Summary of Study ST002874

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, 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.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

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.

Study ID	ST002874
Study Title	Quantification of metabolites in kynurenine pathway
Study Summary	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. Quantification of metabolites in kynurenine pathway was performed using LC-MS/MS.
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 Bangkoknoi, Bangkok 10700, Thailand
Email	sakda.kho@mahidol.edu
Phone	024195511
Submit Date	2023-09-25
Num Groups	2
Total Subjects	117
Publications	https://doi.org/10.1016/j.isci.2021.103355
Raw Data Available	Yes
Raw Data File Type(s)	raw(Waters)
Analysis Type Detail	LC-MS
Release Date	2023-10-10
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

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
Email:	sakda.kho@mahidol.edu
Phone:	024195511
Publications:	https://doi.org/10.1016/j.isci.2021.103355

Subject:

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

Factors:

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

mb_sample_id	local_sample_id	Sample_group	Disease_subclass
SA314348	LN106	LN	All class V
SA314349	LN222	LN	All class V
SA314350	LN236	LN	All class V
SA314351	LN503	LN	All class V
SA314352	LN55	LN	All class V
SA314353	LN882	LN	All class V
SA314354	LN953	LN	All class V
SA314355	LN268	LN	All class V
SA314356	LN277	LN	All class V
SA314357	LN912	LN	All class V
SA314358	LN961	LN	All class V
SA314359	LN709	LN	All class V
SA314360	LN470	LN	All class V
SA314361	LN294	LN	All class V
SA314362	LN45	LN	All class V
SA314363	LN949	LN	All class V
SA314364	LN799	LN	All class V
SA314365	LN57	LN	All class V
SA314366	LN476	LN	All class V
SA314367	LN564	LN	All class V
SA314368	LN269	LN	All class V
SA314369	LN288	LN	All class V
SA314370	LN362	LN	All class V
SA314371	LN343	LN	All class V
SA314372	LN616	LN	All class V
SA314373	LN75	LN	All class V
SA314374	LN197	LN	All class V
SA314375	LN170	LN	All class V
SA314376	LN239	LN	All class V
SA314377	LN257	LN	All class V
SA314378	LN870	LN	All class V
SA314379	LN925	LN	All class V
SA314380	LN473	LN	All class V
SA314381	LN893	LN	Pure class III/IV
SA314382	LN818	LN	Pure class III/IV
SA314383	LN809	LN	Pure class III/IV
SA314384	LN828	LN	Pure class III/IV
SA314385	LN845	LN	Pure class III/IV
SA314386	LN855	LN	Pure class III/IV
SA314387	LN886	LN	Pure class III/IV
SA314388	LN5	LN	Pure class III/IV
SA314389	LN74	LN	Pure class III/IV
SA314390	LN699	LN	Pure class III/IV
SA314391	LN803	LN	Pure class III/IV
SA314392	LN805	LN	Pure class III/IV
SA314393	LN834	LN	Pure class III/IV
SA314394	LN937	LN	Pure class III/IV
SA314395	LN871	LN	Pure class III/IV
SA314396	LN48	LN	Pure class III/IV
SA314397	LN405	LN	Pure class III/IV
SA314398	LN243	LN	Pure class III/IV
SA314399	LN18	LN	Pure class III/IV
SA314400	LN165	LN	Pure class III/IV
SA314401	LN276	LN	Pure class III/IV
SA314402	LN291	LN	Pure class III/IV
SA314403	LN404	LN	Pure class III/IV
SA314404	LN369	LN	Pure class III/IV
SA314405	LN123	LN	Pure class III/IV
SA314406	LN7	LN	Pure class III/IV
SA314407	LN250	LN	Pure class III/IV
SA314408	LN272	LN	Pure class III/IV
SA314409	LN249	LN	Pure class III/IV
SA314410	LN275	LN	Pure class III/IV
SA314411	LN59	LN	Pure class III/IV
SA314412	normal350796	N	N
SA314413	normal358762	N	N
SA314414	normal346675	N	N
SA314415	normal309427	N	N
SA314416	normal358797	N	N
SA314417	normal328154	N	N
SA314418	normal376701	N	N
SA314419	normal378194	N	N
SA314420	normal386006	N	N
SA314421	normal309354	N	N
SA314422	normal374393	N	N
SA314423	normal367346	N	N
SA314424	normal362875	N	N
SA314425	normal302449	N	N
SA314426	normal219541	N	N
SA314427	normal228443	N	N
SA314428	normal190667	N	N
SA314429	normal171808	N	N
SA314430	normal16799	N	N
SA314431	normal275182	N	N
SA314432	normal282901	N	N
SA314433	normal303739	N	N
SA314434	normal388793	N	N
SA314435	normal300195	N	N
SA314436	normal297429	N	N
SA314437	normal304786	N	N
SA314438	normal408913	N	N
SA314439	normal454125	N	N
SA314440	normal456977	N	N
SA314441	normal449032	N	N
SA314442	normal446904	N	N
SA314443	normal441384	N	N
SA314444	normal462020	N	N
SA314445	normal469548	N	N
SA314446	normal61921	N	N
SA314447	normal64947	N	N

Showing page 1 of 2 Results: 1 2 Next Showing results 1 to 100 of 117

Collection:

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:

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.

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 Type	ESI
MS instrument type	Triple quadrupole
MS instrument name	Waters Xevo TQ-S
Ion Mode	POSITIVE
Units	ng/ml

Chromatography:

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:

MS ID:	MS004457
Analysis ID:	AN004711
Instrument Name:	Waters Xevo TQ-S
Instrument Type:	Triple quadrupole
MS Type:	ESI
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.
Ion Mode:	POSITIVE