ONTOLOGY SOURCE REFERENCE
Term Source Name	"OBI"	"NCIT"	"NCBITAXON"	"ERO"	"BTO"	"EFO"	"CHMO"	"MS"
Term Source File	"http://data.bioontology.org/ontologies/OBI"	"http://data.bioontology.org/ontologies/NCIT"	"http://data.bioontology.org/ontologies/NCBITAXON"	"http://data.bioontology.org/ontologies/ERO"	"http://data.bioontology.org/ontologies/BTO"	"http://data.bioontology.org/ontologies/EFO"	"http://data.bioontology.org/ontologies/CHMO"	"http://data.bioontology.org/ontologies/MS"
Term Source Version	"29"	"28"	"2"	"13"	"22"	"113"	"5"	"86"
Term Source Description	"Ontology for Biomedical Investigations"	"National Cancer Institute Thesaurus"	"National Center for Biotechnology Information (NCBI) Organismal Classification"	"Eagle-I Research Resource Ontology"	"BRENDA Tissue and Enzyme Source Ontology"	"Experimental Factor Ontology"	"Chemical Methods Ontology"	"Mass Spectrometry Ontology"
INVESTIGATION
Investigation Identifier	"MTBLS1693"
Investigation Title	"Investigation"
Investigation Description	"Created using the MetaboLights Online Editor (MOE)"
Investigation Submission Date	"2020-05-01"
Investigation Public Release Date	"2020-07-28"
Comment[Created With Configuration]	"MetaboLightsConfig20150707"
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	"MTBLS1693"
Study Title	"Known Metabolite Annotation in Different Biological Samples using Ion Mobility Collision Cross-Section Atlas (AllCCS)"
Study Description	"<p>The metabolome includes not just known but also unknown metabolites; however, metabolite annotation remains the bottleneck in untargeted metabolomics. Ion mobility – mass spectrometry (IM-MS) has emerged as a promising technology by providing multi-dimensional characterizations of metabolites. Here, we curated an ion mobility CCS atlas, namely AllCCS, and developed an integrated strategy for metabolite annotation using known or unknown chemical structures. The AllCCS atlas covers vast chemical structures with &gt;5000 experimental CCS records and ~12 million calculated CCS values for &gt;1.6 million small molecules. We demonstrated the high accuracy and wide applicability of AllCCS with medium relative errors of 0.5-2% for a broad spectrum of small molecules. AllCCS combined with in-silico MS/MS spectra facilitated multi-dimensional match and substantially improved the accuracy and coverage of both known and unknown metabolite annotation from biological samples. Together, AllCCS is a versatile resource that enables confident metabolite annotation, revealing comprehensive chemical and metabolic insights towards biological processes.</p><p><br></p><p><strong>Known Metabolite Annotation in Different Biological Samples assays</strong> are reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS1693' rel='noopener noreferrer' target='_blank'><strong>MTBLS1693</strong></a>.</p><p><strong>Unknown Metabolite Annotation in Mouse Aging assay</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS1622' rel='noopener noreferrer' target='_blank'><strong>MTBLS1622</strong></a>.</p>"
Study Submission Date	"2020-05-01"
Study Public Release Date	"2020-07-28"
Study File Name	"s_MTBLS1693.txt"
STUDY DESIGN DESCRIPTORS
Study Design Type	"Ion mobility spectrometry-mass spectrometry"	"untargeted metabolites"	"ultra-performance liquid chromatography-mass spectrometry"	"tandem mass spectrometry"
Study Design Type Term Accession Number	"http://purl.obolibrary.org/obo/CHMO_0000499"	""	"http://purl.obolibrary.org/obo/CHMO_0000715"	"http://purl.obolibrary.org/obo/CHMO_0000575"
Study Design Type Term Source REF	"CHMO"	""	"CHMO"	"CHMO"
STUDY PUBLICATIONS
Study PubMed ID	""
Study Publication DOI	"10.1038/s41467-020-18171-8"
