#METABOLOMICS WORKBENCH xia_lab_20230726_140432 DATATRACK_ID:4187 STUDY_ID:ST002798 ANALYSIS_ID:AN004552 VERSION 1 CREATED_ON 07-27-2023 #PROJECT PR:PROJECT_TITLE MetaboAnalystR 4.0: towards a unified LC-MS workflow for global metabolomics PR:PROJECT_TYPE MS/MS qualification and MS quantification study PR:PROJECT_SUMMARY Here we introduce MetaboAnalystR 4.0, an open-source R package that have been PR:PROJECT_SUMMARY developed to provide a unified workflow to help address three key bioinformatics PR:PROJECT_SUMMARY bottlenecks facing LC-MS-based global metabolomics, including: 1) auto-optimized PR:PROJECT_SUMMARY LC-MS spectral processing for feature detection and quantification; 2) PR:PROJECT_SUMMARY streamlined MS/MS spectral deconvolution and compound annotation coupled with PR:PROJECT_SUMMARY comprehensive spectral reference databases (~1.5 million MS2 spectra); 3) a PR:PROJECT_SUMMARY sensitive functional interpretation module for functional analysis directly from PR:PROJECT_SUMMARY LC-MS and MS/MS results. During our validation case studies in comparison with PR:PROJECT_SUMMARY other well-established approaches, MetaboAnalystR 4.0 has identified > 10% PR:PROJECT_SUMMARY more high-quality MS and MS/MS features; it has also significantly increased PR:PROJECT_SUMMARY true positive rate of identification (> 40%) without increasing false PR:PROJECT_SUMMARY positives using both data-dependent acquisition (DDA) and data-independent PR:PROJECT_SUMMARY acquisition (DIA) datasets; finally, pathway enrichment analysis integrating PR:PROJECT_SUMMARY LC-MS and MS/MS spectra from COVID-19 datasets has produced results that are PR:PROJECT_SUMMARY better aligned with literature report. PR:INSTITUTE McGill University PR:DEPARTMENT Faculty of Agricultural and Environmental Sciences PR:LABORATORY Xia Lab, Institute of Parasitology PR:LAST_NAME Xia PR:FIRST_NAME Jeff PR:ADDRESS Macdonald Campus, McGill University 21,111 Lakeshore Road PR:EMAIL jeff.xia@mcgill.ca PR:PHONE 5146605018 PR:FUNDING_SOURCE NIH, TIMIC, Genome Canada, Génome Québec PR:DOI http://dx.doi.org/10.21228/M88Q6W PR:CONTRIBUTORS Zhiqiang Pang, Lei Xu, Charles Viau #STUDY ST:STUDY_TITLE Evaluation of quantitative performance with serial dilutions ST:STUDY_TYPE Untargeted Metabolomics ST:STUDY_SUMMARY To benchmark the quantitative performance of MetaboAnalystR, a dilution series ST:STUDY_SUMMARY was prepared by mixing serum and urine in a cross-gradient manner (0:100, ST:STUDY_SUMMARY 1:1024, 1:256, 1:64, 1:16, 1:4, 1:1, 4:1, 16:1, 64:1, 256:1, 1024:1, 100:0). ST:INSTITUTE McGill University ST:DEPARTMENT Faculty of Agricultural and Environmental Sciences ST:LABORATORY Xia Lab, Institute of Parasitology ST:LAST_NAME Xia ST:FIRST_NAME Jeff ST:ADDRESS Macdonald Campus, McGill University 21,111 Lakeshore Road ST:EMAIL jeff.xia@mcgill.ca ST:PHONE 5143988668 ST:SUBMIT_DATE 2023-07-26 #SUBJECT SU:SUBJECT_TYPE Human SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 SU:AGE_OR_AGE_RANGE 22-32 SU:GENDER Male #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS SA_01_C18neg SA_01_C18neg Mode:C18 Negative | Ratio:0;100 MS_mode=MS1; RAW_FILE_NAME=SA_01_C18neg.mzML SUBJECT_SAMPLE_FACTORS SA_02_C18neg SA_02_C18neg Mode:C18 Negative | Ratio:0;100 MS_mode=MS1; RAW_FILE_NAME=SA_02_C18neg.mzML SUBJECT_SAMPLE_FACTORS SA_03_C18neg SA_03_C18neg Mode:C18 Negative | Ratio:0;100 MS_mode=MS1; RAW_FILE_NAME=SA_03_C18neg.mzML SUBJECT_SAMPLE_FACTORS SM_01_C18neg SM_01_C18neg Mode:C18 Negative | Ratio:100;0 MS_mode=MS1; 