ONTOLOGY SOURCE REFERENCE Term Source Name CHMO EFO NCIT OBI Term Source File http://purl.obolibrary.org/obo/chmo.owl http://www.ebi.ac.uk/efo/efo.owl http://purl.obolibrary.org/obo/ncit.owl http://purl.obolibrary.org/obo/obi.owl Term Source Version Term Source Description Chemical Methods Ontology Experimental Factor Ontology MetaboLights Controlled Vocabulary National Cancer Institute Thesaurus Ontology for Biomedical Investigations INVESTIGATION Investigation Identifier Investigation Title Investigation Description Investigation Submission Date Investigation Public Release Date INVESTIGATION PUBLICATIONS Investigation PubMed ID Investigation Publication DOI Investigation Publication Author List Investigation Publication Title Investigation Publication Status Investigation Publication Status Term Accession Number Investigation Publication Status Term Source REF INVESTIGATION CONTACTS Investigation Person Last Name Investigation Person First Name Investigation Person Mid Initials Investigation Person Email Investigation Person Phone Investigation Person Fax Investigation Person Address Investigation Person Affiliation Investigation Person Roles Investigation Person Roles Term Accession Number Investigation Person Roles Term Source REF STUDY Study Identifier MTBLS Study Title Please update the study title Study Description Please update the study abstract/description Study Submission Date Study Public Release Date Study File Name s_Sample.txt Comment[Created At] Comment[License] CC0 1.0 Universal Comment[Sample Template] minimum Comment[Study Template] minimum Comment[Study Category] other Comment[Template Version] 1.0 Comment[Funder] Comment[Funder ROR ID] Comment[Grant Identifier] Comment[Related Data Repository] Comment[Related Data Accession] STUDY DESIGN DESCRIPTORS Study Design Type metabolon ultra-performance liquid chromatography-mass spectrometry untargeted metabolite profiling targeted metabolite profiling Study Design Type Term Accession Number http://purl.obolibrary.org/obo/CHMO_0000715 http://purl.obolibrary.org/obo/MSIO_0000101 http://purl.obolibrary.org/obo/MSIO_0000100 Study Design Type Term Source REF CHMO MSIO MSIO Comment[Study Design Category] Comment[Study Design Source] STUDY PUBLICATIONS Study PubMed ID Study Publication DOI Study Publication Author List Study Publication Title Insert title here - Title should be identical to study title Study Publication Status Study Publication Status Term Accession Number Study Publication Status Term Source REF STUDY FACTORS Study Factor Name Study Factor Type Study Factor Type Term Accession Number Study Factor Type Term Source REF Comment[Study Factor Value Format] Comment[Study Factor Unit] Comment[Study Factor Unit Term Accession Number] Comment[Study Factor Unit Term Source REF] STUDY ASSAYS Study Assay File Name a_MTBLS310_Method1_POS_1_metabolite_profiling_mass_spectrometry Study Assay Measurement Type metabolite profiling assay metabolite profiling assay metabolite profiling assay metabolite profiling assay Study Assay Measurement Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0000366 http://purl.obolibrary.org/obo/OBI_0000366 http://purl.obolibrary.org/obo/OBI_0000366 http://purl.obolibrary.org/obo/OBI_0000366 Study Assay Measurement Type Term Source REF OBI OBI OBI OBI Study Assay Technology Type mass spectrometry assay mass spectrometry assay mass spectrometry assay mass spectrometry assay Study Assay Technology Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0000470 http://purl.obolibrary.org/obo/OBI_0000470 http://purl.obolibrary.org/obo/OBI_0000470 http://purl.obolibrary.org/obo/OBI_0000470 Study Assay Technology Type Term Source REF OBI OBI OBI OBI Study Assay Technology Platform Q Exactive Q Exactive Q Exactive Q Exactive Comment[Assay Identifier] Comment[Assay Result File Format] Comment[Assay Type Label] Comment[Assay Type] Comment[Assay Type Term Source REF] Comment[Assay Type Term Accession Number] Comment[Omics Type] Comment[Omics Type Term Source REF] Comment[Omics Type Term Accession Number] Comment[Assay Descriptor] Comment[Assay Descriptor Term Source REF] Comment[Assay Descriptor Term Accession Number] Comment[Assay Descriptor Category] Comment[Assay Descriptor Source] Comment[Assay Field Name] Comment[Assay Field Default Value] Comment[Assay Field Default Unit] Comment[Assay Field Default Value Source REF] Comment[Assay Field Default Value Accession Number] STUDY PROTOCOLS Study Protocol Name Sample collection Extraction Chromatography Mass spectrometry Data transformation Metabolite identification Study Protocol Type sample collection protocol Extraction Chromatography Mass spectrometry Data transformation Metabolite identification Study Protocol Type Term Accession Number http://www.ebi.ac.uk/efo/EFO_0005518 Study Protocol Type Term Source REF EFO Study Protocol Description Client to add information here Samples are prepared using the automated MicroLab STAR® system from Hamilton Company. Several recovery standards are added prior to the first step in the extraction process for QC purposes. Samples