#METABOLOMICS WORKBENCH ywang99_20190329_125705 DATATRACK_ID:1689 STUDY_ID:ST001162 ANALYSIS_ID:AN001921 PROJECT_ID:PR000778 VERSION 1 CREATED_ON April 1, 2019, 4:02 pm #PROJECT PR:PROJECT_TITLE Evaluation of computational tools using serial mixtures of human plasma and PR:PROJECT_TITLE vegetable juice PR:PROJECT_SUMMARY Mass spectrometry-based metabolomics is developed rapidly in the past few PR:PROJECT_SUMMARY decades. There are few major vendors for LC-MS platform instruments, for PR:PROJECT_SUMMARY example, Thermo ScientificTM LTQ Orbitrap Velos and Agilent 6510 Q-TOF mass PR:PROJECT_SUMMARY spectrometer were used for metabolomics research. The data acquired cross PR:PROJECT_SUMMARY different platform are rarely compared other than the comparison of the PR:PROJECT_SUMMARY instrument itself on resolution, mass accuracy, sensitivity, dynamic range, scan PR:PROJECT_SUMMARY speed etc., which is largely due to the foundation and principle of the PR:PROJECT_SUMMARY instrument design. Other than this, there are many choice for data PR:PROJECT_SUMMARY preprocessing, i.e., the data acquired from the same platform may have been PR:PROJECT_SUMMARY processed with different feature extraction software tools. The discrepancy for PR:PROJECT_SUMMARY the feature detections with different software will lead to the variation of the PR:PROJECT_SUMMARY down-stream statistics analysis and metabolomics pathway interpretation. In PR:PROJECT_SUMMARY addition, the impact of the LC-MS platform and data preprocessing software tools PR:PROJECT_SUMMARY on the quantitative capabilities is also an interesting topic. In this research, PR:PROJECT_SUMMARY XCMS, mzMine 2.37 and apLCMS are three tools used for the feature extraction of PR:PROJECT_SUMMARY data acquired with Thermo ScientificTM LTQ Orbitrap Velos and Agilent 6510 Q-TOF PR:PROJECT_SUMMARY LC-MS platform by serial dilution experiment. The quantification capability is PR:PROJECT_SUMMARY estimated at the same time based on the linearity, accuracy, and precision. PR:INSTITUTE Emory University PR:LAST_NAME Wang PR:FIRST_NAME Yating PR:ADDRESS 615 Michael St. Ste 225, Atlanta, GA, 30322, USA PR:EMAIL yating.wang@emory.edu PR:PHONE 4047275091 #STUDY ST:STUDY_TITLE Evaluation of computational tools using serial mixtures of human plasma and ST:STUDY_TITLE vegetable juice (part - II) ST:STUDY_SUMMARY Mass spectrometry-based metabolomics is developed rapidly in the past few ST:STUDY_SUMMARY decades. There are few major vendors for LC-MS platform instruments, for ST:STUDY_SUMMARY example, Thermo ScientificTM LTQ Orbitrap Velos and Agilent 6510 Q-TOF mass ST:STUDY_SUMMARY spectrometer were used for metabolomics research. The data acquired cross ST:STUDY_SUMMARY different platform are rarely compared other than the comparison of the ST:STUDY_SUMMARY instrument itself on resolution, mass accuracy, sensitivity, dynamic range, scan ST:STUDY_SUMMARY speed etc., which is largely due to the foundation and principle of the ST:STUDY_SUMMARY instrument design. Other than this, there are many choice for data ST:STUDY_SUMMARY preprocessing, i.e., the data acquired from the same platform may have been ST:STUDY_SUMMARY processed with different feature extraction software tools. The discrepancy for ST:STUDY_SUMMARY the feature detections with different software will lead to the variation of the ST:STUDY_SUMMARY down-stream statistics analysis and metabolomics pathway interpretation. In ST:STUDY_SUMMARY addition, the impact of the LC-MS platform and data preprocessing software tools ST:STUDY_SUMMARY on the quantitative capabilities is also an interesting topic. In this research, ST:STUDY_SUMMARY XCMS, mzMine 2.37 and apLCMS are three tools used for the feature extraction of ST:STUDY_SUMMARY data acquired with Thermo ScientificTM LTQ Orbitrap Velos and Agilent 6510 Q-TOF ST:STUDY_SUMMARY LC-MS platform by serial dilution experiment. The quantification capability is ST:STUDY_SUMMARY estimated at the same time based