Metabolite identification was performed by manual curation and verification of the extracted peaks using MassHunter Qualitative 10.0 (Agilent Technologies) and the MassHunter Qualitative workflow 8.0 (Agilent Technologies). A height filter of 5000 counts was used with the MassHunter Qualitative workflow 8.0.
In this study, we are reporting the [M+H]+ and [M-H]- mass-to-charge ratios (m/z) and detected retention times for the compounds of the Human Endosome mixtures, with an identification reliability level 2 (Summer et al. 2007, http://link.springer.com/10.1007/s11306-007-0082-2). When the MS/MS fragments are verified, the reliability will be updated to level 1.
In parallel, an automated strategy is being evaluated to verify, in addition to the m/z match, the isotope pattern match, the detection of multiple related ions, and the MS2 match to reference spectra.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - negative - reverse phase","Liquid Chromatography MS - positive - reverse phase"],"chromatography_protocol":["The reference method and the in-house methods were run on an Agilent 1290 Infinity II UHPLC.
The reference method used reverse-phase chromatography. Eluent A was composed by 100% water with 0.1% formic acid, and eluent B was composed by 100% acetonitrile with 0.1% formic acid. The column was Kinetex C18 100 Å (1.7 µm, 2.1 mm x 100 mm; Phenomenex). The flow was constant at 0.5 mL/min. The injection volume was 1 μL. The chromatographic gradient was as follows (t [min], %B): (0, 5), (1.5, 5), (10, 99.9), (12, 99.9), (12.1, 5), and (15, 5).
The in-house methods, reverse-phase, and HILIC have been previously described by Avella et al. 2025 (https://doi.org/10.26434/chemrxiv-2025-7tbxq).
"],"publication":["HUMAN Ring Trial - Standards detection - Reverse phase."],"submitter_name":["Andres R. Martinez Bilesio","Philippine Louail","Dennisse AVELLA"],"submitter_affiliation":["Eurac Research","Chair of Bioinformatics Jena, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena","Afekta Technologies Ltd."],"organism_part":["blank","reference compound"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["Before collecting aliquots for dilution, the original concentration of NAPS and standard mixtures were vortexed for 10 seconds. Then, they were diluted to 10 ppm with an extraction mixture of 80% water / 20% Acetonitrile before analysis.
Blank solutions were prepared under the same conditions.
"],"organism":["blank","reference compound mix"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS14343"],"author":["Philippine Louail. philippine.louail@eurac.edu.","Olli Kärkkäinen. University of Eastern Finland. olli.karkkainen@uef.fi.","Dennisse Avella. Afekta Technologies LTD.. Mikrokatu 1. dennisse.avella@afekta.com. +358449735026."],"data_transformation_protocol":["The data was acquired using the software MassHunter Acquisition B.05.01 software (Agilent Technologies). No transformation was included.
"],"study_factor":["Mixture type"],"submitter_email":["a.martinez@uni-jena.de","plouail@eurac.edu","dennisse.avella@afekta.com"],"sample_collection_protocol":["A set of 1298 reference standards classified as 'Human Endosome' (HE), 'Food Exposome' (FE), 'Chemical Exposome' (CE), 'Microbiota Exposome' (ME), 'Plant Exposome' (PE), and 'Eukaryotic Exposome (EE) was acquired from the MetaSci metabolite library. The whole set was divided into 83 mixtures, each containing a maximum of 20 standards at about 1000 ppm.
NAPS (N-alkylpyridinium-3-sulfonates) at 700 ppm were also acquired for alignment and retention time indexing.
"],"omics_type":["Metabolomics"],"study_design":["LC-MS data","blank","reference compound","Agilent 6546 LC/Q-TOF","untargeted analysis","Agilent 1290 Infinity II UHPLC","experimental blank","Interlaboratory","reference compound mix"],"curator_keywords":["LC-MS data","blank","reference compound","Agilent 6546 LC/Q-TOF","untargeted analysis","Agilent 1290 Infinity II UHPLC","experimental blank","Interlaboratory","reference compound mix"],"mass_spectrometry_protocol":["Mass spectrometry for the reference method and the in-house methods was performed on an Agilent 6546 LC/Q-TOF with a Jet Stream ESI ion source for positive and negative ionization.
For all the methods, a range of 20-1600 mass-to-charge-ratio (m/z) was used for both MS and MS/MS analysis. Full-scan MS was acquired with a fragmentor voltage of 100 eV, while the collision energies for the MS/MS analysis were fixed at 10, 20, and 40 eV. The four most abundant precursor ions were automatically selected for MS/MS fragmentation, excluded after two acquired MS/MS spectra, and released again from the exclusion list after 0.25 min.