Study Publication Author List	"Zhiwei Zhou, Mingdu Luo, Xi Chen, Yandong Yin, Xin Xiong, Ruohong Wang, and Zheng-Jiang Zhu*"
Study Publication Title	"Ion Mobility Collision Cross-Section Atlas for Known and Unknown Metabolite Annotation in Untargeted Metabolomics"
Study Publication Status	"Published"
Study Publication Status Term Accession Number	"http://www.ebi.ac.uk/efo/EFO_0001796"
Study Publication Status Term Source REF	"EFO"
STUDY FACTORS
Study Factor Name	"Material"
Study Factor Type	"Tissue"
Study Factor Type Term Accession Number	"http://purl.obolibrary.org/obo/NCIT_C12801"
Study Factor Type Term Source REF	"NCIT"
STUDY ASSAYS
Study Assay File Name	"a_MTBLS1693_MEF_POS_LC-MS.txt"	"a_MTBLS1693_Fly_POS_LC-MS.txt"	"a_MTBLS1693_Human_POS_LC-MS.txt"	"a_MTBLS1693_MEF_NEG_LC-MS.txt"	"a_MTBLS1693_Fly_NEG_LC-MS.txt"	"a_MTBLS1693_Human_NEG_LC-MS.txt"
Study Assay Measurement Type	"metabolite profiling"	"metabolite profiling"	"metabolite profiling"	"metabolite profiling"	"metabolite profiling"	"metabolite profiling"
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"	"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"	"OBI"	"OBI"
Study Assay Technology Type	"mass spectrometry"	"mass spectrometry"	"mass spectrometry"	"mass spectrometry"	"mass spectrometry"	"mass spectrometry"
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"	"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"	"OBI"	"OBI"
Study Assay Technology Platform	"Liquid Chromatography MS - positive - hilic"	"Liquid Chromatography MS - positive - hilic"	"Liquid Chromatography MS - positive - hilic"	"Liquid Chromatography MS - negative - hilic"	"Liquid Chromatography MS - negative - hilic"	"Liquid Chromatography MS - negative - hilic"
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	"<p>Brain tissues of wild-type male fruit flies (FlyBase ID: <a href='https://flybase.org/reports/FBst0005905.html' rel='noopener noreferrer' target='_blank'>FBst0005905</a>), MEF cells (Mouse Embryonic Fibroblasts;) and commercial human plasma were used in this study. The standard biological samples (i.e. MEF cell, human plasma, fruit fly) were repeated with 3-6 technical replications.</p>"	"<p>For plasma, 100 μl of human plasma was extracted using 400 μl of solvent mixture of MeOH:ACN (1:1, v/v) in the centrifuge tube, and then the mixture was vortexed for 30 s and sonicated for 10 min at 4 °C water bath. A total of 100 μl of H2O and 800 μl of solvent mixture of ACN:MeOH (1:1, v/v) was added, and vortexed for 30 s, and sonicated for 10 min at 4 °C water bath. After incubation for 1 hour at −20 °C, the sample was further centrifuged for 15 min at 13,000 rpm and 4 °C. The supernatant was collected and evaporated to dryness at 4 °C. The dry extracts were then reconstituted into 100 μl of ACN:H2O (1:1, v/v), followed by sonication at 4 °C for 10 min, and centrifuged at 13,000 rpm and 4 °C for 5 min to remove the insoluble debris before LC-IM-MS/MS analysis.</p><p><br></p><p>For mouse embryonic fibroblasts (MEFs) cells, 1 ml of MeOH:ACN:H2O (2:2:1, v/v/v) solvent mixture was added to the samples, followed by vortex for 30 s and sonication for 10 min at 4 °C water bath. Then the samples were incubated in liquid nitrogen for 1 min, thawed on ice, and sonicated for 10 min at 4 °C water bath. The above vortex–freeze–thaw cycle was repeated 3 times. After incubation for 1 hour at −20 °C, the sample was further centrifuged for 15 min at 13,000 rpm and 4 °C. The supernatant was collected and evaporated to dryness at 4 °C. The dry extracts were then reconstituted into 100 μl of ACN:H2O (1:1, v/v), followed by sonication at 4 °C for 10 min, and centrifuged at 13,000 rpm and 4 °C for 5 min to remove the insoluble debris before LC-IM-MS/MS analysis.