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RAW_FILE_NAME=20220406_URINE_DIA_02_POSITIVE_RPLC.mzML SUBJECT_SAMPLE_FACTORS 20220406_URINE_NonTargetDDMS2_SCAN01_POSITIVE_RPLC 20220406_URINE_NonTargetDDMS2_SCAN01_POSITIVE_RPLC Mode:C18 Positive | Ratio:1;1 MS_mode=MS/MS DDA; RAW_FILE_NAME=20220406_URINE_NonTargetDDMS2_SCAN01_POSITIVE_RPLC.mzML SUBJECT_SAMPLE_FACTORS 20220406_URINE_NonTargetDDMS2_SCAN02_POSITIVE_RPLC 20220406_URINE_NonTargetDDMS2_SCAN02_POSITIVE_RPLC Mode:C18 Positive | Ratio:1;1 MS_mode=MS/MS DDA; RAW_FILE_NAME=20220406_URINE_NonTargetDDMS2_SCAN02_POSITIVE_RPLC.mzML SUBJECT_SAMPLE_FACTORS 20220406_URINE_NonTargetDDMS2_SCAN03_POSITIVE_RPLC 20220406_URINE_NonTargetDDMS2_SCAN03_POSITIVE_RPLC Mode:C18 Positive | Ratio:1;1 MS_mode=MS/MS DDA; RAW_FILE_NAME=20220406_URINE_NonTargetDDMS2_SCAN03_POSITIVE_RPLC.mzML SUBJECT_SAMPLE_FACTORS 20220406_URINE_NonTargetDDMS2_SCAN04_POSITIVE_RPLC 20220406_URINE_NonTargetDDMS2_SCAN04_POSITIVE_RPLC Mode:C18 Positive | Ratio:1;1 MS_mode=MS/MS DDA; RAW_FILE_NAME=20220406_URINE_NonTargetDDMS2_SCAN04_POSITIVE_RPLC.mzML SUBJECT_SAMPLE_FACTORS 20220406_URINE_NonTargetDDMS2_SCAN05_POSITIVE_RPLC 20220406_URINE_NonTargetDDMS2_SCAN05_POSITIVE_RPLC Mode:C18 Positive | Ratio:1;1 MS_mode=MS/MS DDA; 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RAW_FILE_NAME=URINEDIA2_C18pos.mzML SUBJECT_SAMPLE_FACTORS URINEDIA3_1_C18pos URINEDIA3_1_C18pos Mode:C18 Positive | Ratio:1;1 MS_mode=MS/MS SWATH-DIA; RAW_FILE_NAME=URINEDIA3_1_C18pos.mzML SUBJECT_SAMPLE_FACTORS URINEDIA3_C18pos URINEDIA3_C18pos Mode:C18 Positive | Ratio:1;1 MS_mode=MS/MS SWATH-DIA; RAW_FILE_NAME=URINEDIA3_C18pos.mzML SUBJECT_SAMPLE_FACTORS SB_01_C18pos SB_01_C18pos Mode:C18 Positive | Ratio:1;1024 MS_mode=MS1; RAW_FILE_NAME=SB_01_C18pos.mzML SUBJECT_SAMPLE_FACTORS SB_02_C18pos SB_02_C18pos Mode:C18 Positive | Ratio:1;1024 MS_mode=MS1; RAW_FILE_NAME=SB_02_C18pos.mzML SUBJECT_SAMPLE_FACTORS SB_03_C18pos SB_03_C18pos Mode:C18 Positive | Ratio:1;1024 MS_mode=MS1; RAW_FILE_NAME=SB_03_C18pos.mzML SUBJECT_SAMPLE_FACTORS SE_01_C18pos SE_01_C18pos Mode:C18 Positive | Ratio:1;16 MS_mode=MS1; RAW_FILE_NAME=SE_01_C18pos.mzML SUBJECT_SAMPLE_FACTORS SE_02_C18pos SE_02_C18pos Mode:C18 Positive | Ratio:1;16 MS_mode=MS1; RAW_FILE_NAME=SE_02_C18pos.mzML SUBJECT_SAMPLE_FACTORS SE_03_C18pos SE_03_C18pos Mode:C18 Positive | Ratio:1;16 MS_mode=MS1; RAW_FILE_NAME=SE_03_C18pos.mzML SUBJECT_SAMPLE_FACTORS SC_01_C18pos SC_01_C18pos Mode:C18 Positive | Ratio:1;256 MS_mode=MS1; RAW_FILE_NAME=SC_01_C18pos.mzML SUBJECT_SAMPLE_FACTORS SC_02_C18pos SC_02_C18pos Mode:C18 Positive | Ratio:1;256 MS_mode=MS1; RAW_FILE_NAME=SC_02_C18pos.mzML SUBJECT_SAMPLE_FACTORS SC_03_C18pos SC_03_C18pos Mode:C18 Positive | Ratio:1;256 MS_mode=MS1; RAW_FILE_NAME=SC_03_C18pos.mzML SUBJECT_SAMPLE_FACTORS SF_01_C18pos SF_01_C18pos Mode:C18 Positive | Ratio:1;4 MS_mode=MS1; RAW_FILE_NAME=SF_01_C18pos.mzML SUBJECT_SAMPLE_FACTORS SF_02_C18pos SF_02_C18pos Mode:C18 Positive | Ratio:1;4 MS_mode=MS1; RAW_FILE_NAME=SF_02_C18pos.mzML SUBJECT_SAMPLE_FACTORS SF_03_C18pos SF_03_C18pos Mode:C18 Positive | Ratio:1;4 MS_mode=MS1; RAW_FILE_NAME=SF_03_C18pos.mzML SUBJECT_SAMPLE_FACTORS SI_01_C18pos SI_01_C18pos Mode:C18 Positive | Ratio:16;1 MS_mode=MS1; RAW_FILE_NAME=SI_01_C18pos.mzML SUBJECT_SAMPLE_FACTORS SI_02_C18pos SI_02_C18pos Mode:C18 Positive | Ratio:16;1 MS_mode=MS1; RAW_FILE_NAME=SI_02_C18pos.mzML SUBJECT_SAMPLE_FACTORS SI_03_C18pos SI_03_C18pos Mode:C18 Positive | Ratio:16;1 MS_mode=MS1; RAW_FILE_NAME=SI_03_C18pos.mzML SUBJECT_SAMPLE_FACTORS