Summary of Study ST001450

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 PR000996. The data can be accessed directly via it's Project DOI: 10.21228/M8Z692 This work is supported by NIH grant, U2C- DK119886.

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

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Study ID	ST001450
Study Title	Five Easy Metrics of Data Quality for LC-MS based Global Metabolomics
Study Summary	Data quality in global metabolomics is of great importance for biomarker discovery and systems biology studies. However, comprehensive metrics and methods to evaluate and compare the data quality of global metabolomics data sets are lacking. In this work, we combine newly developed metrics, along with well-known measures, to comprehensively and quantitatively characterize the data quality across two similar LC-MS platforms, with the goal of providing an efficient and improved ability to evaluate the data quality in global metabolite profiling experiments. A pooled human serum sample was run 50 times on two high-resolution LC-QTOF-MS platforms to provide profile and centroid MS data. These data were processed using Progenesis Qi software and then analyzed using five important data quality measures, including retention time drift, compound coverage, missing values and MS reproducibility (2 measures). The coverage was fit to a Gamma distribution versus compound abundance, which was normalized to allow comparison of different platforms. To evaluate missing values, characteristic curves were obtained by plotting the compound detection percentage versus extraction frequency. To characterize reproducibility, the accumulative coefficient of variation (CV) versus percentage of total compounds detected and CV vs intra-class correlation coefficient (ICC) were investigated. Key findings include significantly better performance using profile mode data compared to centroid mode as well quantitatively better performance from the newer, higher resolution instrument. A summary of the results given in tabulated form gives a snapshot of the experimental results and provides a template to evaluate the global metabolite profiling workflow. In total, these measures give a good overall view of data quality in global profiling and allow comparisons of data acquisition strategies and platforms as well as optimization of parameters.
Institute	University of Washington
Department	Anesthesiology and Pain
Laboratory	Daniel Raftery
Last Name	Zhang
First Name	Xinyu
Address	850 Republican Street, Seattle, Washington 98109, United States
Email	xinyu.z@live.com
Phone	850-567-2757
Submit Date	2020-08-18
Raw Data Available	Yes
Raw Data File Type(s)	d
Analysis Type Detail	LC-MS
Release Date	2020-09-10
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR000996
Project DOI:	doi: 10.21228/M8Z692
Project Title:	Five Easy Metrics of Data Quality for LC-MS based Global Metabolomics
Project Type:	MS global profiling
Project Summary:	Data quality in global metabolomics is of great importance for biomarker discovery and systems biology studies. However, comprehensive metrics and methods to evaluate and compare the data quality of global metabolomics data sets are lacking. In this work, we combine newly developed metrics, along with well-known measures, to comprehensively and quantitatively characterize the data quality across two similar LC-MS platforms, with the goal of providing an efficient and improved ability to evaluate the data quality in global metabolite profiling experiments. A pooled human serum sample was run 50 times on two high-resolution LC-QTOF-MS platforms to provide profile and centroid MS data. These data were processed using Progenesis Qi software and then analyzed using five important data quality measures, including retention time drift, compound coverage, missing values and MS reproducibility (2 measures). The coverage was fit to a Gamma distribution versus compound abundance, which was normalized to allow comparison of different platforms. To evaluate missing values, characteristic curves were obtained by plotting the compound detection percentage versus extraction frequency. To characterize reproducibility, the accumulative coefficient of variation (CV) versus percentage of total compounds detected and CV vs intra-class correlation coefficient (ICC) were investigated. Key findings include significantly better performance using profile mode data compared to centroid mode as well quantitatively better performance from the newer, higher resolution instrument. A summary of the results given in tabulated form gives a snapshot of the experimental results and provides a template to evaluate the global metabolite profiling workflow. In total, these measures give a good overall view of data quality in global profiling and allow comparisons of data acquisition strategies and platforms as well as optimization of parameters.
Institute:	University of Washington
Department:	Anesthesiology and Pain
Laboratory:	Daniel Raftery
Last Name:	Zhang
First Name:	Xinyu
Address:	850 Republican Street, Seattle, WA, 98109, USA
Email:	xinyu.z@live.com
Phone:	8505672757

Subject:

