#METABOLOMICS WORKBENCH bm_garcia_20220214_054444 DATATRACK_ID:3083 STUDY_ID:ST002092 ANALYSIS_ID:AN003418 VERSION 1 CREATED_ON 02-08-2024 #PROJECT PR:PROJECT_TITLE Addressing batch effects in large-scale metabolomics with augmented experimental PR:PROJECT_TITLE design and meta-analysis PR:PROJECT_SUMMARY Untargeted LC-MS study conducted using RP and HILIC chromatography on three PR:PROJECT_SUMMARY groups of C. elegans: natural isolates, central metabolism mutants, and PR:PROJECT_SUMMARY UDP-glucuronosyltransferase mutants. An augmented study design, rank PR:PROJECT_SUMMARY transformation of the raw data, strict QA/QC followed by a meta-analysis was PR:PROJECT_SUMMARY used for data analysis. PR:INSTITUTE University of Georgia - Complex Carbohydrate Research Center PR:LABORATORY Edison Lab PR:LAST_NAME Garcia PR:FIRST_NAME Brianna PR:ADDRESS 315 Riverbend Road, Athens, GA 30602 PR:EMAIL brianna.garcia@uga.edu PR:PHONE 7065424401 PR:FUNDING_SOURCE U2CES030167 PR:DOI http://dx.doi.org/10.21228/M82978 PR:CONTRIBUTORS Amanda O. Shaver, Goncalo J. Gouveia, Alison M. Morse, Zihao Liu, Carter K. PR:CONTRIBUTORS Asef, Ricardo M. Borges, Franklin E. Leach III, Erik C. Andersen, I. Jonathan PR:CONTRIBUTORS Amster, Facundo M. Fernández, Arthur S. Edison, and Lauren M. McIntyre #STUDY ST:STUDY_TITLE Addressing batch effects in large-scale metabolomics with augmented experimental ST:STUDY_TITLE design and meta-analysis ST:STUDY_SUMMARY Untargeted LC-MS study conducted using RP and HILIC chromatography on three ST:STUDY_SUMMARY groups of C. elegans: natural isolates, central metabolism mutants, and ST:STUDY_SUMMARY UDP-glucuronosyltransferase mutants. An augmented study design, rank ST:STUDY_SUMMARY transformation of the raw data, strict QA/QC followed by a meta-analysis was ST:STUDY_SUMMARY used for data analysis. ST:INSTITUTE University of Georgia - Complex Carbohydrate Research Center ST:LABORATORY Edison Lab ST:LAST_NAME Garcia ST:FIRST_NAME Brianna ST:ADDRESS 315 Riverbend Road ST:EMAIL brianna.garcia@uga.edu ST:PHONE 7065424401 ST:SUBMIT_DATE 2022-02-14 #SUBJECT SU:SUBJECT_TYPE Invertebrate SU:SUBJECT_SPECIES Caenorhabditis elegans SU:TAXONOMY_ID 6239 SU:GENDER Hermaphrodite #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS - b5_aos_51 Strain:AUM2073 | Sample type:sample RAW_FILE_NAME=b5_aos_51.mzML; Batch=5; Set=3 SUBJECT_SAMPLE_FACTORS - b5_aos_79 Strain:AUM2073 | Sample type:sample RAW_FILE_NAME=b5_aos_79.mzML; Batch=5; Set=3 SUBJECT_SAMPLE_FACTORS - b5_aos_91 Strain:AUM2073 | Sample type:sample RAW_FILE_NAME=b5_aos_91.mzML; Batch=5; Set=3 SUBJECT_SAMPLE_FACTORS - b6_aos_120 Strain:AUM2073 | Sample type:sample RAW_FILE_NAME=b6_aos_120.mzML; Batch=6; Set=3 SUBJECT_SAMPLE_FACTORS - b6_aos_135 Strain:AUM2073 | Sample type:sample RAW_FILE_NAME=b6_aos_135.mzML; Batch=6; Set=3 SUBJECT_SAMPLE_FACTORS - b6_aos_169 Strain:AUM2073 | Sample type:sample RAW_FILE_NAME=b6_aos_169.mzML; Batch=6; Set=3 SUBJECT_SAMPLE_FACTORS - b1_aos_142 Strain:CB4856 | Sample type:sample