SD_01_C18pos SD_01_C18pos Mode:C18 Positive | Ratio:1;64 MS_mode=MS1; RAW_FILE_NAME=SD_01_C18pos.mzML SUBJECT_SAMPLE_FACTORS SD_02_C18pos SD_02_C18pos Mode:C18 Positive | Ratio:1;64 MS_mode=MS1; RAW_FILE_NAME=SD_02_C18pos.mzML SUBJECT_SAMPLE_FACTORS SD_03_C18pos SD_03_C18pos Mode:C18 Positive | Ratio:1;64 MS_mode=MS1; RAW_FILE_NAME=SD_03_C18pos.mzML SUBJECT_SAMPLE_FACTORS SK_01_C18pos SK_01_C18pos Mode:C18 Positive | Ratio:256;1 MS_mode=MS1; RAW_FILE_NAME=SK_01_C18pos.mzML SUBJECT_SAMPLE_FACTORS SK_02_C18pos SK_02_C18pos Mode:C18 Positive | Ratio:256;1 MS_mode=MS1; RAW_FILE_NAME=SK_02_C18pos.mzML SUBJECT_SAMPLE_FACTORS SK_03_C18pos SK_03_C18pos Mode:C18 Positive | Ratio:256;1 MS_mode=MS1; RAW_FILE_NAME=SK_03_C18pos.mzML SUBJECT_SAMPLE_FACTORS SH_01_C18pos SH_01_C18pos Mode:C18 Positive | Ratio:4;1 MS_mode=MS1; RAW_FILE_NAME=SH_01_C18pos.mzML SUBJECT_SAMPLE_FACTORS SH_02_C18pos SH_02_C18pos Mode:C18 Positive | Ratio:4;1 MS_mode=MS1; RAW_FILE_NAME=SH_02_C18pos.mzML SUBJECT_SAMPLE_FACTORS SH_03_C18pos SH_03_C18pos Mode:C18 Positive | Ratio:4;1 MS_mode=MS1; RAW_FILE_NAME=SH_03_C18pos.mzML SUBJECT_SAMPLE_FACTORS SJ_01_C18pos SJ_01_C18pos Mode:C18 Positive | Ratio:64;1 MS_mode=MS1; RAW_FILE_NAME=SJ_01_C18pos.mzML SUBJECT_SAMPLE_FACTORS SJ_02_C18pos SJ_02_C18pos Mode:C18 Positive | Ratio:64;1 MS_mode=MS1; RAW_FILE_NAME=SJ_02_C18pos.mzML SUBJECT_SAMPLE_FACTORS SJ_03_C18pos SJ_03_C18pos Mode:C18 Positive | Ratio:64;1 MS_mode=MS1; RAW_FILE_NAME=SJ_03_C18pos.mzML SUBJECT_SAMPLE_FACTORS SA_01_HILICneg SA_01_HILICneg Mode:HILIC Negative | Ratio:0;100 MS_mode=MS1; RAW_FILE_NAME=SA_01_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SA_02_HILICneg SA_02_HILICneg Mode:HILIC Negative | Ratio:0;100 MS_mode=MS1; RAW_FILE_NAME=SA_02_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SA_03_HILICneg SA_03_HILICneg Mode:HILIC Negative | Ratio:0;100 MS_mode=MS1; RAW_FILE_NAME=SA_03_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SM_01_HILICneg SM_01_HILICneg Mode:HILIC Negative | Ratio:100;0 MS_mode=MS1; RAW_FILE_NAME=SM_01_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SM_02_HILICneg SM_02_HILICneg Mode:HILIC Negative | Ratio:100;0 MS_mode=MS1; RAW_FILE_NAME=SM_02_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SM_03_HILICneg SM_03_HILICneg Mode:HILIC Negative | Ratio:100;0 MS_mode=MS1; RAW_FILE_NAME=SM_03_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SL_01_HILICneg SL_01_HILICneg Mode:HILIC Negative | Ratio:1024;1 MS_mode=MS1; RAW_FILE_NAME=SL_01_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SL_02_HILICneg SL_02_HILICneg Mode:HILIC Negative | Ratio:1024;1 MS_mode=MS1; RAW_FILE_NAME=SL_02_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SL_03_HILICneg SL_03_HILICneg Mode:HILIC Negative | Ratio:1024;1 MS_mode=MS1; RAW_FILE_NAME=SL_03_HILICneg.mzML SUBJECT_SAMPLE_FACTORS 20210908urineHILICDDMS_HILICneg 20210908urineHILICDDMS_HILICneg Mode:HILIC Negative | Ratio:1;1 MS_mode=MS/MS DDA; RAW_FILE_NAME=20210908urineHILICDDMS_HILICneg.mzML SUBJECT_SAMPLE_FACTORS 20210908urineHILICDIA1_HILICneg 20210908urineHILICDIA1_HILICneg Mode:HILIC Negative | Ratio:1;1 MS_mode=MS/MS SWATH-DIA; RAW_FILE_NAME=20210908urineHILICDIA1_HILICneg.mzML SUBJECT_SAMPLE_FACTORS 20210908urineHILICDIA2_HILICneg 20210908urineHILICDIA2_HILICneg Mode:HILIC Negative | Ratio:1;1 MS_mode=MS/MS SWATH-DIA; RAW_FILE_NAME=20210908urineHILICDIA2_HILICneg.mzML SUBJECT_SAMPLE_FACTORS 20210908urineHILICDIA3_HILICneg 20210908urineHILICDIA3_HILICneg Mode:HILIC Negative | Ratio:1;1 