Summary of Study ST002874

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR001796. The data can be accessed directly via it's Project DOI: 10.21228/M8JX52 This work is supported by NIH grant, U2C- DK119886.


This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST002874
Study TitleQuantification of metabolites in kynurenine pathway
Study SummaryUrine samples were collected from two independent cohorts. Patients with LN were classified into proliferative (class III/IV) and membranous (class V) by kidney histopathology. Quantification of metabolites in kynurenine pathway was performed using LC-MS/MS.
Mahidol University
DepartmentSiriraj Metabolomics and Phenomics Center
LaboratorySiriraj Center of Research Excellence in Metabolomics and Systems Biology
Last NameKhoomrung
First NameSakda
Address2 Wanglang Road Bangkoknoi, Bangkok 10700, Thailand
Submit Date2023-09-25
Num Groups2
Total Subjects117
Raw Data AvailableYes
Raw Data File Type(s)raw(Waters)
Analysis Type DetailLC-MS
Release Date2023-10-10
Release Version1
Sakda Khoomrung Sakda Khoomrung application/zip

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Project ID:PR001796
Project DOI:doi: 10.21228/M8JX52
Project Title:Predicting lupus membranous nephritis using reduced picolinic acid to tryptophan ratio as a urinary biomarker
Project Type:MS quantitative analysis
Project Summary:The current gold standard for classifying lupus nephritis (LN) progression is a renal biopsy, which is an invasive procedure. Undergoing a series of biopsies for monitoring disease progression and treatments is unlikely suitable for patients with LN. Thus, there is an urgent need for non-invasive alternative biomarkers that can facilitate LN class diagnosis. Such biomarkers will be very useful in guiding intervention strategies to mitigate or treat patients with LN. Urine samples were collected from two independent cohorts. Patients with LN were classified into proliferative (class III/IV) and membranous (class V) by kidney histopathology. Metabolomics was performed to identify potential metabolites, which could be specific for the classification of membranous LN. The ratio of picolinic acid (Pic) to tryptophan (Trp) ([Pic/Trp] ratio) was found to be a promising candidate for LN diagnostic and membranous classification. It has high potential as an alternative biomarker for the non-invasive diagnosis of LN.
Institute:Mahidol University
Department:Siriraj Metabolomics and Phenomics Center
Laboratory:Siriraj Center of Research Excellence in Metabolomics and Systems Biology
Last Name:Khoomrung
First Name:Sakda
Address:2 Wanglang Road, Bangkok, Bangkok, 10700, Thailand


Subject ID:SU002987
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Male and female


Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Sample_group Disease_subclass
SA314348LN106LN All class V
SA314349LN222LN All class V
SA314350LN236LN All class V
SA314351LN503LN All class V
SA314352LN55LN All class V
SA314353LN882LN All class V
SA314354LN953LN All class V
SA314355LN268LN All class V
SA314356LN277LN All class V
SA314357LN912LN All class V
SA314358LN961LN All class V
SA314359LN709LN All class V
SA314360LN470LN All class V
SA314361LN294LN All class V
SA314362LN45LN All class V
SA314363LN949LN All class V
SA314364LN799LN All class V
SA314365LN57LN All class V
SA314366LN476LN All class V
SA314367LN564LN All class V
SA314368LN269LN All class V
SA314369LN288LN All class V
SA314370LN362LN All class V
SA314371LN343LN All class V
SA314372LN616LN All class V
SA314373LN75LN All class V
SA314374LN197LN All class V
SA314375LN170LN All class V
SA314376LN239LN All class V
SA314377LN257LN All class V
SA314378LN870LN All class V
SA314379LN925LN All class V
SA314380LN473LN All class V
SA314381LN893LN Pure class III/IV
SA314382LN818LN Pure class III/IV
SA314383LN809LN Pure class III/IV
SA314384LN828LN Pure class III/IV
SA314385LN845LN Pure class III/IV
SA314386LN855LN Pure class III/IV
SA314387LN886LN Pure class III/IV
SA314388LN5LN Pure class III/IV
SA314389LN74LN Pure class III/IV
SA314390LN699LN Pure class III/IV
SA314391LN803LN Pure class III/IV
SA314392LN805LN Pure class III/IV
SA314393LN834LN Pure class III/IV
SA314394LN937LN Pure class III/IV
SA314395LN871LN Pure class III/IV
SA314396LN48LN Pure class III/IV
SA314397LN405LN Pure class III/IV
SA314398LN243LN Pure class III/IV
SA314399LN18LN Pure class III/IV
SA314400LN165LN Pure class III/IV
SA314401LN276LN Pure class III/IV
SA314402LN291LN Pure class III/IV
SA314403LN404LN Pure class III/IV
SA314404LN369LN Pure class III/IV
SA314405LN123LN Pure class III/IV
SA314406LN7LN Pure class III/IV
SA314407LN250LN Pure class III/IV
SA314408LN272LN Pure class III/IV
SA314409LN249LN Pure class III/IV
SA314410LN275LN Pure class III/IV
SA314411LN59LN Pure class III/IV
SA314412normal350796N N
SA314413normal358762N N
SA314414normal346675N N
SA314415normal309427N N
SA314416normal358797N N
SA314417normal328154N N
SA314418normal376701N N
SA314419normal378194N N
SA314420normal386006N N
SA314421normal309354N N
SA314422normal374393N N
SA314423normal367346N N
SA314424normal362875N N
SA314425normal302449N N
SA314426normal219541N N
SA314427normal228443N N
SA314428normal190667N N
SA314429normal171808N N
SA314430normal16799N N
SA314431normal275182N N
SA314432normal282901N N
SA314433normal303739N N
SA314434normal388793N N
SA314435normal300195N N
SA314436normal297429N N
SA314437normal304786N N
SA314438normal408913N N
SA314439normal454125N N
SA314440normal456977N N
SA314441normal449032N N
SA314442normal446904N N
SA314443normal441384N N
SA314444normal462020N N
SA314445normal469548N N
SA314446normal61921N N
SA314447normal64947N N
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Collection ID:CO002980
Collection Summary:Both morning urine and blood samples were collected under sterile conditions within the same day of biopsy/recruitment. Urine samples were centrifuged at 3,500 rpm for 10 min at 4°C. The supernatant was then aliquoted and stored at −80°C until the analysis. Common blood biochemical parameters were measured by an ISO 15189 accredited laboratory. Serum creatinine (SCr) and urine creatinine (UCr) were measured by an enzymatic assay using a Dimension ExL analyzer (Siemens Healthcare Diagnostics, Newark, DE, USA). Urine protein (Uprot) was measured by a modified pyrogallol red-molybdate method. Uprot was reported as urine protein creatinine ratio (UPCR in mg/mgCr). The estimated glomerular filtration rate (eGFR in mL/min/1.73 m2) was calculated using the CKD-EPI equation (Levey et al., 2009):
Sample Type:Urine


