Summary of Study ST002196

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 PR001400. The data can be accessed directly via it's Project DOI: 10.21228/M8RM5T 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	ST002196
Study Title	Metabolic signature of idiopathic inflammatory myopathy
Study Summary	Objective of this study was to find Metabolic signature of idiopathic inflammatory myopathy (IIM). We used the serum samples of healthy control, IIM, ankylosing spondylitis. Metabolites were quantified using biocrates p180 kit. First, we found IIM specific metabolites by using ANOVA with post-hoc analysis. With set of metabolite panel, we made prediction model using logistic regression (LR), support vector machine (SVM), and random forest (RF). We found 7 metabolites as biomarker for classifying IIM from healthy control and ankylosing spondylitis. Also, we validate our model using 5 cross validation method. Out set of metabolites showed the AUC values of 0.955 (LR), 0.908 (RF) and 0.918 (SVM).
Institute	Seoul National University
Last Name	Kang
First Name	Jihyun
Address	502ho Intergrative Biomedical Education Research Building, 101 Deahakro, Jongro-gu, Seoul, 03080, Korea, South Korea
Email	jikang@snu.ac.kr
Phone	+821071014069
Submit Date	2022-06-09
Raw Data Available	Yes
Raw Data File Type(s)	wiff
Analysis Type Detail	LC-MS
Release Date	2022-07-14
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001400
Project DOI:	doi: 10.21228/M8RM5T
Project Title:	Myositis metabolomics
Project Type:	MS quantitative analysis
Project Summary:	Targeted metabolomics study for idiopathic inflammatory myositis patients and C-protein induced myositis mouse model
Institute:	Seoul national university
Last Name:	Kang
First Name:	Jihyun
Address:	502ho Intergrative Biomedical Education Research Building, 101 Deahakro, Jongro-gu, Seoul, 03080, Korea, South
Email:	jikang@snu.ac.kr
Phone:	+821071014069

Subject:

Subject ID:	SU002282
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606

Factors:

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

mb_sample_id	local_sample_id	Factor
SA210483	67	AS
SA210484	68	AS
SA210485	70	AS
SA210486	65	AS
SA210487	69	AS
SA210488	64	AS
SA210489	61	AS
SA210490	62	AS
SA210491	63	AS
SA210492	71	AS
SA210493	72	AS
SA210494	78	AS
SA210495	79	AS
SA210496	80	AS
SA210497	77	AS
SA210498	76	AS
SA210499	73	AS
SA210500	74	AS
SA210501	75	AS
SA210502	2_61	AS
SA210503	66	AS
SA210504	2_68	AS
SA210505	2_69	AS
SA210506	2_62	AS
SA210507	2_67	AS
SA210508	2_70	AS
SA210509	2_63	AS
SA210510	2_65	AS
SA210511	2_64	AS
SA210512	2_66	AS
SA210513	2_54	Healthy control
SA210514	2_55	Healthy control
SA210515	2_56	Healthy control
SA210516	2_53	Healthy control
SA210517	2_60	Healthy control
SA210518	2_57	Healthy control
SA210519	2_58	Healthy control
SA210520	2_59	Healthy control
SA210521	2_51	Healthy control
SA210522	2_52	Healthy control
SA210523	2_49	IIM
SA210524	2_48	IIM
SA210525	2_50	IIM
SA210526	2_77	IIM
SA210527	2_73	IIM
SA210528	2_72	IIM
SA210529	2_71	IIM
SA210530	2_47	IIM
SA210531	2_74	IIM
SA210532	2_75	IIM
SA210533	2_79	IIM
SA210534	2_78	IIM
SA210535	2_76	IIM
SA210536	2_80	IIM
SA210537	2_32	IIM
SA210538	51	IIM
SA210539	50	IIM
SA210540	49	IIM
SA210541	52	IIM
SA210542	53	IIM
SA210543	55	IIM
SA210544	54	IIM
SA210545	48	IIM
SA210546	47	IIM
SA210547	42	IIM
SA210548	41	IIM
SA210549	40	IIM
SA210550	43	IIM
SA210551	44	IIM
SA210552	46	IIM
SA210553	45	IIM
SA210554	56	IIM
SA210555	57	IIM
SA210556	2_41	IIM
SA210557	2_40	IIM
SA210558	2_38	IIM
SA210559	2_42	IIM
SA210560	2_43	IIM
SA210561	2_45	IIM
SA210562	2_44	IIM
SA210563	2_36	IIM
SA210564	2_34	IIM
SA210565	60	IIM
SA210566	59	IIM
SA210567	58	IIM
SA210568	2_26	IIM
SA210569	2_28	IIM
SA210570	39	IIM
SA210571	2_30	IIM
SA210572	2_46	IIM

