevis embryos. A portion of the identified D11 cell was microaspirated using a fabricated microcapillary.","COLLECTION_PROTOCOL_ID":"Liu 2018 Metabolomics Workbench Protocol.pdf","SAMPLE_TYPE":"Embryonic cells","COLLECTION_METHOD":"Microaspiration of cell content","COLLECTION_FREQUENCY":"1 collection per cell","COLLECTION_DURATION":"5 s for aspiration","VOLUMEORAMOUNT_COLLECTED":"Ca. 10 nL per aspiration","STORAGE_CONDITIONS":"-80℃","COLLECTION_TUBE_TEMP":"chilled on ice"}, "TREATMENT":{"TREATMENT_SUMMARY":"All protocols related to the handling and manipulation of animals were approved by the Institutional Animal Care and Use Committee (IACUC) of the George Washington University (Washington, DC) and the University of Maryland, College Park (College Park, MD).","TREATMENT_PROTOCOL_ID":"IACUC #A311 (George Washington University) and IACUC #R-DEC-17-57 (University of Maryland, College Park)","TREATMENT_PROTOCOL_FILENAME":"Liu 2018 Metabolomics Workbench Protocol.pdf","TREATMENT_PROTOCOL_COMMENTS":"Embryos were dejellied using 2% cystine solution, cultured in 100% Steinberg's solution (media), and used without further treatment."}, "SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Ca. 10 nL of cell content were aspirated from identified cells. The aspirated material was ejected into ~4 uL of aqueous mixture of 40% acetonitrile and 40% methanol to extract metabolites.","SAMPLEPREP_PROTOCOL_ID":"Cold aqueous acetonitrile-methanold extraction","SAMPLEPREP_PROTOCOL_FILENAME":"Liu 2018 Metabolomics Workbench Protocol.pdf","PROCESSING_STORAGE_CONDITIONS":"On ice","EXTRACTION_METHOD":"In cold aqueous mixture of 40% acetonitrile and 40% methanol.","EXTRACT_STORAGE":"-80℃","SAMPLE_RESUSPENSION":"None. The cells were stored in the extraction solution. The extract was not dried or processed further.","SUBCELLULAR_LOCATION":"Unknown"}, "CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"CE","INSTRUMENT_NAME":"Custom built CE system","COLUMN_NAME":"Bare fused silica capillary"}, "ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"Nemes Laboratory","OPERATOR_NAME":"Erika Portero","SOFTWARE_VERSION":"Compass ver. 4.3","ACQUISITION_DATE":"2016 Feb-to-June","DATA_FORMAT":".d (Bruker)"}, "MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Bruker Impact HD","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"POSITIVE","ACQUISITION_DATE":"2016 Feb-to-June","CAPILLARY_TEMPERATURE":"Ca. 100 degC","CAPILLARY_VOLTAGE":"-1700 V","DRY_GAS_FLOW":"2 L/min","DRY_GAS_TEMP":"100 degC","ION_SOURCE_TEMPERATURE":"100 degC","MASS_ACCURACY":"<10 ppm","RESOLUTION_SETTING":"~45000 FWHM","SCANNING_CYCLE":"2 Hz spectral","SCANNING_RANGE":"m/z 50-550","MS_RESULTS_FILE":"ST001028_AN001686_Results.txt UNITS:PeakAreaInCounts"} }