Subject ID:	SU001524
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	Data type
SA123799	67	Agilent 6520 centroid data
SA123800	68	Agilent 6520 centroid data
SA123801	66	Agilent 6520 centroid data
SA123802	65	Agilent 6520 centroid data
SA123803	64	Agilent 6520 centroid data
SA123804	69	Agilent 6520 centroid data
SA123805	70	Agilent 6520 centroid data
SA123806	74	Agilent 6520 centroid data
SA123807	73	Agilent 6520 centroid data
SA123808	72	Agilent 6520 centroid data
SA123809	71	Agilent 6520 centroid data
SA123810	63	Agilent 6520 centroid data
SA123811	62	Agilent 6520 centroid data
SA123812	55	Agilent 6520 centroid data
SA123813	54	Agilent 6520 centroid data
SA123814	53	Agilent 6520 centroid data
SA123815	52	Agilent 6520 centroid data
SA123816	56	Agilent 6520 centroid data
SA123817	57	Agilent 6520 centroid data
SA123818	61	Agilent 6520 centroid data
SA123819	60	Agilent 6520 centroid data
SA123820	59	Agilent 6520 centroid data
SA123821	58	Agilent 6520 centroid data
SA123822	75	Agilent 6520 centroid data
SA123823	78	Agilent 6520 centroid data
SA123824	93	Agilent 6520 centroid data
SA123825	94	Agilent 6520 centroid data
SA123826	92	Agilent 6520 centroid data
SA123827	91	Agilent 6520 centroid data
SA123828	90	Agilent 6520 centroid data
SA123829	95	Agilent 6520 centroid data
SA123830	96	Agilent 6520 centroid data
SA123831	100	Agilent 6520 centroid data
SA123832	99	Agilent 6520 centroid data
SA123833	98	Agilent 6520 centroid data
SA123834	97	Agilent 6520 centroid data
SA123835	89	Agilent 6520 centroid data
SA123836	88	Agilent 6520 centroid data
SA123837	81	Agilent 6520 centroid data
SA123838	80	Agilent 6520 centroid data
SA123839	79	Agilent 6520 centroid data
SA123840	51	Agilent 6520 centroid data
SA123841	82	Agilent 6520 centroid data
SA123842	83	Agilent 6520 centroid data
SA123843	87	Agilent 6520 centroid data
SA123844	86	Agilent 6520 centroid data
SA123845	85	Agilent 6520 centroid data
SA123846	84	Agilent 6520 centroid data
SA123847	77	Agilent 6520 centroid data
SA123848	76	Agilent 6520 centroid data
SA123849	17	Agilent 6520 profile data
SA123850	18	Agilent 6520 profile data
SA123851	16	Agilent 6520 profile data
SA123852	15	Agilent 6520 profile data
SA123853	14	Agilent 6520 profile data
SA123854	19	Agilent 6520 profile data
SA123855	20	Agilent 6520 profile data
SA123856	24	Agilent 6520 profile data
SA123857	23	Agilent 6520 profile data
SA123858	22	Agilent 6520 profile data
SA123859	21	Agilent 6520 profile data
SA123860	13	Agilent 6520 profile data
SA123861	12	Agilent 6520 profile data
SA123862	4	Agilent 6520 profile data
SA123863	5	Agilent 6520 profile data
SA123864	3	Agilent 6520 profile data
SA123865	50	Agilent 6520 profile data
SA123866	2	Agilent 6520 profile data
SA123867	6	Agilent 6520 profile data
SA123868	7	Agilent 6520 profile data
SA123869	11	Agilent 6520 profile data
SA123870	10	Agilent 6520 profile data
SA123871	9	Agilent 6520 profile data
SA123872	8	Agilent 6520 profile data
SA123873	25	Agilent 6520 profile data
SA123874	1	Agilent 6520 profile data
SA123875	42	Agilent 6520 profile data
SA123876	43	Agilent 6520 profile data
SA123877	41	Agilent 6520 profile data
SA123878	40	Agilent 6520 profile data
SA123879	39	Agilent 6520 profile data
SA123880	44	Agilent 6520 profile data
SA123881	45	Agilent 6520 profile data
SA123882	26	Agilent 6520 profile data
SA123883	48	Agilent 6520 profile data
SA123884	47	Agilent 6520 profile data
SA123885	46	Agilent 6520 profile data
SA123886	38	Agilent 6520 profile data
SA123887	49	Agilent 6520 profile data
SA123888	37	Agilent 6520 profile data
SA123889	29	Agilent 6520 profile data
SA123890	28	Agilent 6520 profile data
SA123891	27	Agilent 6520 profile data
SA123892	31	Agilent 6520 profile data
SA123893	30	Agilent 6520 profile data
SA123894	32	Agilent 6520 profile data
SA123895	35	Agilent 6520 profile data
SA123896	36	Agilent 6520 profile data
SA123897	34	Agilent 6520 profile data
SA123898	33	Agilent 6520 profile data