Showing results 1 to 90 of 90

Showing results 1 to 90 of 90

Collection:

Collection ID:	CO002275
Collection Summary:	Patients recruited for 10 years with IIM. Patients with other rheumatic disease were excluded. Healthy control and ankylosing spondylitis samples were also collected for this study. Serum was collected in Seoul national university hospital.
Sample Type:	Blood (serum)

Treatment:

Treatment ID:	TR002294
Treatment Summary:	N/A

Sample Preparation:

Sampleprep ID:	SP002288
Sampleprep Summary:	Centrifuge the calibration standards, QC, and ISTD mix vials before opening at 10 000 x g (rcf) for 2 min. Dissolve calibration standards (red caps) in 100 µL water. Dissolve QCs (green, blue and yellow caps) in 100 µL water. Dissolve ISTD mix (orange cap) in 1200 µL water. Shake all vials (Cal, QCs, ISTD) for 15 min at 1200 rpm and vortex several times. Centrifuge the QCs and your plasma samples for 5 min at 2750 x g (rcf) and 4 °C. Add 10 µL of the ISTD mix to each well of the Kit plate except A1. Pipette 10 µL PBS / Cal / QC / sample according to your plate layout generated by MetIDQTM. Dry for 30 min under nitrogen (using a Nitrogen Evaporator or a Pressure Manifold). Prepare the pre-mix for derivatization in the plastic tube of the Kit box (1900 µL of each: ethanol, water and pyridine). Add 300 µL phenylisothiocyanate (PITC) and vortex rigorously (at least 10 sec) until the derivatization solution is clear. Make half of the solution for the starter kit. Add 50 µL of the derivatization solution to each well using a repeater at maximum dispensing speed. Cover the plate with the plastic lid and incubate for 25 min, then dry for 60 min under nitrogen. Prepare extraction solvent and add 300 µL to each well. You can use the repeater at low dispensing speed or an 8-channel pipette. Shake for 30 min at 450 rpm (on the scale of min-max 0-1400 rpm). Centrifuge for 2 min at 500 x g (rcf) or use a Pressure Manifold. Visually check that the fill level is the same in all wells of the capture plate. If not, repeat and apply higher g or higher pressure, respectively. Carefully remove the upper filter plate and transfer the volume specified for your instrument to another empty 96-deep well plate that you find in the Kit box (label “LC plate”). Use an 8-channel pipette. Finish the LC plate and dilute the extracts as described for your instrument Prepare the FIA plate and dilute the original extracts as described for your instrument Seal both plates with the silicon mat. Firmly press the mat’s naps into the wells. Shake both plates for 2 min at 600 rpm. Put the plates in the autosampler.