RAW_FILE_NAME=b1_aos_142.mzML; Batch=1; Set=1 SUBJECT_SAMPLE_FACTORS - b1_aos_145 Strain:CB4856 | Sample type:sample RAW_FILE_NAME=b1_aos_145.mzML; Batch=1; Set=1 SUBJECT_SAMPLE_FACTORS - b2_aos_130 Strain:CB4856 | Sample type:sample RAW_FILE_NAME=b2_aos_130.mzML; Batch=2; Set=1 SUBJECT_SAMPLE_FACTORS - b2_aos_170 Strain:CB4856 | Sample type:sample RAW_FILE_NAME=b2_aos_170.mzML; Batch=2; Set=1 SUBJECT_SAMPLE_FACTORS - b1_aos_127 Strain:CX11314 | Sample type:sample RAW_FILE_NAME=b1_aos_127.mzML; Batch=1; Set=1 SUBJECT_SAMPLE_FACTORS - b1_aos_25 Strain:CX11314 | Sample type:sample RAW_FILE_NAME=b1_aos_25.mzML; Batch=1; Set=1 SUBJECT_SAMPLE_FACTORS - b1_aos_76 Strain:CX11314 | Sample type:sample RAW_FILE_NAME=b1_aos_76.mzML; Batch=1; Set=1 SUBJECT_SAMPLE_FACTORS - b2_aos_103 Strain:CX11314 | Sample type:sample RAW_FILE_NAME=b2_aos_103.mzML; Batch=2; Set=1 SUBJECT_SAMPLE_FACTORS - b2_aos_175 Strain:CX11314 | Sample type:sample RAW_FILE_NAME=b2_aos_175.mzML; Batch=2; Set=1 SUBJECT_SAMPLE_FACTORS - b2_aos_199 Strain:CX11314 | Sample type:sample RAW_FILE_NAME=b2_aos_199.mzML; Batch=2; Set=1 SUBJECT_SAMPLE_FACTORS - b1_aos_46 Strain:DL238 | Sample type:sample RAW_FILE_NAME=b1_aos_46.mzML; Batch=1; Set=1 SUBJECT_SAMPLE_FACTORS - b1_aos_50 Strain:DL238 | Sample type:sample RAW_FILE_NAME=b1_aos_50.mzML; Batch=1; Set=1 SUBJECT_SAMPLE_FACTORS - b1_aos_65 Strain:DL238 | Sample type:sample RAW_FILE_NAME=b1_aos_65.mzML; Batch=1; Set=1 SUBJECT_SAMPLE_FACTORS - b2_aos_165 Strain:DL238 | Sample type:sample RAW_FILE_NAME=b2_aos_165.mzML; Batch=2; Set=1 SUBJECT_SAMPLE_FACTORS - b2_aos_174 Strain:DL238 | Sample type:sample RAW_FILE_NAME=b2_aos_174.mzML; Batch=2; Set=1 SUBJECT_SAMPLE_FACTORS - b2_aos_192 Strain:DL238 | Sample type:sample RAW_FILE_NAME=b2_aos_192.mzML; Batch=2; Set=1 SUBJECT_SAMPLE_FACTORS - b3_aos_28 Strain:KJ550 | Sample type:sample RAW_FILE_NAME=b3_aos_28.mzML; Batch=3; Set=2 SUBJECT_SAMPLE_FACTORS - b3_aos_86 Strain:KJ550 | Sample type:sample RAW_FILE_NAME=b3_aos_86.mzML; Batch=3; Set=2 SUBJECT_SAMPLE_FACTORS - b4_aos_100 Strain:KJ550 | Sample type:sample RAW_FILE_NAME=b4_aos_100.mzML; Batch=4; Set=2 SUBJECT_SAMPLE_FACTORS - b4_aos_109 Strain:KJ550 | Sample type:sample RAW_FILE_NAME=b4_aos_109.mzML; Batch=4; Set=2 SUBJECT_SAMPLE_FACTORS - b4_aos_134 Strain:KJ550 | Sample type:sample RAW_FILE_NAME=b4_aos_134.mzML; Batch=4; Set=2 SUBJECT_SAMPLE_FACTORS - b1_aos_48 Strain:N2 | Sample type:sample RAW_FILE_NAME=b1_aos_48.mzML; Batch=1; Set=1 SUBJECT_SAMPLE_FACTORS - b1_aos_58 Strain:N2 | Sample type:sample RAW_FILE_NAME=b1_aos_58.mzML; Batch=1; Set=1 SUBJECT_SAMPLE_FACTORS - b1_aos_67 Strain:N2 | Sample type:sample RAW_FILE_NAME=b1_aos_67.mzML; Batch=1; Set=1 SUBJECT_SAMPLE_FACTORS - b2_aos_106 Strain:N2 | Sample type:sample RAW_FILE_NAME=b2_aos_106.mzML; Batch=2; Set=1 SUBJECT_SAMPLE_FACTORS - b2_aos_56 Strain:N2 | Sample type:sample RAW_FILE_NAME=b2_aos_56.mzML; Batch=2; Set=1 SUBJECT_SAMPLE_FACTORS - b1_aos_129 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b1_aos_129.mzML; Batch=1; Set=1 