Showing page 1 of 2 Results: 1 2 Next Showing results 1 to 100 of 200

Collection:

Collection ID:	CO001519
Collection Summary:	Human serum was frozen at -80 C.
Sample Type:	Blood (serum)

Treatment:

Treatment ID:	TR001539
Treatment Summary:	See sampleprep

Sample Preparation:

Sampleprep ID:	SP001532
Sampleprep Summary:	4 mL frozen commercial pooled human serum (Innovative Research, Novi, MI, USA) was thawed at 4 °C, vortexed and aliquoted into 50 µL portions in 2 mL Eppendorf vials. Every 50 µL portion was mixed with 250 µL cold methanol and vortexed to precipitate proteins.38 After 20 min incubation at −20 °C, these mixtures were centrifuged at 20,800 x g for 10 min at 4 °C. The supernatants were transferred into clean 2.0 mL Eppendorf vials and then dried in an Eppendorf Vacufuge (Brinkmann Instruments, Westbury, NY, USA). The residue in each Eppendorf vial was reconstituted in 50 µL H2O:ACN (2:3 v/v), vortexed and centrifuged at 20,800 x g for 10 min at 4 °C. The supernatant in all Eppendorf vials was pooled into a 5 mL Eppendorf vial, vortexed and centrifuged at xx,xxx x g (To Dan: I should have used 5000 rpm or a typical rpm in the big centrifuge in the biosample prep lab) for 10 min at 4 °C to further remove any solid residue. The resultant supernatant was aliquoted into 50 µL portions in 1.5 mL Eppendorf vials and stored at −80 °C. Prior to repeated injections to LC-MS in this work, 8 portions were diluted to 200 µL each with H2O:ACN (2:3 v/v), pooled into a 2 mL LC vial and vortexed.

Sampleprep ID:

SP001532

Sampleprep Summary:

4 mL frozen commercial pooled human serum (Innovative Research, Novi, MI, USA) was thawed at 4 °C, vortexed and aliquoted into 50 µL portions in 2 mL Eppendorf vials. Every 50 µL portion was mixed with 250 µL cold methanol and vortexed to precipitate proteins.38 After 20 min incubation at −20 °C, these mixtures were centrifuged at 20,800 x g for 10 min at 4 °C. The supernatants were transferred into clean 2.0 mL Eppendorf vials and then dried in an Eppendorf Vacufuge (Brinkmann Instruments, Westbury, NY, USA). The residue in each Eppendorf vial was reconstituted in 50 µL H2O:ACN (2:3 v/v), vortexed and centrifuged at 20,800 x g for 10 min at 4 °C. The supernatant in all Eppendorf vials was pooled into a 5 mL Eppendorf vial, vortexed and centrifuged at xx,xxx x g (To Dan: I should have used 5000 rpm or a typical rpm in the big centrifuge in the biosample prep lab) for 10 min at 4 °C to further remove any solid residue. The resultant supernatant was aliquoted into 50 µL portions in 1.5 mL Eppendorf vials and stored at −80 °C. Prior to repeated injections to LC-MS in this work, 8 portions were diluted to 200 µL each with H2O:ACN (2:3 v/v), pooled into a 2 mL LC vial and vortexed.

Combined analysis:

Analysis ID	AN002421	AN002422	AN002423	AN002424
Analysis type	MS	MS	MS	MS
Chromatography type	HILIC	HILIC	HILIC	HILIC
Chromatography system	Agilent 1260 Infinity	Agilent 1260 Infinity	Agilent 1290 Infinity	Agilent 1290 Infinity
Column	Waters XBridge BEH Amide (15 cm x 2.1mm,2.5um)	Waters XBridge BEH Amide (15 cm x 2.1mm,2.5um)	Waters XBridge BEH Amide (15 cm x 2.1mm,2.5um)	Waters XBridge BEH Amide (15 cm x 2.1mm,2.5um)
MS Type	ESI	ESI	ESI	ESI
MS instrument type	QTOF	QTOF	QTOF	QTOF
MS instrument name	Agilent 6520 QTOF	Agilent 6520 QTOF	Agilent 6545 QTOF	Agilent 6545 QTOF
Ion Mode	POSITIVE	POSITIVE	POSITIVE	POSITIVE
Units	Peak area	Peak area	Peak area	Peak area

Chromatography:

