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"PROJECT":{"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"},

"STUDY":{"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"},

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"Additional sample data":{"RAW_FILE_NAME":"135"}
},
{
"Subject ID":"-",
"Sample ID":"136",
"Factors":{"Data type":"Agilent 6545 profile data"},
"Additional sample data":{"RAW_FILE_NAME":"136"}
},
{
"Subject ID":"-",
"Sample ID":"137",
"Factors":{"Data type":"Agilent 6545 profile data"},
"Additional sample data":{"RAW_FILE_NAME":"137"}
},
{
"Subject ID":"-",
"Sample ID":"138",
"Factors":{"Data type":"Agilent 6545 profile data"},
"Additional sample data":{"RAW_FILE_NAME":"138"}
},
{
"Subject ID":"-",
"Sample ID":"139",
"Factors":{"Data type":"Agilent 6545 profile data"},
"Additional sample data":{"RAW_FILE_NAME":"139"}
},
{
"Subject ID":"-",
"Sample ID":"140",
"Factors":{"Data type":"Agilent 6545 profile data"},
"Additional sample data":{"RAW_FILE_NAME":"140"}
},
{
"Subject ID":"-",
"Sample ID":"141",
"Factors":{"Data type":"Agilent 6545 profile data"},
"Additional sample data":{"RAW_FILE_NAME":"141"}
},
{
"Subject ID":"-",
"Sample ID":"142",
"Factors":{"Data type":"Agilent 6545 profile data"},
"Additional sample data":{"RAW_FILE_NAME":"142"}
},
{
"Subject ID":"-",
"Sample ID":"143",
"Factors":{"Data type":"Agilent 6545 profile data"},
"Additional sample data":{"RAW_FILE_NAME":"143"}
},
{
"Subject ID":"-",
"Sample ID":"144",
"Factors":{"Data type":"Agilent 6545 profile data"},
"Additional sample data":{"RAW_FILE_NAME":"144"}
},
{
"Subject ID":"-",
"Sample ID":"145",
"Factors":{"Data type":"Agilent 6545 profile data"},
"Additional sample data":{"RAW_FILE_NAME":"145"}
},
{
"Subject ID":"-",
"Sample ID":"146",
"Factors":{"Data type":"Agilent 6545 profile data"},
"Additional sample data":{"RAW_FILE_NAME":"146"}
},
{
"Subject ID":"-",
"Sample ID":"147",
"Factors":{"Data type":"Agilent 6545 profile data"},
"Additional sample data":{"RAW_FILE_NAME":"147"}
},
{
"Subject ID":"-",
"Sample ID":"148",
"Factors":{"Data type":"Agilent 6545 profile data"},
"Additional sample data":{"RAW_FILE_NAME":"148"}
},
{
"Subject ID":"-",
"Sample ID":"149",
"Factors":{"Data type":"Agilent 6545 profile data"},
"Additional sample data":{"RAW_FILE_NAME":"149"}
},
{
"Subject ID":"-",
"Sample ID":"150",
"Factors":{"Data type":"Agilent 6545 profile data"},
"Additional sample data":{"RAW_FILE_NAME":"150"}
},
{
"Subject ID":"-",
"Sample ID":"151",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"151"}
},
{
"Subject ID":"-",
"Sample ID":"152",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"152"}
},
{
"Subject ID":"-",
"Sample ID":"153",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"153"}
},
{
"Subject ID":"-",
"Sample ID":"154",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"154"}
},
{
"Subject ID":"-",
"Sample ID":"155",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"155"}
},
{
"Subject ID":"-",
"Sample ID":"156",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"156"}
},
{
"Subject ID":"-",
"Sample ID":"157",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"157"}
},
{
"Subject ID":"-",
"Sample ID":"158",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"158"}
},
{
"Subject ID":"-",
"Sample ID":"159",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"159"}
},
{
"Subject ID":"-",
"Sample ID":"160",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"160"}
},
{
"Subject ID":"-",
"Sample ID":"161",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"161"}
},
{
"Subject ID":"-",
"Sample ID":"162",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"162"}
},
{
"Subject ID":"-",
"Sample ID":"163",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"163"}
},
{
"Subject ID":"-",
"Sample ID":"164",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"164"}
},
{
"Subject ID":"-",
"Sample ID":"165",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"165"}
},
{
"Subject ID":"-",
"Sample ID":"166",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"166"}
},
{
"Subject ID":"-",
"Sample ID":"167",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"167"}
},
{
"Subject ID":"-",