</p><p><br></p><p>For fruit fly head samples, the sample collection and extraction followed our previous publication<strong>[1]</strong>. Briefly, wild-type male fruit flies (FlyBase ID: <a href='https://flybase.org/reports/FBst0005905.html' rel='noopener noreferrer' target='_blank'>FBst0005905</a>) were cultured in standard media (temperature, 25 °C; humidity, 60%; and a 12 h light and 12 h dark cycle). At day 3 (3-day) and day 30 (30-day), 100 fruit flies were collected and divided into 10 samples (10 flies in each sample, n = 10 in each group, and 20 samples in total). The fruit flies were killed with 75% ethanol. The heads of the fruit flies were collected and placed into microcentrifuge tubes. The tubes were immediately frozen with liquid nitrogen and stored at −80 °C until metabolite extraction. The Drosophila aging samples were defrosted on ice. The Drosophila aging samples were then homogenized with 200 μl of H2O and 20 ceramic beads (diameter, 0.1 mm) using a homogenizer (Precellys 24, Bertin Technologies). A mixture of ACN:MeOH (1:1, v/v; 800 μl) was added to the samples, which were then vortexed for 30 s, followed by incubation in liquid nitrogen for 1 min, and then thawed on ice. This vortex–freeze–thaw cycle was repeated 3 times. The samples were incubated for 1 h at −20 °C for protein precipitation, followed by centrifugation at 16,200 x g and 4 °C for 15 min. The supernatant solution was removed and evaporated to dryness in a vacuum concentrator (Labconco, USA). A mixture of ACN:H2O (1:1, v/v; 100 µl) was then added to reconstitute the dry extracts, followed by sonication (50 Hz, 4 °C) for 10 min. The solutions were centrifuged at 16,200 x g and 4 °C for 5 min to precipitate the insoluble debris. Finally, the supernatant solutions were transferred to HPLC glass vials and stored at −80 °C prior to LC-IM-MS/MS analysis.</p><p><br></p><p><strong>Ref:</strong></p><p><strong>[1]</strong> Shen X, Wang R, Xiong X, Yin Y, Cai Y, Ma Z, Liu N, Zhu ZJ. Metabolic reaction network-based recursive metabolite annotation for untargeted metabolomics. Nat Commun. 2019 Apr 3;10(1):1516. doi:10.1038/s41467-019-09550-x. PMID:30944337</p>"	"<p>A UHPLC system (Agilent 1290 series) coupled to a quadruple time-of-flight mass spectrometer equipped with an ion-mobility drift tube (Agilent DTIM-QTOF-MS 6560, Agilent Technologies, USA) was used for LC-IM-MS/MS data acquisition. The LC separation was performed on a Waters BEH Amide column (particle size, 1.7 μm; 100 mm (length) x 2.1 mm (i.d.)) maintained at 25 °C. The solvent A was 100% H2O with 25 mM NH4OAc and 25 mM NH4OH, and solvent B was 100% ACN. The flow rate was 0.3 ml/min, and the gradient was described as follows: 0-1 min: 95% B, 1-14 min: 95% B to 65% B, 14-16 min: 65% B to 40% B, 16-18 min: 40% B, 18-18.1 min: 40% B to 95% B and 18.1-23 min: 95% B. The sample injection volume was 2 μl.</p>"	"<p>The data acquisition was operated in IM-Q-TOF mode. The source parameters were set as follows: sheath gas temperature, 325 °C or 275 °C in positive or negative modes; dry gas temperature, 300 °C; sheath gas flow, 11 l/min; dry gas flow, 8 l/min; capillary voltage, 4000 V or -3000 V in positive or negative modes, respectively; and nebulizer pressure, 20 psi or 25 psi in positive or negative modes, respectively. The TOF mass range was set as m/z 50 – 1700 Da. For ion mobility parameters, the nitrogen (N2) was used for the drift gas. Other related IM parameters were set as follows: entrance and exit voltages of drift tube, 1600 V and 250 V; trap filling and trap release times, 20000 μs and 150 μs. The pressure of drift tube was set at 3.95 Torr. The MS/MS spectra were acquired in the 'Alternating frames' mode, and the collision energy was fixed at 20 V in frame 2. The CCS values were calculated with single electric field method. All data acquisitions were carried out using MassHunter Workstation Data Acquisition Software (Version B.08.00, Agilent Technologies, USA).