MS_mode=MS/MS SWATH-DIA; RAW_FILE_NAME=20210908urineHILICDIA3_HILICneg.mzML SUBJECT_SAMPLE_FACTORS 20220413_URINE_HILIC_DIA01_NEGATIVE 20220413_URINE_HILIC_DIA01_NEGATIVE Mode:HILIC Negative | Ratio:1;1 MS_mode=MS/MS SWATH-DIA; RAW_FILE_NAME=20220413_URINE_HILIC_DIA01_NEGATIVE.mzML SUBJECT_SAMPLE_FACTORS 20220413_URINE_HILIC_DIA02_NEGATIVE 20220413_URINE_HILIC_DIA02_NEGATIVE Mode:HILIC Negative | Ratio:1;1 MS_mode=MS/MS SWATH-DIA; RAW_FILE_NAME=20220413_URINE_HILIC_DIA02_NEGATIVE.mzML SUBJECT_SAMPLE_FACTORS 20220413_URINE_HILIC_NonTargetedDDMS_SCAN01_NEGATIVE 20220413_URINE_HILIC_NonTargetedDDMS_SCAN01_NEGATIVE Mode:HILIC Negative | Ratio:1;1 MS_mode=MS/MS DDA; RAW_FILE_NAME=20220413_URINE_HILIC_NonTargetedDDMS_SCAN01_NEGATIVE.mzML SUBJECT_SAMPLE_FACTORS 20220413_URINE_HILIC_NonTargetedDDMS_SCAN02_NEGATIVE 20220413_URINE_HILIC_NonTargetedDDMS_SCAN02_NEGATIVE Mode:HILIC Negative | Ratio:1;1 MS_mode=MS/MS DDA; RAW_FILE_NAME=20220413_URINE_HILIC_NonTargetedDDMS_SCAN02_NEGATIVE.mzML SUBJECT_SAMPLE_FACTORS 20220413_URINE_HILIC_NonTargetedDDMS_SCAN03_NEGATIVE 20220413_URINE_HILIC_NonTargetedDDMS_SCAN03_NEGATIVE Mode:HILIC Negative | Ratio:1;1 MS_mode=MS/MS DDA; RAW_FILE_NAME=20220413_URINE_HILIC_NonTargetedDDMS_SCAN03_NEGATIVE.mzML SUBJECT_SAMPLE_FACTORS 20220413_URINE_HILIC_NonTargetedDDMS_SCAN04_NEGATIVE 20220413_URINE_HILIC_NonTargetedDDMS_SCAN04_NEGATIVE Mode:HILIC Negative | Ratio:1;1 MS_mode=MS/MS DDA; RAW_FILE_NAME=20220413_URINE_HILIC_NonTargetedDDMS_SCAN04_NEGATIVE.mzML SUBJECT_SAMPLE_FACTORS 20220413_URINE_HILIC_NonTargetedDDMS_SCAN05_NEGATIVE 20220413_URINE_HILIC_NonTargetedDDMS_SCAN05_NEGATIVE Mode:HILIC Negative | Ratio:1;1 MS_mode=MS/MS DDA; RAW_FILE_NAME=20220413_URINE_HILIC_NonTargetedDDMS_SCAN05_NEGATIVE.mzML SUBJECT_SAMPLE_FACTORS 20220413_URINE_HILIC_NonTargetedDDMS_SCAN06_NEGATIVE 20220413_URINE_HILIC_NonTargetedDDMS_SCAN06_NEGATIVE Mode:HILIC Negative | Ratio:1;1 MS_mode=MS/MS DDA; RAW_FILE_NAME=20220413_URINE_HILIC_NonTargetedDDMS_SCAN06_NEGATIVE.mzML SUBJECT_SAMPLE_FACTORS SG_01_HILICneg SG_01_HILICneg Mode:HILIC Negative | Ratio:1;1 MS_mode=MS1; RAW_FILE_NAME=SG_01_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SG_02_HILICneg SG_02_HILICneg Mode:HILIC Negative | Ratio:1;1 MS_mode=MS1; RAW_FILE_NAME=SG_02_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SG_03_HILICneg SG_03_HILICneg Mode:HILIC Negative | Ratio:1;1 MS_mode=MS1; RAW_FILE_NAME=SG_03_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SB_01_HILICneg SB_01_HILICneg Mode:HILIC Negative | Ratio:1;1024 MS_mode=MS1; RAW_FILE_NAME=SB_01_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SB_02_HILICneg SB_02_HILICneg Mode:HILIC Negative | Ratio:1;1024 MS_mode=MS1; RAW_FILE_NAME=SB_02_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SB_03_HILICneg SB_03_HILICneg Mode:HILIC Negative | Ratio:1;1024 MS_mode=MS1; RAW_FILE_NAME=SB_03_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SE_01_HILICneg SE_01_HILICneg Mode:HILIC Negative | Ratio:1;16 MS_mode=MS1; RAW_FILE_NAME=SE_01_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SE_02_HILICneg SE_02_HILICneg Mode:HILIC Negative | Ratio:1;16 MS_mode=MS1; RAW_FILE_NAME=SE_02_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SE_03_HILICneg SE_03_HILICneg Mode:HILIC Negative | Ratio:1;16 MS_mode=MS1; RAW_FILE_NAME=SE_03_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SC_01_HILICneg SC_01_HILICneg Mode:HILIC Negative | Ratio:1;256 MS_mode=MS1; RAW_FILE_NAME=SC_01_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SC_02_HILICneg