"Sample ID":"168",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"168"}
},
{
"Subject ID":"-",
"Sample ID":"169",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"169"}
},
{
"Subject ID":"-",
"Sample ID":"170",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"170"}
},
{
"Subject ID":"-",
"Sample ID":"171",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"171"}
},
{
"Subject ID":"-",
"Sample ID":"172",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"172"}
},
{
"Subject ID":"-",
"Sample ID":"173",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"173"}
},
{
"Subject ID":"-",
"Sample ID":"174",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"174"}
},
{
"Subject ID":"-",
"Sample ID":"175",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"175"}
},
{
"Subject ID":"-",
"Sample ID":"176",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"176"}
},
{
"Subject ID":"-",
"Sample ID":"177",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"177"}
},
{
"Subject ID":"-",
"Sample ID":"178",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"178"}
},
{
"Subject ID":"-",
"Sample ID":"179",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"179"}
},
{
"Subject ID":"-",
"Sample ID":"180",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"180"}
},
{
"Subject ID":"-",
"Sample ID":"181",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"181"}
},
{
"Subject ID":"-",
"Sample ID":"182",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"182"}
},
{
"Subject ID":"-",
"Sample ID":"183",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"183"}
},
{
"Subject ID":"-",
"Sample ID":"184",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"184"}
},
{
"Subject ID":"-",
"Sample ID":"185",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"185"}
},
{
"Subject ID":"-",
"Sample ID":"186",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"186"}
},
{
"Subject ID":"-",
"Sample ID":"187",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"187"}
},
{
"Subject ID":"-",
"Sample ID":"188",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"188"}
},
{
"Subject ID":"-",
"Sample ID":"189",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"189"}
},
{
"Subject ID":"-",
"Sample ID":"190",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"190"}
},
{
"Subject ID":"-",
"Sample ID":"191",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"191"}
},
{
"Subject ID":"-",
"Sample ID":"192",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"192"}
},
{
"Subject ID":"-",
"Sample ID":"193",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"193"}
},
{
"Subject ID":"-",
"Sample ID":"194",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"194"}
},
{
"Subject ID":"-",
"Sample ID":"195",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"195"}
},
{
"Subject ID":"-",
"Sample ID":"196",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"196"}
},
{
"Subject ID":"-",
"Sample ID":"197",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"197"}
},
{
"Subject ID":"-",
"Sample ID":"198",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"198"}
},
{
"Subject ID":"-",
"Sample ID":"199",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"199"}
},
{
"Subject ID":"-",
"Sample ID":"200",
"Factors":{"Data type":"Agilent 6545 centroid data"},
"Additional sample data":{"RAW_FILE_NAME":"200"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Human serum was frozen at -80 C.","SAMPLE_TYPE":"Blood (serum)"},

"TREATMENT":{"TREATMENT_SUMMARY":"See sampleprep"},

"SAMPLEPREP":{"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."},

"CHROMATOGRAPHY":{"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.","CHROMATOGRAPHY_TYPE":"HILIC","INSTRUMENT_NAME":"Agilent 1290 Infinity","COLUMN_NAME":"Waters XBridge BEH Amide column (15 cm x 2.1 mm, 2.5 µm)"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","DATA_FORMAT":".mzxml (centroid)"},

"MS":{"INSTRUMENT_NAME":"Agilent 6545 QTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"POSITIVE","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.","MS_RESULTS_FILE":"ST001450_AN002424_Results.txt UNITS:Peak area Has m/z:Yes Has RT:Yes RT units:Minutes"}

}