SUBJECT_SAMPLE_FACTORS - b1_aos_149 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b1_aos_149.mzML; Batch=1; Set=1 SUBJECT_SAMPLE_FACTORS - b1_aos_27 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b1_aos_27.mzML; Batch=1; Set=1 SUBJECT_SAMPLE_FACTORS - b1_aos_43 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b1_aos_43.mzML; Batch=1; Set=1 SUBJECT_SAMPLE_FACTORS - b1_aos_54 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b1_aos_54.mzML; Batch=1; Set=1 SUBJECT_SAMPLE_FACTORS - b1_aos_78 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b1_aos_78.mzML; Batch=1; Set=1 SUBJECT_SAMPLE_FACTORS - b2_aos_102 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b2_aos_102.mzML; Batch=2; Set=1 SUBJECT_SAMPLE_FACTORS - b2_aos_107 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b2_aos_107.mzML; Batch=2; Set=1 SUBJECT_SAMPLE_FACTORS - b2_aos_124 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b2_aos_124.mzML; Batch=2; Set=1 SUBJECT_SAMPLE_FACTORS - b2_aos_167 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b2_aos_167.mzML; Batch=2; Set=1 SUBJECT_SAMPLE_FACTORS - b2_aos_188 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b2_aos_188.mzML; Batch=2; Set=1 SUBJECT_SAMPLE_FACTORS - b2_aos_200 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b2_aos_200.mzML; Batch=2; Set=1 SUBJECT_SAMPLE_FACTORS - b2_aos_53 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b2_aos_53.mzML; Batch=2; Set=1 SUBJECT_SAMPLE_FACTORS - b3_aos_185 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b3_aos_185.mzML; Batch=3; Set=2 SUBJECT_SAMPLE_FACTORS - b3_aos_27 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b3_aos_27.mzML; Batch=3; Set=2 SUBJECT_SAMPLE_FACTORS - b3_aos_38 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b3_aos_38.mzML; Batch=3; Set=2 SUBJECT_SAMPLE_FACTORS - b3_aos_43 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b3_aos_43.mzML; Batch=3; Set=2 SUBJECT_SAMPLE_FACTORS - b3_aos_54 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b3_aos_54.mzML; Batch=3; Set=2 SUBJECT_SAMPLE_FACTORS - b3_aos_78 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b3_aos_78.mzML; Batch=3; Set=2 SUBJECT_SAMPLE_FACTORS - b3_aos_90 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b3_aos_90.mzML; Batch=3; Set=2 SUBJECT_SAMPLE_FACTORS - b3_aos_99 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b3_aos_99.mzML; Batch=3; Set=2 SUBJECT_SAMPLE_FACTORS - b4_aos_107 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b4_aos_107.mzML; Batch=4; Set=2 SUBJECT_SAMPLE_FACTORS - b4_aos_124 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b4_aos_124.mzML; Batch=4; Set=2 SUBJECT_SAMPLE_FACTORS - b4_aos_140 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b4_aos_140.mzML; Batch=4; Set=2 SUBJECT_SAMPLE_FACTORS - b4_aos_180 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b4_aos_180.mzML; Batch=4; Set=2 SUBJECT_SAMPLE_FACTORS - b4_aos_87 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b4_aos_87.mzML; Batch=4; Set=2 