SC_02_HILICneg Mode:HILIC Negative | Ratio:1;256 MS_mode=MS1; RAW_FILE_NAME=SC_02_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SC_03_HILICneg SC_03_HILICneg Mode:HILIC Negative | Ratio:1;256 MS_mode=MS1; RAW_FILE_NAME=SC_03_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SF_01_HILICneg SF_01_HILICneg Mode:HILIC Negative | Ratio:1;4 MS_mode=MS1; RAW_FILE_NAME=SF_01_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SF_02_HILICneg SF_02_HILICneg Mode:HILIC Negative | Ratio:1;4 MS_mode=MS1; RAW_FILE_NAME=SF_02_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SF_03_HILICneg SF_03_HILICneg Mode:HILIC Negative | Ratio:1;4 MS_mode=MS1; RAW_FILE_NAME=SF_03_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SI_01_HILICneg SI_01_HILICneg Mode:HILIC Negative | Ratio:16;1 MS_mode=MS1; RAW_FILE_NAME=SI_01_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SI_02_HILICneg SI_02_HILICneg Mode:HILIC Negative | Ratio:16;1 MS_mode=MS1; RAW_FILE_NAME=SI_02_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SI_03_HILICneg SI_03_HILICneg Mode:HILIC Negative | Ratio:16;1 MS_mode=MS1; RAW_FILE_NAME=SI_03_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SD_01_HILICneg SD_01_HILICneg Mode:HILIC Negative | Ratio:1;64 MS_mode=MS1; RAW_FILE_NAME=SD_01_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SD_02_HILICneg SD_02_HILICneg Mode:HILIC Negative | Ratio:1;64 MS_mode=MS1; RAW_FILE_NAME=SD_02_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SD_03_HILICneg SD_03_HILICneg Mode:HILIC Negative | Ratio:1;64 MS_mode=MS1; RAW_FILE_NAME=SD_03_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SK_01_HILICneg SK_01_HILICneg Mode:HILIC Negative | Ratio:256;1 MS_mode=MS1; RAW_FILE_NAME=SK_01_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SK_02_HILICneg SK_02_HILICneg Mode:HILIC Negative | Ratio:256;1 MS_mode=MS1; RAW_FILE_NAME=SK_02_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SK_03_HILICneg SK_03_HILICneg Mode:HILIC Negative | Ratio:256;1 MS_mode=MS1; RAW_FILE_NAME=SK_03_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SH_01_HILICneg SH_01_HILICneg Mode:HILIC Negative | Ratio:4;1 MS_mode=MS1; RAW_FILE_NAME=SH_01_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SH_02_HILICneg SH_02_HILICneg Mode:HILIC Negative | Ratio:4;1 MS_mode=MS1; RAW_FILE_NAME=SH_02_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SH_03_HILICneg SH_03_HILICneg Mode:HILIC Negative | Ratio:4;1 MS_mode=MS1; RAW_FILE_NAME=SH_03_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SJ_01_HILICneg SJ_01_HILICneg Mode:HILIC Negative | Ratio:64;1 MS_mode=MS1; RAW_FILE_NAME=SJ_01_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SJ_02_HILICneg SJ_02_HILICneg Mode:HILIC Negative | Ratio:64;1 MS_mode=MS1; RAW_FILE_NAME=SJ_02_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SJ_03_HILICneg SJ_03_HILICneg Mode:HILIC Negative | Ratio:64;1 MS_mode=MS1; RAW_FILE_NAME=SJ_03_HILICneg.mzML SUBJECT_SAMPLE_FACTORS SA_01_HILICpos SA_01_HILICpos Mode:HILIC Positive | Ratio:0;100 MS_mode=MS1; RAW_FILE_NAME=SA_01_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SA_02_HILICpos SA_02_HILICpos Mode:HILIC Positive | Ratio:0;100 MS_mode=MS1; RAW_FILE_NAME=SA_02_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SA_03_HILICpos SA_03_HILICpos Mode:HILIC Positive | Ratio:0;100 MS_mode=MS1; RAW_FILE_NAME=SA_03_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SM_01_HILICpos SM_01_HILICpos Mode:HILIC Positive | Ratio:100;0 MS_mode=MS1; RAW_FILE_NAME=SM_01_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SM_02_HILICpos