ONTOLOGY SOURCE REFERENCE
Term Source Name	"BTO"	"BAO"	"OBI"	"MS"	"NCIT"	"NCBITAXON"	"CHMO"	"CHEBI"	
Term Source File	"http://data.bioontology.org/ontologies/BTO"	"http://data.bioontology.org/ontologies/BAO"	"http://data.bioontology.org/ontologies/OBI"	"http://data.bioontology.org/ontologies/MS"	"http://data.bioontology.org/ontologies/NCIT"	"http://data.bioontology.org/ontologies/NCBITAXON"	"http://data.bioontology.org/ontologies/CHMO"	"http://data.bioontology.org/ontologies/CHEBI"	
Term Source Version	"26"	"25"	"25"	"103"	"40"	"4"	"16"	"93"	
Term Source Description	"BRENDA Tissue and Enzyme Source Ontology"	"BioAssay Ontology"	"Ontology for Biomedical Investigations"	"Mass Spectrometry Ontology"	"National Cancer Institute Thesaurus"	"National Center for Biotechnology Information (NCBI) Organismal Classification"	"Chemical Methods Ontology"	"Chemical Entities of Biological Interest Ontology"	
INVESTIGATION
Investigation Identifier	"MTBLS6"
Investigation Title	"Investigation"
Investigation Description	""
Investigation Submission Date	""
Investigation Public Release Date	""
Comment[Created With Configuration]	"/Users/rms72/Configurations/isaconfig-201229_live"
Comment[Last Opened With Configuration]	"MetaboLightsConfig20150707"
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	"MTBLS6"
Study Title	"Development and validation of the PyMS Mass Spectrometry software"
Study Description	"To provide useful data for development and validation of the PyMS Mass Spectrometry software, a test dataset was run at Metabolomics Australia. A biologically complex mix of a biological background material (foetal calf serum), spiked with 2-fold increasing amounts of a mix of metabolite standards. In addition, a single sample consisting of a simple mix of 45 metabolites representing a variety of chemical classes (sufars, organic acids, amino acids, sugar phosphates), was run through a standard Metabolomics Australia GC-MS analysis. The resulting data is a valuable tool in testing GC-MS data analysis software."
Study Submission Date	"2012-03-29"
Study Public Release Date	"2012-03-29"
Study File Name	"s_live10_mtbl.txt"
STUDY DESIGN DESCRIPTORS
Study Design Type	"PyMS"	"gas chromatography-mass spectrometry"	"data processing software"	"Validation"
Study Design Type Term Accession Number	""	"http://purl.obolibrary.org/obo/CHMO_0000497"	"http://purl.obolibrary.org/obo/MS_1001457"	"http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C16237"
Study Design Type Term Source REF	""	"CHMO"	"MS"	"NCIT"
STUDY PUBLICATIONS
Study PubMed ID	""
Study Publication DOI	""
Study Publication Author List	""
Study Publication Title	"Development and validation of the PyMS Mass Spectrometry software"
Study Publication Status	""
Study Publication Status Term Accession Number	""
Study Publication Status Term Source REF	""
STUDY FACTORS
Study Factor Name	"Sample type"	"Spike in volume"	"Gap Penalty"	"Retention Time Modulation"	"Threshold"	"Min Number Ions"	"Relative Intensity"	"Skewing"	"Window"
Study Factor Type	"Sample plate type"	"Spike in volume"	"Gap Penalty"	"Retention Time Modulation"	"Threshold"	"Min Number Ions"	"Relative Intensity"	"Skewing"	"Window"
Study Factor Type Term Accession Number	""	""	""	""	""	""	""	""	""
Study Factor Type Term Source REF	""	""	""	""	""	""	""	""	""
STUDY ASSAYS
Study Assay File Name	"a_live10_mtbl_metabolite profiling_mass spectrometry.txt"
Study Assay Measurement Type	"metabolite profiling"
Study Assay Measurement Type Term Accession Number	"http://purl.obolibrary.org/obo/OBI_0000366"
Study Assay Measurement Type Term Source REF	"OBI"
Study Assay Technology Type	"mass spectrometry"
Study Assay Technology Type Term Accession Number	"http://purl.obolibrary.org/obo/OBI_0000470"
Study Assay Technology Type Term Source REF	"OBI"
Study Assay Technology Platform	"Agilent 5975E GC/MSD (Agilent)"
STUDY PROTOCOLS