"],"metabolite_name":["2'-deoxyadenosine 5'-monophosphate","N(alpha)-acetyl-L-arginine","(R)-carnitine","ethylmalonic acid","undecanedioic acid","L-arginine","PE 14:0/14:0","serotonin","alpha-D-glucosamine 6-phosphate","isonicotinic acid","glutaric acid","D-ribofuranose","thymidine","cysteamine","N-acetyl-L-valine","N-acetyl-L-cysteine","3-(methylthio)propionic acid","Dimethyl succinate","2'-deoxyadenosine","L-glutamine","cytidine","5-phenylpentanoic acid","skatole","N-acetyl-L-tryptophan","cortisol","D-lysine","taurochenodeoxycholic acid","creatine","2'-deoxycytidine","L-aspartic acid","kynurenic acid","L-isoleucine","N-acetyl-L-isoleucine","L-methionine","L-lysine","homovanillic acid","2-hydroxyoctanoic acid","esculin","bilirubin IXalpha","itaconic acid","L-thyroxine","4-hydroxy-L-proline","creatinine","L-citrulline","cytosine","N(2)-phenylacetyl-L-glutamine","5,6-dihydroxyindole","N-isovalerylglycine","2'-deoxyguanosine","2-phenylethylamine","N-acetyl-L-alanine","L-cystine","N-benzoylglycine","L-glutamic acid","L-threonine","LMFA01170001","xanthurenic acid","citraconic acid","6-methyladenine","N-acetyl-L-phenylalanine","L-homoarginine","glycinamide","guanosine","3-amino-L-alanine","N-acetyl-L-glutamine","xanthosine","1-hexadecanoyl-sn-glycero-3-phosphocholine","corticosterone","5-aminolevulinic acid","dopamine","glutathione disulfide","taurocholic acid","4-pyridoxic acid","quinolinic acid","picolinic acid","1H-imidazole","L-tryptophan","2-hydroxy-4-(methylthio)butanoic acid","N-acetyl-alpha-D-galactosamine","estrone","D-asparagine","2-Methyl-4-pentenoic acid","3,3',5-triiodo-L-thyronine","phloretic acid","3-hydroxyisovaleric acid","alpha-D-mannose","1-stearoyl-sn-glycerol","(R)-adrenaline","cysteic acid","N-alpha-acetyl-L-asparagine","agmatine","3,5-diiodo-L-tyrosine","lithocholic acid","N-acetyl-L-aspartic acid","trans-3-coumaric acid","glycerol","O-propanoyl-L-carnitine","(6S)-5-formyltetrahydrofolic acid","homocystine","3-methyladipic acid","N-acetyl-L-methionine","N(2)-acetyl-L-lysine","nicotinic acid","L-arabinitol","taurodeoxycholic acid","4-guanidinobutanoic acid","L-dopa","5-aminoimidazole-4-carboxamide","alpha-D-glucuronic acid","N-acetyl-L-serine","N-carbamoyl-beta-alanine","L-leucine","Homocysteine thiolactone","3-hydroxyphenylacetic acid","alloxanthine","Dipropyl hexanedioate","L-homocitrulline","ethanolamine","(5-hydroxyindol-3-yl)acetic acid","3-nitro-L-tyrosine","folic acid","N-acetyl-beta-neuraminic acid","5,6-dimethylbenzimidazole","6-hydroxynicotinic acid","fumaric acid","guanosine 5'-monophosphate","L-homoserine","tricaproin","chlorphenamine","cytidine 5'-monophosphate","9H-xanthine","3-amino-3-(4-hydroxyphenyl)propanoic acid","D-leucine","Gly-Phe","N-acetyl-beta-D-mannosamine","ritalinic acid","(3,4-dihydroxyphenyl)acetic acid","N-acetyl-L-proline","indole-3-butyric acid","trans-3-hexenedioic acid","uracil","cholest-4-en-3-one","melatonin","O-phospho-L-serine","pyridoxal","thymine","inosine","5-hydroxy-L-tryptophan","all-trans-retinal","3,3-dimethylglutaric acid","pyrrolidin-2-one","D-glucono-1,5-lactone","dihydroorotic acid","hypoxanthine","homogentisic acid","glycine","taurocyamine","hexadecanedioic acid","3-hydroxybenzoic acid","undecanoic acid","(S)-methylsuccinic acid","cis-4-hydroxy-D-proline","tyramine","NAD zwitterion","2-aminoisobutyric acid","trans-cinnamic acid","citric