SM_02_HILICpos Mode:HILIC Positive | Ratio:100;0 MS_mode=MS1; RAW_FILE_NAME=SM_02_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SM_03_HILICpos SM_03_HILICpos Mode:HILIC Positive | Ratio:100;0 MS_mode=MS1; RAW_FILE_NAME=SM_03_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SL_01_HILICpos SL_01_HILICpos Mode:HILIC Positive | Ratio:1024;1 MS_mode=MS1; RAW_FILE_NAME=SL_01_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SL_02_HILICpos SL_02_HILICpos Mode:HILIC Positive | Ratio:1024;1 MS_mode=MS1; RAW_FILE_NAME=SL_02_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SL_03_HILICpos SL_03_HILICpos Mode:HILIC Positive | Ratio:1024;1 MS_mode=MS1; RAW_FILE_NAME=SL_03_HILICpos.mzML SUBJECT_SAMPLE_FACTORS 20210908urineHILICDDMS_HILICpos 20210908urineHILICDDMS_HILICpos Mode:HILIC Positive | Ratio:1;1 MS_mode=MS/MS DDA; RAW_FILE_NAME=20210908urineHILICDDMS_HILICpos.mzML SUBJECT_SAMPLE_FACTORS 20210908urineHILICDIA1_HILICpos 20210908urineHILICDIA1_HILICpos Mode:HILIC Positive | Ratio:1;1 MS_mode=MS/MS SWATH-DIA; RAW_FILE_NAME=20210908urineHILICDIA1_HILICpos.mzML SUBJECT_SAMPLE_FACTORS 20210908urineHILICDIA2_HILICpos 20210908urineHILICDIA2_HILICpos Mode:HILIC Positive | Ratio:1;1 MS_mode=MS/MS SWATH-DIA; RAW_FILE_NAME=20210908urineHILICDIA2_HILICpos.mzML SUBJECT_SAMPLE_FACTORS 20210908urineHILICDIA3_HILICpos 20210908urineHILICDIA3_HILICpos Mode:HILIC Positive | Ratio:1;1 MS_mode=MS/MS SWATH-DIA; RAW_FILE_NAME=20210908urineHILICDIA3_HILICpos.mzML SUBJECT_SAMPLE_FACTORS 20220412_URINE_HILIC_DIA_01_POS 20220412_URINE_HILIC_DIA_01_POS Mode:HILIC Positive | Ratio:1;1 MS_mode=MS/MS SWATH-DIA; RAW_FILE_NAME=20220412_URINE_HILIC_DIA_01_POS.mzML SUBJECT_SAMPLE_FACTORS 20220412_URINE_HILIC_DIA_02_POS 20220412_URINE_HILIC_DIA_02_POS Mode:HILIC Positive | Ratio:1;1 MS_mode=MS/MS SWATH-DIA; RAW_FILE_NAME=20220412_URINE_HILIC_DIA_02_POS.mzML SUBJECT_SAMPLE_FACTORS 20220412_URINE_HILIC_NonTargetedDDMS_SCAN01_POS 20220412_URINE_HILIC_NonTargetedDDMS_SCAN01_POS Mode:HILIC Positive | Ratio:1;1 MS_mode=MS/MS DDA; RAW_FILE_NAME=20220412_URINE_HILIC_NonTargetedDDMS_SCAN01_POS.mzML SUBJECT_SAMPLE_FACTORS 20220412_URINE_HILIC_NonTargetedDDMS_SCAN02_POS 20220412_URINE_HILIC_NonTargetedDDMS_SCAN02_POS Mode:HILIC Positive | Ratio:1;1 MS_mode=MS/MS DDA; RAW_FILE_NAME=20220412_URINE_HILIC_NonTargetedDDMS_SCAN02_POS.mzML SUBJECT_SAMPLE_FACTORS 20220412_URINE_HILIC_NonTargetedDDMS_SCAN03_POS 20220412_URINE_HILIC_NonTargetedDDMS_SCAN03_POS Mode:HILIC Positive | Ratio:1;1 MS_mode=MS/MS DDA; RAW_FILE_NAME=20220412_URINE_HILIC_NonTargetedDDMS_SCAN03_POS.mzML SUBJECT_SAMPLE_FACTORS 20220412_URINE_HILIC_NonTargetedDDMS_SCAN04_POS 20220412_URINE_HILIC_NonTargetedDDMS_SCAN04_POS Mode:HILIC Positive | Ratio:1;1 MS_mode=MS/MS DDA; RAW_FILE_NAME=20220412_URINE_HILIC_NonTargetedDDMS_SCAN04_POS.mzML SUBJECT_SAMPLE_FACTORS 20220412_URINE_HILIC_NonTargetedDDMS_SCAN05_POS 20220412_URINE_HILIC_NonTargetedDDMS_SCAN05_POS Mode:HILIC Positive | Ratio:1;1 MS_mode=MS/MS DDA; RAW_FILE_NAME=20220412_URINE_HILIC_NonTargetedDDMS_SCAN05_POS.mzML SUBJECT_SAMPLE_FACTORS 20220412_URINE_HILIC_NonTargetedDDMS_SCAN06_POS 20220412_URINE_HILIC_NonTargetedDDMS_SCAN06_POS Mode:HILIC Positive | Ratio:1;1 MS_mode=MS/MS DDA; RAW_FILE_NAME=20220412_URINE_HILIC_NonTargetedDDMS_SCAN06_POS.mzML SUBJECT_SAMPLE_FACTORS SG_01_HILICpos SG_01_HILICpos Mode:HILIC Positive | Ratio:1;1 MS_mode=MS1; RAW_FILE_NAME=SG_01_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SG_02_HILICpos SG_02_HILICpos Mode:HILIC