Chromatography ID:	CH001778
Chromatography Summary:	The mobile phase consisted of (A) H2O:ACN (95:5, v/v) with 5 mM ammonium acetate and 0.1% acetic acid, and (B) H2O:ACN (5:95, v/v), 5 mM ammonium acetate and 0.1% acetic acid. Gradient elution was performed as follows: 100% mobile phase B for 1.5 min, 100 to 78% B from 1.5-6.0 min, 78 to 50% B from 6.0-9.0 min, 50% B from 9.0-15.0 min, restoration to 100% B from 15.0-17.0 min, and continued 100% B from 17.0-30.0 to equilibrate the LC column. The flow rate was 0.3 mL/min, the injection volume was 5 µL, followed by an H2O:ACN (5:95, v/v) needle wash for 10 s, and the column temperature was 35 oC.
Instrument Name:	Agilent 1260 Infinity
Column Name:	Waters XBridge BEH Amide (15 cm x 2.1mm,2.5um)
Column Temperature:	35
Flow Gradient:	100% mobile phase B for 1.5 min, 100 to 78% B from 1.5-6.0 min, 78 to 50% B from 6.0-9.0 min, 50% B from 9.0-15.0 min, restoration to 100% B from 15.0-17.0 min, and continued 100% B from 17.0-30.0 to equilibrate the LC column.
Flow Rate:	0.3 mL/min
Solvent A:	95% water/5% acetonitrile; 0.1% acetic acid; 5 mM ammonium acetate
Solvent B:	5% water/95% acetonitrile; 0.1% acetic acid; 5 mM ammonium acetate
Chromatography Type:	HILIC

Chromatography ID:	CH001779
Chromatography Summary:	The mobile phase consisted of (A) H2O:ACN (95:5, v/v) with 5 mM ammonium acetate and 0.1% acetic acid, and (B) H2O:ACN (5:95, v/v), 5 mM ammonium acetate and 0.1% acetic acid. Gradient elution was performed as follows: 100% mobile phase B for 1.5 min, 100 to 78% B from 1.5-6.0 min, 78 to 50% B from 6.0-9.0 min, 50% B from 9.0-15.0 min, restoration to 100% B from 15.0-17.0 min, and continued 100% B from 17.0-30.0 to equilibrate the LC column. The flow rate was 0.3 mL/min, the injection volume was 5 µL, followed by an H2O:ACN (5:95, v/v) needle wash for 10 s, and the column temperature was 35 oC.
Instrument Name:	Agilent 1260 Infinity
Column Name:	Waters XBridge BEH Amide (15 cm x 2.1mm,2.5um)
Column Temperature:	35
Flow Gradient:	100% mobile phase B for 1.5 min, 100 to 78% B from 1.5-6.0 min, 78 to 50% B from 6.0-9.0 min, 50% B from 9.0-15.0 min, restoration to 100% B from 15.0-17.0 min, and continued 100% B from 17.0-30.0 to equilibrate the LC column.
Flow Rate:	0.3 mL/min
Solvent A:	95% water/5% acetonitrile; 0.1% acetic acid; 5 mM ammonium acetate
Solvent B:	5% water/95% acetonitrile; 0.1% acetic acid; 5 mM ammonium acetate
Chromatography Type:	HILIC

Chromatography ID:	CH001780
Chromatography Summary:	The mobile phase consisted of (A) H2O:ACN (95:5, v/v) with 5 mM ammonium acetate and 0.1% acetic acid, and (B) H2O:ACN (5:95, v/v), 5 mM ammonium acetate and 0.1% acetic acid. Gradient elution was performed as follows: 100% mobile phase B for 1.5 min, 100 to 78% B from 1.5-6.0 min, 78 to 50% B from 6.0-9.0 min, 50% B from 9.0-15.0 min, restoration to 100% B from 15.0-17.0 min, and continued 100% B from 17.0-30.0 to equilibrate the LC column. The flow rate was 0.3 mL/min, the injection volume was 5 µL, followed by an H2O:ACN (5:95, v/v) needle wash for 10 s, and the column temperature was 35 oC.
Instrument Name:	Agilent 1290 Infinity
Column Name:	Waters XBridge BEH Amide (15 cm x 2.1mm,2.5um)
Column Temperature:	35
Flow Gradient:	100% mobile phase B for 1.5 min, 100 to 78% B from 1.5-6.0 min, 78 to 50% B from 6.0-9.0 min, 50% B from 9.0-15.0 min, restoration to 100% B from 15.0-17.0 min, and continued 100% B from 17.0-30.0 to equilibrate the LC column.
Flow Rate:	0.3 mL/min
Solvent A:	95% water/5% acetonitrile; 0.1% acetic acid; 5 mM ammonium acetate
Solvent B:	5% water/95% acetonitrile; 0.1% acetic acid; 5 mM ammonium acetate
Chromatography Type:	HILIC