on the linearity, accuracy, and precision. ST:INSTITUTE Emory University ST:LAST_NAME Wang ST:FIRST_NAME Yating ST:ADDRESS 615 Michael St. Ste 225, Atlanta, GA, 30322, USA ST:EMAIL yating.wang@emory.edu ST:PHONE 4047275091 #SUBJECT SU:SUBJECT_TYPE Other SU:SUBJECT_SPECIES Homo sapiens #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS Pure vegetable juice 0-1_100v8 Sample.Composition:food SUBJECT_SAMPLE_FACTORS Mixture of vegetable juice and plasma 0-2_1024_1_vq Sample.Composition:food and human plasma SUBJECT_SAMPLE_FACTORS Mixture of vegetable juice and plasma 0-3_256_1_vq Sample.Composition:food and human plasma SUBJECT_SAMPLE_FACTORS Mixture of vegetable juice and plasma 0-4_64_1_vq Sample.Composition:food and human plasma SUBJECT_SAMPLE_FACTORS Mixture of vegetable juice and plasma 0-5_16_1_vq Sample.Composition:food and human plasma SUBJECT_SAMPLE_FACTORS Mixture of vegetable juice and plasma 0-6_4_1_vq Sample.Composition:food and human plasma SUBJECT_SAMPLE_FACTORS Mixture of vegetable juice and plasma 0-7_1_1_vq Sample.Composition:food and human plasma SUBJECT_SAMPLE_FACTORS Mixture of vegetable juice and plasma 0-8_1_4_vq Sample.Composition:food and human plasma SUBJECT_SAMPLE_FACTORS Mixture of vegetable juice and plasma 0-9_1_16_vq Sample.Composition:food and human plasma SUBJECT_SAMPLE_FACTORS Mixture of vegetable juice and plasma 0-10_1_64_vq Sample.Composition:food and human plasma SUBJECT_SAMPLE_FACTORS Mixture of vegetable juice and plasma 0-11_1_256_vq Sample.Composition:food and human plasma SUBJECT_SAMPLE_FACTORS Mixture of vegetable juice and plasma 0-12_1_1024_vq Sample.Composition:food and human plasma SUBJECT_SAMPLE_FACTORS Pure plasma 0-13_100q3 Sample.Composition:human plasma #COLLECTION CO:COLLECTION_SUMMARY Commercially available CO:SAMPLE_TYPE Blood (plasma) #TREATMENT TR:TREATMENT_SUMMARY Samples were prepared by mixing commercially available vegetable juice and human TR:TREATMENT_SUMMARY plsama Qstandard. Smaples were mixed in the ratio of vegetable jucie to plasma TR:TREATMENT_SUMMARY at 1024:1, 256:1,64:1, 16:1, 4:1, 1:1, 1:4, 1:16, 1:256, 1:1024. Prior to TR:TREATMENT_SUMMARY analysis, samples were stored in -80 degree C. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Samples were prepared for metabolomics analysis using established SP:SAMPLEPREP_SUMMARY methods(Johnson et al. (2010). Analyst; Go et al. (2015). Tox Sci). Prior to SP:SAMPLEPREP_SUMMARY analysis, plasma aliquots were removed from storage at -80 degrees C and thawed SP:SAMPLEPREP_SUMMARY on ice. Each cryotube was then vortexed briefly to ensure homogeneity, and 50 SP:SAMPLEPREP_SUMMARY microliters was transferred to a clean microfuge tube. Immediately after, the SP:SAMPLEPREP_SUMMARY plasma was treated with 100 microliters of ice-cold LC-MS grade SP:SAMPLEPREP_SUMMARY acetonitrile(Sigma Aldrich) containing 2.5 microliters of internal standard SP:SAMPLEPREP_SUMMARY solution with eleven stable isotopic chemicals selected to cover a range of SP:SAMPLEPREP_SUMMARY chemical properties. Following addition of acetonitrile, samples were SP:SAMPLEPREP_SUMMARY equilibrated for 30 min on ice, upon which precipitated proteins were removed by SP:SAMPLEPREP_SUMMARY centrifuge (14,000rpm at 4 degrees C for 10 min). The resulting supernatant (100 SP:SAMPLEPREP_SUMMARY microliters) was removed, added to a low volume autosampler vial and maintained SP:SAMPLEPREP_SUMMARY at 4 degrees C until analysis (<22 h). #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE HILIC CH:INSTRUMENT_NAME Agilent 6560 CH:COLUMN_NAME Waters XBridge Amide (100 x 4.6mm, 3.5um) #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Agilent 6560 Ion Mobility MS:INSTRUMENT_TYPE QTOF MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS Convert to mzXML format using MSConvert; XCMS R package was used to extract MS:MS_COMMENTS feature table MS:MS_RESULTS_FILE ST001162_AN001921_Results.txt UNITS:Peak Area Has m/z:Yes Has RT:Yes RT units:Seconds #END