acid","D-arabinitol","O-phosphoethanolamine","L-alanine","L-phenylalanine","N-acetylserotonin","D-arginine","sn-glycerol 3-phosphate","2-phenylbutyric acid","pyridin-2-ol","3-chloro-L-tyrosine","5-hydroxymethyl-2-furoic acid","D-serine","3-iodo-L-tyrosine","gamma-caprolactone","O(4)-phospho-L-tyrosine","L-tryptophanamide","estriol","Dimethyl adipate","L-serine","beta-alanine","hyodeoxycholic acid","phenylacetylglycine","nicotinamide","L-histidine","N-acetyl-L-glutamic acid","trans-urocanic acid","tauroursodeoxycholic acid","3-methoxytyramine","D-cysteine","5-hydroxymethyluracil","biotin","pyridoxamine","5-oxo-L-proline","taurine","lipoamide","L-pipecolic acid","5-methoxysalicylic acid","IMP","Gly-Pro","2-hydroxy-2-methylbutyric acid","guanine","(3S,5R)-fluvastatin","(R)-noradrenaline","4-acetamidobutanoic acid","2'-deoxyinosine","(S)-lipoic acid","5-methoxytryptamine","2-Methylheptanoic acid","N-acetyl-L-leucine","glutathione","progesterone","Acetylcarnosine","D-proline","imidazol-4-ylacetic acid","2'-deoxyuridine","urea","uridine","L-proline","5-aminopentanoic acid","L-ornithine","3,5-Diiodothyronine","gallic acid","3,4,5-Trimethoxycinnamic acid","methylmalonic acid","N-carbamoylglutamic acid","carnosine","L-valine","N(6)-acetyl-L-lysine","pregnenolone","N-acetyl-L-tyrosine","Phenylglyoxal","N(4)-acetylcytidine","vanillin","chenodeoxycholic acid"],"additional_accession":[]},"is_claimable":false,"name":"HUMAN Ring Trial - Standards detection - Reverse phase","description":"To better understand the effect of different LC-MS setups on metabolite detection, five laboratories analyzed 1298 standard compounds obtained from the MetaSci metabolite standard library, classified as 'Human Endosome' (HE), 'Food Exposome' (FE), 'Chemical Exposome' (CE), 'Microbiota Exposome' (ME), 'Plant Exposome' (PE), and 'Eukaryotic Exposome' (EE), using a common reference reverse-phase method in both positive and negative ionization modes and different in-house methods. NAPS were used for alignment and retention time indexing.
In our laboratory, we ran the reference reverse-phase method, an in-house reverse-phase method, and an in-house HILIC method, all three with positive and negative ionization, using an LC-MS with a Q-ToF analyzer. In this study, we present data from the reference reverse-phase method and the in-house reverse-phase method.
","dates":{"publication":"2026-04-24","submission":"2026-04-22"},"accession":"MTBLS14343","cross_references":{"HMDB":["HMDB0000650","HMDB0000883","HMDB0000719","HMDB0000182","HMDB0001890","HMDB0006028","HMDB0000904","HMDB0000206","HMDB0000472","HMDB0000033","HMDB0001254","HMDB0006049","HMDB0000575","HMDB0000125","HMDB0000288","HMDB0001397","HMDB0000532","HMDB0000812","HMDB0006029","HMDB0000679","HMDB0062795","HMDB0000929","HMDB0000645","HMDB0005923","HMDB0000095","HMDB0000175","HMDB0000121","HMDB0000902","HMDB0001487","HMDB0001906","HMDB0000574","HMDB0033780","HMDB0000214","HMDB0000517","HMDB0000446","HMDB0001138","HMDB0000181","HMDB0000133","HMDB0000230","HMDB0000295","HMDB0000064","HMDB0000224","HMDB0003405","HMDB0002931","HMDB0000568","HMDB0000714","HMDB0000272","HMDB0000670","HMDB0000296","HMDB0006344","HMDB0000905","HMDB0003337","HMDB0000161","HMDB0002006","HMDB0000187","HMDB0000766","HMDB0000191","HMDB0000641","HMDB0000148","HMDB0002757","HMDB0000126","HMDB0003416","HMDB0000866","HMDB0000