Positive | Ratio:1;1 MS_mode=MS1; RAW_FILE_NAME=SG_02_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SG_03_HILICpos SG_03_HILICpos Mode:HILIC Positive | Ratio:1;1 MS_mode=MS1; RAW_FILE_NAME=SG_03_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SB_01_HILICpos SB_01_HILICpos Mode:HILIC Positive | Ratio:1;1024 MS_mode=MS1; RAW_FILE_NAME=SB_01_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SB_02_HILICpos SB_02_HILICpos Mode:HILIC Positive | Ratio:1;1024 MS_mode=MS1; RAW_FILE_NAME=SB_02_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SB_03_HILICpos SB_03_HILICpos Mode:HILIC Positive | Ratio:1;1024 MS_mode=MS1; RAW_FILE_NAME=SB_03_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SE_01_HILICpos SE_01_HILICpos Mode:HILIC Positive | Ratio:1;16 MS_mode=MS1; RAW_FILE_NAME=SE_01_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SE_02_HILICpos SE_02_HILICpos Mode:HILIC Positive | Ratio:1;16 MS_mode=MS1; RAW_FILE_NAME=SE_02_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SE_03_HILICpos SE_03_HILICpos Mode:HILIC Positive | Ratio:1;16 MS_mode=MS1; RAW_FILE_NAME=SE_03_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SC_01_HILICpos SC_01_HILICpos Mode:HILIC Positive | Ratio:1;256 MS_mode=MS1; RAW_FILE_NAME=SC_01_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SC_02_HILICpos SC_02_HILICpos Mode:HILIC Positive | Ratio:1;256 MS_mode=MS1; RAW_FILE_NAME=SC_02_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SC_03_HILICpos SC_03_HILICpos Mode:HILIC Positive | Ratio:1;256 MS_mode=MS1; RAW_FILE_NAME=SC_03_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SF_01_HILICpos SF_01_HILICpos Mode:HILIC Positive | Ratio:1;4 MS_mode=MS1; RAW_FILE_NAME=SF_01_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SF_02_HILICpos SF_02_HILICpos Mode:HILIC Positive | Ratio:1;4 MS_mode=MS1; RAW_FILE_NAME=SF_02_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SF_03_HILICpos SF_03_HILICpos Mode:HILIC Positive | Ratio:1;4 MS_mode=MS1; RAW_FILE_NAME=SF_03_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SI_01_HILICpos SI_01_HILICpos Mode:HILIC Positive | Ratio:16;1 MS_mode=MS1; RAW_FILE_NAME=SI_01_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SI_02_HILICpos SI_02_HILICpos Mode:HILIC Positive | Ratio:16;1 MS_mode=MS1; RAW_FILE_NAME=SI_02_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SI_03_HILICpos SI_03_HILICpos Mode:HILIC Positive | Ratio:16;1 MS_mode=MS1; RAW_FILE_NAME=SI_03_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SD_01_HILICpos SD_01_HILICpos Mode:HILIC Positive | Ratio:1;64 MS_mode=MS1; RAW_FILE_NAME=SD_01_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SD_02_HILICpos SD_02_HILICpos Mode:HILIC Positive | Ratio:1;64 MS_mode=MS1; RAW_FILE_NAME=SD_02_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SD_03_HILICpos SD_03_HILICpos Mode:HILIC Positive | Ratio:1;64 MS_mode=MS1; RAW_FILE_NAME=SD_03_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SK_01_HILICpos SK_01_HILICpos Mode:HILIC Positive | Ratio:256;1 MS_mode=MS1; RAW_FILE_NAME=SK_01_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SK_02_HILICpos SK_02_HILICpos Mode:HILIC Positive | Ratio:256;1 MS_mode=MS1; RAW_FILE_NAME=SK_02_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SK_03_HILICpos SK_03_HILICpos Mode:HILIC Positive | Ratio:256;1 MS_mode=MS1; RAW_FILE_NAME=SK_03_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SH_01_HILICpos SH_01_HILICpos Mode:HILIC Positive | Ratio:4;1 MS_mode=MS1; RAW_FILE_NAME=SH_01_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SH_02_HILICpos