Treatment ID:TR002996
Treatment Summary:LN patients and health subjects (N) were recruited from Ramathibodi Hospital, Bangkok, Thailand. Patients, who fulfilled at least four of the American College of Rheumatology 1982 revised criteria for SLE (Hochberg, 1997) and were referred to kidney biopsy for clinical indications of proteinuria ≥ 0.5g/24 hours (Fanouriakis et al., 2020) were included.

Sample Preparation:

Sampleprep ID:SP002993
Sampleprep Summary:The urine samples were prepared based on a previously published protocol (Zhu et al., 2019) with minor modifications. Briefly, a 50 μL of each urine sample was mixed with 200 μL of MeOH/ACN (1:1, v/v) containing 100 ng of anthranilic acid C13 (Ant-C13) as an internal standard (IS). The mixture was vortexed for 30 s and sonicated for 10 min (room temperature). The mixture was then left overnight (−20°C) for protein precipitation before centrifugation at 13,000 rpm (4°C) for 15 min. The supernatant was transferred to a new test tube and evaporated to dryness (room temperature) using a vacuum concentrator (Labconco, MO, USA). The dried sample was reconstituted in 100 μL of Milli-Q H2O (containing 0.1% formic acid), vortexed for 30 s, and sonicated (room temperature) for 10 min. The reconstituted sample was centrifuged at 13,000 rpm (4°C) for 15 min. The supernatant was kept at −80°C before analysis.

Combined analysis:

Analysis ID AN004711
Analysis type MS
Chromatography type Normal phase
Chromatography system Waters Acquity I-Class
Column Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um)
MS instrument type Single quadrupole
MS instrument name Waters Xevo-TQ-S
Units ng/ml


Chromatography ID:CH003547
Chromatography Summary:A volume of 5 μL of a standard or sample was injected onto an HSS T3 column, 2.1 × 100 mm, 1.8 μM column (Waters, Milford, MA, USA) at 30°C with a constant flow rate of 0.3 mL/min. Mobile phases consisted of (A) 0.1% formic acid in Milli-Q water and (B) 0.1% formic acid in ACN. The gradient program started at 99% A, decreased to 70% over 7.0 min, then decreased to 30% at 9 min, and return to the initial condition at 10 min and held for 4.0 min. The total runtime was 14 min. The weak and strong needles wash solutions were 5% ACN and H2O/ACN/MeOH/IPA (1:1:1:1), respectively.
Instrument Name:Waters Acquity I-Class
Column Name:Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um)
Column Temperature:30
Flow Gradient:The gradient program started at 99% A, decreased to 70% over 7.0 min, then decreased to 30% at 9 min and return to the initial condition at 10 min and held for 4.0 min. The total runtime was 14 min. The weak and strong needles wash solutions were 5% ACN and H2O/ACN/MeOH/IPA (1:1:1:1), respectively.
Flow Rate:0.4ml/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:Normal phase


MS ID:MS004457
Analysis ID:AN004711
Instrument Name:Waters Xevo-TQ-S
Instrument Type:Single quadrupole
MS Comments:Quantitative analysis (absolute quantification) was achieved by external calibration curves of each standard prepared in pooled urine samples (standard addition) (Limjiasahapong et al., 2021). The linear ranges of the calibration standards are as follows: 3.5–1,000 ng/mL for Ant; 4.5–80 ng/mL for Cin; 8–2,500 ng/ml for Kyna; 8–5,000 ng/ml for Kyn; 1.4–400 ng/ml for Pic; 40–5000 ng/ml for Qui; 7–2000 ng/ml for Trp; 2–200 ng/ml for Xan; 900–14,000 ng/ml for 3OH-Kyn; 300–2,500 ng/ml for 3OH-Ant and 8–2,000 ng/ml for Ant-C13.