192","HMDB0000089","HMDB0001586","HMDB0001520","HMDB0003406","HMDB0000167","HMDB0003417","HMDB0001851","HMDB0000177","HMDB0001885","HMDB0004620","HMDB0001562","HMDB0000202","HMDB0059712","HMDB0003192","HMDB0000687","HMDB0000622","HMDB0004058","HMDB0000292","HMDB0000073","HMDB0000159","HMDB0001431","HMDB0028848","HMDB0000085","HMDB0031125","HMDB0062472","HMDB0000131","HMDB0000300","HMDB0000716","HMDB0006055","HMDB0000746","HMDB0000301","HMDB0000678","HMDB0000232","HMDB0000022","HMDB0000289","HMDB0000169","HMDB0000763","HMDB0000127","HMDB0000267","HMDB0000661","HMDB0000306","HMDB0000696","HMDB0000786","HMDB0094701","HMDB0001713","HMDB0001868","HMDB0000150","HMDB0000118","HMDB0000715","HMDB0000512","HMDB0000030","HMDB0000021","HMDB0001547","HMDB0000265","HMDB0000112","HMDB0000162","HMDB0002024","HMDB0002658","HMDB0000393","HMDB0037115","HMDB0003584","HMDB0005807","HMDB0011756","HMDB0000259","HMDB0000068","HMDB0001238","HMDB0000012","HMDB0013713","HMDB0000071","HMDB0000562","HMDB0031158","HMDB0002287","HMDB0000634","HMDB0001844","HMDB0003464","HMDB0003701","HMDB0000062","HMDB0002199","HMDB0041606","HMDB0004095","HMDB0013318","HMDB0000212","HMDB0000101","HMDB0014879","HMDB0010382","HMDB0013751","HMDB0012275","HMDB0002243","HMDB0000805","HMDB0001149","HMDB0060460","HMDB0000026","HMDB0061916","HMDB0000157","HMDB0002466","HMDB0002432","HMDB0000930","HMDB0014997","HMDB0000283","HMDB0011757","HMDB0001545","HMDB0000881","HMDB0000195","HMDB0002039","HMDB0003355","HMDB0060665","HMDB0000466","HMDB0000469","HMDB0000132","HMDB0000555","HMDB0000821","HMDB0002096","HMDB0000962","HMDB0000299","HMDB0030820","HMDB0000056","HMDB0003843","HMDB0000254","HMDB0003681","HMDB0033837","HMDB0002099","HMDB0000440","HMDB0002441","HMDB0061684","HMDB0000017","HMDB0000824","HMDB0001129","HMDB0001389","HMDB0002511","HMDB0001525","HMDB0000630","HMDB0000754","HMDB0002092","HMDB0000172","HMDB0000156","HMDB0000174","HMDB0001336","HMDB0003831","HMDB0001904","HMDB0000014","HMDB0000273","HMDB0001944","HMDB0003474","HMDB0000582","HMDB0000190","HMDB0003411","HMDB0000134","HMDB0001406","HMDB0001488","HMDB0000251","HMDB0000262","HMDB0001432","HMDB0013773","HMDB0012308","HMDB0000528","HMDB0000130","HMDB0000216","HMDB0000721","HMDB0011745","HMDB0032306","HMDB0042008","HMDB0031587","HMDB0000543","HMDB0000888","HMDB0000151","HMDB0000761","HMDB0015227","HMDB0000951","HMDB0000896","HMDB0007098","HMDB0007866","HMDB0006740","HMDB0008923","HMDB0001918","HMDB0005806","HMDB0000329","HMDB0000145","HMDB0001358","HMDB0000672","HMDB0000253","HMDB0011131","HMDB0000921","HMDB0000733","HMDB0000619","HMDB0000256","HMDB0000874","HMDB0000036","HMDB0000918","HMDB0000593","HMDB0005414","HMDB0000711","HMDB0002043","HMDB0000947","HMDB0014312","HMDB0041614","HMDB0000153","HMDB0001830","HMDB0000518","HMDB0000946","HMDB0008821","HMDB0009059","HMDB0008991","HMDB0000271","HMDB0000163","HMDB0000613","HMDB0012881","HMDB0001401","HMDB0000740","HMDB0001262","HMDB0060079","HMDB0000123","HMDB0000286","HMDB0000205","HMDB0000291","HMDB0000691","HMDB0001987","HMDB0000005","HMDB0000243","HMDB0000407","HMDB0000703","HMDB0000263","HMDB0000139","HMDB0001051","HMDB0000008","HMDB0000491","HMDB0000208","HMDB0000707","HMDB0000119","HMDB0001527","HMDB0003903","HMDB0040733","HMDB0000944","HMDB0000220","HMDB0000452","HMDB0000193","HMDB0000094","HMDB0000149","HMDB0002991","HMDB0000294","HMDB0000054"]}}