Chromatography ID:	CH001781
Chromatography Summary:	The mobile phase consisted of (A) H2O:ACN (95:5, v/v) with 5 mM ammonium acetate and 0.1% acetic acid, and (B) H2O:ACN (5:95, v/v), 5 mM ammonium acetate and 0.1% acetic acid. Gradient elution was performed as follows: 100% mobile phase B for 1.5 min, 100 to 78% B from 1.5-6.0 min, 78 to 50% B from 6.0-9.0 min, 50% B from 9.0-15.0 min, restoration to 100% B from 15.0-17.0 min, and continued 100% B from 17.0-30.0 to equilibrate the LC column. The flow rate was 0.3 mL/min, the injection volume was 5 µL, followed by an H2O:ACN (5:95, v/v) needle wash for 10 s, and the column temperature was 35 oC.
Instrument Name:	Agilent 1290 Infinity
Column Name:	Waters XBridge BEH Amide (15 cm x 2.1mm,2.5um)
Column Temperature:	35
Flow Gradient:	100% mobile phase B for 1.5 min, 100 to 78% B from 1.5-6.0 min, 78 to 50% B from 6.0-9.0 min, 50% B from 9.0-15.0 min, restoration to 100% B from 15.0-17.0 min, and continued 100% B from 17.0-30.0 to equilibrate the LC column.
Flow Rate:	0.3 mL/min
Solvent A:	95% water/5% acetonitrile; 0.1% acetic acid; 5 mM ammonium acetate
Solvent B:	5% water/95% acetonitrile; 0.1% acetic acid; 5 mM ammonium acetate
Chromatography Type:	HILIC

MS:

MS ID:	MS002258
Analysis ID:	AN002421
Instrument Name:	Agilent 6520 QTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	The ESI conditions were as follows: Electrospray ion source ESI Agilent Jet Stream Technology in positive ionization mode; voltage 3.8 kV; desolvation temperature 325 °C; cone flow 20 L/h; desolvation gas flow 600 L/h; nebulizer pressure 45 psi, N2 drying gas; MS scan rate of 1.03 spectra/s across the range m/z 60-1000. The software, Progenesis Qi, was used to process raw data. In the results, every compound (feature) had at least two ions, like an ion and its isotope ion or adduct ion. Compounds with single ions were filtered out. If a compound had m/z information only, the m/z was directly used in the compound name. If a compound had neutral mass information, the neutral mass was converted to m/z.
Ion Mode:	POSITIVE

MS ID:	MS002259
Analysis ID:	AN002422
Instrument Name:	Agilent 6520 QTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	The ESI conditions were as follows: Electrospray ion source ESI Agilent Jet Stream Technology in positive ionization mode; voltage 3.8 kV; desolvation temperature 325 °C; cone flow 20 L/h; desolvation gas flow 600 L/h; nebulizer pressure 45 psi, N2 drying gas; MS scan rate of 1.03 spectra/s across the range m/z 60-1000. The software, Progenesis Qi, was used to process raw data. In the results, every compound (feature) had at least two ions, like an ion and its isotope ion or adduct ion. Compounds with single ions were filtered out. If a compound had m/z information only, the m/z was directly used in the compound name. If a compound had neutral mass information, the neutral mass was converted to m/z.
Ion Mode:	POSITIVE

MS ID:	MS002260
Analysis ID:	AN002423
Instrument Name:	Agilent 6545 QTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	(Agilent 6545) MS scan rate of 1.03 spectra/s across the range m/z 60-1000. The software, Progenesis Qi, was used to process raw data. In the results, every compound (feature) had at least two ions, like an ion and its isotope ion or adduct ion. Compounds with single ions were filtered out. If a compound had m/z information only, the m/z was directly used in the compound name. If a compound had neutral mass information, the neutral mass was converted to m/z.
Ion Mode:	POSITIVE

MS ID:	MS002261
Analysis ID:	AN002424
Instrument Name:	Agilent 6545 QTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	(Agilent 6545) MS scan rate of 1.03 spectra/s across the range m/z 60-1000. The software, Progenesis Qi, was used to process raw data. In the results, every compound (feature) had at least two ions, like an ion and its isotope ion or adduct ion. Compounds with single ions were filtered out. If a compound had m/z information only, the m/z was directly used in the compound name. If a compound had neutral mass information, the neutral mass was converted to m/z.
Ion Mode:	POSITIVE