are extracted with methanol under vigorous shaking for 2 min (Glen Mills GenoGrinder 2000) to precipitate protein and dissociate small molecules bound to protein or trapped in the precipitated protein matrix, followed by centrifugation to recover chemically diverse metabolites. The resulting extract is divided into five fractions: two for analysis by two separate reverse phase (RP)/UPLC-MS/MS methods using positive ion mode electrospray ionization (ESI), one for analysis by RP/UPLC-MS/MS using negative ion mode ESI, one for analysis by HILIC/UPLC-MS/MS using negative ion mode ESI, and one reserved for backup. Samples are placed briefly on a TurboVap® (Zymark) to remove the organic solvent and stored overnight under nitrogen. In preparation for analysis, samples are then reconstituted in solvents compatible to each of the four methods. All methods utilize a Waters ACQUITY ultra-performance liquid chromatography (UPLC). Each reconstitution solvent contains a series of standards at fixed concentrations to ensure injection and chromatographic consistency. Method 1/Pos 1: One aliquot is analyzed using acidic positive ion conditions, chromatographically optimized for more hydrophilic compounds. In this method, the extract is gradient-eluted from a C18 column (Waters UPLC BEH C18-2.1x100 mm, 1.7 um) using water and methanol, containing 0.05% perfluoropentanoic acid (PFPA) and 0.1% formic acid (FA). Method 2/Pos 2: A second aliquot is also analyzed using acidic positive ion conditions, but is chromatographically optimized for more hydrophobic compounds. In this method, the extract is gradient eluted from the aforementioned C18 column using methanol, acetonitrile, water, 0.05% PFPA and 0.01% FA, and is operated at an overall higher organic content. Method 3/Neg 1: A third aliquot is analyzed using basic negative ion optimized conditions using a separate dedicated C18 column. The basic extracts are gradient-eluted from the column using methanol and water, however with 6.5 mM Ammonium Bicarbonate at pH 8. Method 4/Neg 2: The fourth aliquot is analyzed via negative ionization following elution from a HILIC column (Waters UPLC BEH Amide 2.1x150 mm, 1.7 um) using a gradient consisting of water and acetonitrile with 10 mM Ammonium Formate, pH 10.8. A Thermo Scientific Q-Exactive high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution was used. The MS analysis alternates between MS and data-dependent MSn scans using dynamic exclusion. Raw data were extracted, peak-identified, and QC processed using Metabolon's hardware and software. These systems are built on a web-service platform utilizing Microsoft's .NET technologies, which run on high-performance application servers and fiber-channel storage arrays in clusters to provide active failover and load-balancing. Compounds were identified by comparison to library entries of purified standards or recurrent unknown entities. Metabolon maintains a library based on authenticated standards that contains the retention time/index (RI), mass to charge ratio (m/z), and chromatographic data (including MS/MS spectral data) on all molecules present in the library. More than 4500 commercially available purified standard compounds have been acquired and registered into LIMS for analysis on all platforms for determination of their analytical characteristics. Additional mass spectral entries have been created for structurally unnamed biochemicals, which have been identified by virtue of their recurrent nature (both chromatographic and mass spectral). These compounds have the potential to be identified by future acquisition of a matching purified standard or by classical structural analysis. Study Protocol URI Study Protocol Version Study Protocol Parameters Name Post Extraction;Derivatization Chromatography Instrument;Column type;Column model Instrument software;Detector mode;Spectrum representation;Inlet type;Number of scans;Scan m/z range;Detector;Instrument serial number;Raw data file checksum type;Mass analyzer;Instrument manufacturer;Raw data file format;Scan polarity;Raw data file checksum value;Instrument software version;Native spectrum identifier format;Instrument;Data file content;Time range;Ion source;Data file checksum type Data Transformation software;Data Transformation software version Study Protocol Parameters Name Term Accession Number ; ;; ;;;;;;;;;;;;;;;;;;;; ; Study Protocol Parameters Name Term Source REF ; ;; ;;;;;;;;;;;;;;;;;;;; ; Study Protocol Components Name Study Protocol Components Type Study Protocol Components Type Term Accession Number Study Protocol Components Type Term Source REF Comment[Study Protocol Parameters Value Format] ; ;; ;;;;;;;;;;;;;;;;;;;; ; STUDY CONTACTS Study Person Last Name Study Person First Name Study Person Mid Initials Study Person Email Study Person Phone Study Person Fax Study Person Address Study Person Affiliation Study Person Roles Study Person Roles Term Accession Number Study Person Roles Term Source REF Comment[Study Person ORCID] Comment[Study Person Additional Email] Comment[Study Person Affiliation ROR ID]