SUBJECT_SAMPLE_FACTORS - b4_aos_92 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b4_aos_92.mzML; Batch=4; Set=2 SUBJECT_SAMPLE_FACTORS - b5_aos_181 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b5_aos_181.mzML; Batch=5; Set=3 SUBJECT_SAMPLE_FACTORS - b5_aos_196 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b5_aos_196.mzML; Batch=5; Set=3 SUBJECT_SAMPLE_FACTORS - b5_aos_41 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b5_aos_41.mzML; Batch=5; Set=3 SUBJECT_SAMPLE_FACTORS - b5_aos_43 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b5_aos_43.mzML; Batch=5; Set=3 SUBJECT_SAMPLE_FACTORS - b5_aos_54 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b5_aos_54.mzML; Batch=5; Set=3 SUBJECT_SAMPLE_FACTORS - b5_aos_75 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b5_aos_75.mzML; Batch=5; Set=3 SUBJECT_SAMPLE_FACTORS - b5_aos_78 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b5_aos_78.mzML; Batch=5; Set=3 SUBJECT_SAMPLE_FACTORS - b5_aos_87 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b5_aos_87.mzML; Batch=5; Set=3 SUBJECT_SAMPLE_FACTORS - b6_aos_102 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b6_aos_102.mzML; Batch=6; Set=3 SUBJECT_SAMPLE_FACTORS - b6_aos_107 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b6_aos_107.mzML; Batch=6; Set=3 SUBJECT_SAMPLE_FACTORS - b6_aos_140 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b6_aos_140.mzML; Batch=6; Set=3 SUBJECT_SAMPLE_FACTORS - b6_aos_167 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b6_aos_167.mzML; Batch=6; Set=3 SUBJECT_SAMPLE_FACTORS - b6_aos_188 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b6_aos_188.mzML; Batch=6; Set=3 SUBJECT_SAMPLE_FACTORS - b6_aos_198 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b6_aos_198.mzML; Batch=6; Set=3 SUBJECT_SAMPLE_FACTORS - b6_aos_90 Strain:PD1074 | Sample type:sample RAW_FILE_NAME=b6_aos_90.mzML; Batch=6; Set=3 SUBJECT_SAMPLE_FACTORS - b1_aos_122 Strain:RB2011 | Sample type:sample RAW_FILE_NAME=b1_aos_122.mzML; Batch=1; Set=1 SUBJECT_SAMPLE_FACTORS - b1_aos_32 Strain:RB2011 | Sample type:sample RAW_FILE_NAME=b1_aos_32.mzML; Batch=1; Set=1 SUBJECT_SAMPLE_FACTORS - b2_aos_108 Strain:RB2011 | Sample type:sample RAW_FILE_NAME=b2_aos_108.mzML; Batch=2; Set=1 SUBJECT_SAMPLE_FACTORS - b2_aos_173 Strain:RB2011 | Sample type:sample RAW_FILE_NAME=b2_aos_173.mzML; Batch=2; Set=1 SUBJECT_SAMPLE_FACTORS - b5_aos_26 Strain:RB2055 | Sample type:sample RAW_FILE_NAME=b5_aos_26.mzML; Batch=5; Set=3 SUBJECT_SAMPLE_FACTORS - b5_aos_45 Strain:RB2055 | Sample type:sample RAW_FILE_NAME=b5_aos_45.mzML; Batch=5; Set=3 SUBJECT_SAMPLE_FACTORS - b5_aos_83 Strain:RB2055 | Sample type:sample RAW_FILE_NAME=b5_aos_83.mzML; Batch=5; Set=3 SUBJECT_SAMPLE_FACTORS - b6_aos_114 Strain:RB2055 | Sample type:sample RAW_FILE_NAME=b6_aos_114.mzML; Batch=6; Set=3 SUBJECT_SAMPLE_FACTORS - b6_aos_118 Strain:RB2055 | Sample type:sample RAW_FILE_NAME=b6_aos_118.mzML; Batch=6; Set=3 SUBJECT_SAMPLE_FACTORS - b6_aos_186 