SH_02_HILICpos Mode:HILIC Positive | Ratio:4;1 MS_mode=MS1; RAW_FILE_NAME=SH_02_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SH_03_HILICpos SH_03_HILICpos Mode:HILIC Positive | Ratio:4;1 MS_mode=MS1; RAW_FILE_NAME=SH_03_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SJ_01_HILICpos SJ_01_HILICpos Mode:HILIC Positive | Ratio:64;1 MS_mode=MS1; RAW_FILE_NAME=SJ_01_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SJ_02_HILICpos SJ_02_HILICpos Mode:HILIC Positive | Ratio:64;1 MS_mode=MS1; RAW_FILE_NAME=SJ_02_HILICpos.mzML SUBJECT_SAMPLE_FACTORS SJ_03_HILICpos SJ_03_HILICpos Mode:HILIC Positive | Ratio:64;1 MS_mode=MS1; RAW_FILE_NAME=SJ_03_HILICpos.mzML #COLLECTION CO:COLLECTION_SUMMARY serum standards and an urine sample is mixed based on a series of dilution ratio CO:SAMPLE_TYPE Urine CO:STORAGE_CONDITIONS -80℃ #TREATMENT TR:TREATMENT_SUMMARY Healthy volunteers were recruited. About 1 mL urine were collected. The urine TR:TREATMENT_SUMMARY sample was mixed with a serum sample then. No other treatment applied. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY A urine sample was collected from a donor of McGill University45. A total of SP:SAMPLEPREP_SUMMARY 100mL urine was sub-sampled and frozen at -80°C. A human standard serum sample SP:SAMPLEPREP_SUMMARY (Sigma-Aldrich, Sigma, St. Louis, MO, USA) and the urine were thawed in ice for SP:SAMPLEPREP_SUMMARY 1 hour, and then vortexed for 30 seconds to ensure homogeneity. A total of 13 SP:SAMPLEPREP_SUMMARY Eppendorf microcentrifuge tubes were prepared and labelled from A to M. For SP:SAMPLEPREP_SUMMARY tubes A to E, 150 µl urine was transferred into each of them. For tube G to K, SP:SAMPLEPREP_SUMMARY 150 µl standard serum was transferred into each of them. 250 µl pure urine SP:SAMPLEPREP_SUMMARY were transferred into tube L, and 250 µl pure serum were transferred into tube SP:SAMPLEPREP_SUMMARY M. Then, 50 µl pure serum were extracted and mixed into tube E. Then, 50 µl SP:SAMPLEPREP_SUMMARY liquids were extracted and mixed into tube D, and so on until tube A. Same SP:SAMPLEPREP_SUMMARY operations were repeated for pure urine tube L, and tube G-K. Finally, 75 µl SP:SAMPLEPREP_SUMMARY pure urine and serum were extracted respectively and mixed into tube F. At a SP:SAMPLEPREP_SUMMARY result, a total of 11 dilution mixtures and 2 pure samples were generated. SP:PROCESSING_STORAGE_CONDITIONS On ice SP:EXTRACTION_METHOD Organic reagent SP:EXTRACT_STORAGE On ice #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY For C18 columns, the composition of the mobile phases A and B were 0.1% FA in CH:CHROMATOGRAPHY_SUMMARY water and 0.1% FA in ACN, respectively. CH:INSTRUMENT_NAME Thermo Vanquish CH:COLUMN_NAME Thermo Hypersil GOLD aQ (100 x 2.1mm,1.9um) CH:COLUMN_TEMPERATURE 40 CH:FLOW_GRADIENT 0-1min: 95%A; 1-3min:50%A; 3-15min:20%A; 15-15.5:0%A; 15.5-19.5min: 0%A; CH:FLOW_GRADIENT 19.5%-20: 95%A CH:FLOW_RATE 0.4 mL/min CH:SOLVENT_A 100% water; 0.1% formic acid CH:SOLVENT_B 100% acetonitrile; 0.1% formic acid CH:CHROMATOGRAPHY_TYPE Reversed phase #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo Q Exactive Orbitrap MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:MS_COMMENTS For the C18 column, an electrospray ion (ESI) source with a spray voltage of 4 MS:MS_COMMENTS keV in positive mode and 3.5 keV in negative mode were used MS:ION_MODE POSITIVE and NEGATIVE MS:MS_RESULTS_FILE ST002798_AN004552_Results.txt UNITS:Peak area Has m/z:Yes Has RT:Yes RT units:Seconds #END