Study Protocol Name	"Sample collection"	"Extraction"	"Chromatography"	"Mass spectrometry"	"Data transformation"	"Metabolite identification"
Study Protocol Type	"Sample collection"	"Extraction"	"Chromatography"	"Mass spectrometry"	"Data transformation"	"Metabolite identification"
Study Protocol Type Term Accession Number	""	""	""	""	""	""
Study Protocol Type Term Source REF	""	""	""	""	""	""
Study Protocol Description	"Two types of samples were prepared. A mixture of 45 metabolites, representing a variety of chemical classes (sugars, organic acids, amino acids, sugar phosphates), was prepared for GC-MS analysis. 10 µl of the mixture was transferred to a GC-MS vial insert and evaporated to dryness in vacuo. The samples were resuspended in 20 mg/ml methoxyamine in pyridine (20 µl, 16 hr, 25 °C) with continuous shaking, followed by derivatization with BSTFA + 1% TMCS (Pierce; 20 µl, 1 hr, 25 °C) using a Gerstel MPS2 autosampler robot. Second group a Foetal calf serum was spiked with 2-fold increasing amounts of a mix of metabolite standards."	"The Foetal calf serum samples (120 µl) were extracted by the addition of 200 µl of 3:2 chloroform:methanol, followed by vigorous mixing and incubation on ice for 10 min. Samples were centrifuged at 4 °C for 10 mins at 16,000 rpm to enable biphasic sparation. 15 µl of the upper aqueous phase was transferred to GC-MS vial inserts and dried in vacuo. The samples were resuspended in 20 mg/ml methoxyamine in pyridine (20 µl, 16 hr, 25 °C) with continuous shaking, followed by derivatization with BSTFA + 1% TMCS (Pierce; 20 µl, 1 hr, 25 °C) using a Gerstel MPS2 autosampler robot."	"Gas chromatography was performed using a 30 m VF5-MS column with 0.25 mm inner diameter and 0.25 mm film thickness (Varian Inc.). Agilent 7890A gas chromatograph interfaced with a 5975C mass selective detector."	"The injection temperature was 250 °C, the interface set at 280 °C, and the ionsource adjusted to 250 °C. The carrier gas was helium (flow rate 1 ml/min). The temperature program was 1 min isothermal heating at 70 °C, followed by a 1 °C/min oven temperature ramp to 76 °C, then 5 °C/min to 325 °C and held for 10 min. Mass spectra were recorded at 2.66 scans/s (m/z 50–600)."	"Data Analysis was performed using the PyMS software package (code.google.com/p/pyms). There are two steps, deconvolution (peak picking), and alignment. Each step produces output – for each sample a peak list was created. Deconvolution was carried out using PyMS with the following parameters: Threshold: 6000, Window: 13 scan, Num Ions per Peak: 3, Relative Intensity: 2 and Spectral Skewing parameter: 2 for the Foetal Calf Serum and Threshold: 3000, and Window: 5 scans difference for the Metabolite mix sample. Alignment was carried out using PyMS, with gap penalty 0.3 and retention time modulation parameter 2.5."	"No metabolites were identified."
Study Protocol URI	""	""	""	""	""	""
Study Protocol Version	""	""	""	""	""	""
Study Protocol Parameters Name	""	"Post Extraction;Derivatization"	"Chromatography Instrument;Column type;Column model"	"Scan polarity;Scan m/z range;Instrument;Mass analyzer;Ion source"	""	""
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	""	""	""	""	""	""
STUDY CONTACTS
Study Person Last Name	"De Souza"	"O'Callaghan"
Study Person First Name	"David"	"Sean"
Study Person Mid Initials	"P"	""
Study Person Email	"desouzad@unimelb.edu.au"	"spoc@unimelb.edu.au"
Study Person Phone	"+61383442487"	"+61383442479"
Study Person Fax	""	""
Study Person Address	"Bio 21 Institute, 30 Fleminton Road, University Of Melbourne, VIC 3010, Australia"	"Bio 21 Institute, 30 Fleminton Road, University Of Melbourne, VIC 3010, Australia"
Study Person Affiliation	"Metabolomics Australia"	"Metabolomics Australia"
Study Person Roles	"Operational research officer"	"Bioinformatics"
Study Person Roles Term Accession Number	""	""
Study Person Roles Term Source REF	""	""