Sampleprep ID:

SP002288

Sampleprep Summary:

Centrifuge the calibration standards, QC, and ISTD mix vials before opening at 10 000 x g (rcf) for 2 min. Dissolve calibration standards (red caps) in 100 µL water. Dissolve QCs (green, blue and yellow caps) in 100 µL water. Dissolve ISTD mix (orange cap) in 1200 µL water. Shake all vials (Cal, QCs, ISTD) for 15 min at 1200 rpm and vortex several times. Centrifuge the QCs and your plasma samples for 5 min at 2750 x g (rcf) and 4 °C. Add 10 µL of the ISTD mix to each well of the Kit plate except A1. Pipette 10 µL PBS / Cal / QC / sample according to your plate layout generated by MetIDQTM. Dry for 30 min under nitrogen (using a Nitrogen Evaporator or a Pressure Manifold). Prepare the pre-mix for derivatization in the plastic tube of the Kit box (1900 µL of each: ethanol, water and pyridine). Add 300 µL phenylisothiocyanate (PITC) and vortex rigorously (at least 10 sec) until the derivatization solution is clear. Make half of the solution for the starter kit. Add 50 µL of the derivatization solution to each well using a repeater at maximum dispensing speed. Cover the plate with the plastic lid and incubate for 25 min, then dry for 60 min under nitrogen. Prepare extraction solvent and add 300 µL to each well. You can use the repeater at low dispensing speed or an 8-channel pipette. Shake for 30 min at 450 rpm (on the scale of min-max 0-1400 rpm). Centrifuge for 2 min at 500 x g (rcf) or use a Pressure Manifold. Visually check that the fill level is the same in all wells of the capture plate. If not, repeat and apply higher g or higher pressure, respectively. Carefully remove the upper filter plate and transfer the volume specified for your instrument to another empty 96-deep well plate that you find in the Kit box (label “LC plate”). Use an 8-channel pipette. Finish the LC plate and dilute the extracts as described for your instrument Prepare the FIA plate and dilute the original extracts as described for your instrument Seal both plates with the silicon mat. Firmly press the mat’s naps into the wells. Shake both plates for 2 min at 600 rpm. Put the plates in the autosampler.

Combined analysis:

Analysis ID	AN003595
Analysis type	MS
Chromatography type	Reversed phase
Chromatography system	AB SCIEX QTRAP 5500
Column	Waters ACQUITY UPLC BEH C18 (75 x 2.1mm,1.7um)
MS Type	ESI
MS instrument type	QTRAP
MS instrument name	ABI Sciex 5500 QTrap
Ion Mode	POSITIVE
Units	ng/mL

Chromatography:

Chromatography ID:	CH002656
Instrument Name:	AB SCIEX QTRAP 5500
Column Name:	Waters ACQUITY UPLC BEH C18 (75 x 2.1mm,1.7um)
Solvent A:	100% water; 0.2% formic acid
Solvent B:	100% acetonitrile; 0.2% formic acid
Chromatography Type:	Reversed phase

MS:

MS ID:	MS003350
Analysis ID:	AN003595
Instrument Name:	ABI Sciex 5500 QTrap
Instrument Type:	QTRAP
MS Type:	ESI
MS Comments:	For LC part: Mobile phase A: 1000 mL water + 2 mL formic acid (FA) Mobile phase B: 500 mL ACN + 1 mL FA Wash solvent 1: 500 mL ACN + 200 mL MeOH + 150 mL iPrOH + 150 mL water + 2.5 mL FA Wash solvent 2: water Install column and precolumn (if required). Wash the column at 95% B and condition to 100% For FIA part: Deactivate “Use flat files for scan data” in the Analyst software FIA mobile phase: FIA Mobile Phase Additive (1x glass ampule) + 290 mL MeOH Wash solvent 1: 500 mL ACN + 200 mL MeOH + 150 mL iPrOH + 150 mL water + 2.5 mL FA Wash solvent 2 (if possible): 333 mL MeOH + 333 mL iPrOH + 333 mL water For data processing: Adjust the retention times in the quantitation method and if necessary some integration parameters. Process the LC-MS data using the Quantitation Wizard. Save the results. Import the results export (TXT file) into MetIDQTM  Parse the FIA-MS WIFF files directly into MetIDQTM. Evaluate results, perform statistics (e.g. using MetaboINDICATOR™, StatPack, MetaboAnalyst).
Ion Mode:	POSITIVE