</p><p><br></p><p>Chemical standards were first dissolved at 0.01 mg/ml in either H2O, MeOH, CH2Cl2, DMSO or their mixture with different proportions depending on compound polarity and solubility, and subject to measurements of CCS values and MS/MS spectra. The CCS values were independently measured 3 times across 2 months using a single-field approach on Agilent DTIM-QTOF-MS 6560 instrument according to our previous publication<strong>[1].</strong> The MS/MS spectra were acquired using targeted MS/MS method with 3 different collision energy levels (10 V, 20 V, and 40 V).</p><p><br></p><p><strong>Ref:</strong></p><p><strong>[1]</strong> Zhou Z, Shen X, Tu J, Zhu ZJ. Large-Scale Prediction of Collision Cross-Section Values for Metabolites in Ion Mobility-Mass Spectrometry. Anal Chem. 2016 Nov 15;88(22):11084-11091. doi:10.1021/acs.analchem.6b03091. PMID: 27768289</p>"	"<p>Raw MS data files (.d) were first recalibrated using IM-MS Reprocessor (Version B.08.00, Agilent Technologies). Then, the smoothing and saturation repair were performed using PNNL PreProcessor (Version 2018.06.02). The CCS calibration was performed by IM-MS Browser software (Version B.08.01, Agilent Technologies). The pre-processed data files were submitted for feature finding, alignment, and MS/MS spectra extraction using Mass Profiler (Version 10.0, Agilent Technologies). Finally, the peak table and MS/MS spectra (.CEF format) files were exported for metabolite annotation.</p>"	"<p>The metabolites were annotated using multi-dimensional match as we described before. The m/z tolerance was set at 25 ppm, and only [M+H]+ and [M-H]- adducts were considered for positive and negative modes, respectively. The MS-FINDER was used for in-silico MS/MS match. The known metabolite database (KEGG and HMDB) and the extended database were used for known and unknown metabolite annotation, respectively.</p>"
Study Protocol URI	""	""	""	""	""	""
Study Protocol Version	""	""	""	""	""	""
Study Protocol Parameters Name	""	"Post Extraction;Derivatization"	"Chromatography Instrument;Autosampler model;Column model;Column type;Guard column"	"Scan polarity;Scan m/z range;Instrument;Ion source;Mass analyzer"	""	""
Study Protocol Parameters Name Term Accession Number	""	";"	";;;;"	";;;;"	""	""
Study Protocol Parameters Name Term Source REF	""	";"	";;;;"	";;;;"	""	""
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STUDY CONTACTS
Study Person Last Name	"Zhiwei"	"Zheng-jiang"
Study Person First Name	"Zhou"	"Zhu"
Study Person Mid Initials	""	""
Study Person Email	"zhouzw@sioc.ac.cn"	"jiangzhu@sioc.ac.cn"
Study Person Phone	"+86-1752133825"	"+86-21-68582296"
Study Person Fax	""	""
Study Person Address	""	"26 Qiuyue Road, Pudong, Shanghai, China 201210"
Study Person Affiliation	"Interdisciplinary Research Center on Biology and Chemistry (IRCBC), Shanghai Institute of Organic Chemistry (SIOC), Chinese Academy of Sciences (CAS)"	"Interdisciplinary Research Center on Biology and Chemistry (IRCBC), Shanghai Institute of Organic Chemistry (SIOC), Chinese Academy of Sciences (CAS)"
Study Person Roles	"Graduate student role"	"Principal Investigator"
Study Person Roles Term Accession Number	"http://purl.obolibrary.org/obo/ERO_0000785"	"http://purl.obolibrary.org/obo/NCIT_C19924"
Study Person Roles Term Source REF	"ERO"	"NCIT"