Strain:RB2055 | Sample type:sample RAW_FILE_NAME=b6_aos_186.mzML; Batch=6; Set=3 SUBJECT_SAMPLE_FACTORS - b3_aos_36 Strain:RB2347 | Sample type:sample RAW_FILE_NAME=b3_aos_36.mzML; Batch=3; Set=2 SUBJECT_SAMPLE_FACTORS - b3_aos_37 Strain:RB2347 | Sample type:sample RAW_FILE_NAME=b3_aos_37.mzML; Batch=3; Set=2 SUBJECT_SAMPLE_FACTORS - b3_aos_74 Strain:RB2347 | Sample type:sample RAW_FILE_NAME=b3_aos_74.mzML; Batch=3; Set=2 SUBJECT_SAMPLE_FACTORS - b4_aos_116 Strain:RB2347 | Sample type:sample RAW_FILE_NAME=b4_aos_116.mzML; Batch=4; Set=2 SUBJECT_SAMPLE_FACTORS - b4_aos_171 Strain:RB2347 | Sample type:sample RAW_FILE_NAME=b4_aos_171.mzML; Batch=4; Set=2 SUBJECT_SAMPLE_FACTORS - b4_aos_82 Strain:RB2347 | Sample type:sample RAW_FILE_NAME=b4_aos_82.mzML; Batch=4; Set=2 SUBJECT_SAMPLE_FACTORS - b4_aos_95 Strain:RB2347 | Sample type:sample RAW_FILE_NAME=b4_aos_95.mzML; Batch=4; Set=2 SUBJECT_SAMPLE_FACTORS - b3_aos_35 Strain:RB2550 | Sample type:sample RAW_FILE_NAME=b3_aos_35.mzML; Batch=3; Set=2 SUBJECT_SAMPLE_FACTORS - b3_aos_40 Strain:RB2550 | Sample type:sample RAW_FILE_NAME=b3_aos_40.mzML; Batch=3; Set=2 SUBJECT_SAMPLE_FACTORS - b3_aos_71 Strain:RB2550 | Sample type:sample RAW_FILE_NAME=b3_aos_71.mzML; Batch=3; Set=2 SUBJECT_SAMPLE_FACTORS - b4_aos_111 Strain:RB2550 | Sample type:sample RAW_FILE_NAME=b4_aos_111.mzML; Batch=4; Set=2 SUBJECT_SAMPLE_FACTORS - b4_aos_81 Strain:RB2550 | Sample type:sample RAW_FILE_NAME=b4_aos_81.mzML; Batch=4; Set=2 SUBJECT_SAMPLE_FACTORS - b4_aos_96 Strain:RB2550 | Sample type:sample RAW_FILE_NAME=b4_aos_96.mzML; Batch=4; Set=2 SUBJECT_SAMPLE_FACTORS - b5_aos_39 Strain:RB2607 | Sample type:sample RAW_FILE_NAME=b5_aos_39.mzML; Batch=5; Set=3 SUBJECT_SAMPLE_FACTORS - b6_aos_101 Strain:RB2607 | Sample type:sample RAW_FILE_NAME=b6_aos_101.mzML; Batch=6; Set=3 SUBJECT_SAMPLE_FACTORS - b6_aos_133 Strain:RB2607 | Sample type:sample RAW_FILE_NAME=b6_aos_133.mzML; Batch=6; Set=3 SUBJECT_SAMPLE_FACTORS - b6_aos_166 Strain:RB2607 | Sample type:sample RAW_FILE_NAME=b6_aos_166.mzML; Batch=6; Set=3 SUBJECT_SAMPLE_FACTORS - b6_aos_88 Strain:RB2607 | Sample type:sample RAW_FILE_NAME=b6_aos_88.mzML; Batch=6; Set=3 SUBJECT_SAMPLE_FACTORS - b1_pool_mutant_b1_01 Strain:- | Sample type:pool_mutant RAW_FILE_NAME=b1_pool_mutant_b1_01.mzML; Batch=1; Set=1 SUBJECT_SAMPLE_FACTORS - b1_pool_mutant_b1_02 Strain:- | Sample type:pool_mutant RAW_FILE_NAME=b1_pool_mutant_b1_02.mzML; Batch=1; Set=1 SUBJECT_SAMPLE_FACTORS - b2_pool_mutant_b2_01 Strain:- | Sample type:pool_mutant RAW_FILE_NAME=b2_pool_mutant_b2_01.mzML; Batch=2; Set=1 SUBJECT_SAMPLE_FACTORS - b2_pool_mutant_b2_02 Strain:- | Sample type:pool_mutant RAW_FILE_NAME=b2_pool_mutant_b2_02.mzML; Batch=2; Set=1 SUBJECT_SAMPLE_FACTORS - b3_pool_mutant_b3_01 Strain:- | Sample type:pool_mutant RAW_FILE_NAME=b3_pool_mutant_b3_01.mzML; Batch=3; Set=2 SUBJECT_SAMPLE_FACTORS - b3_pool_mutant_b3_02 Strain:- | Sample type:pool_mutant RAW_FILE_NAME=b3_pool_mutant_b3_02.mzML; Batch=3; Set=2 SUBJECT_SAMPLE_FACTORS - b4_pool_mutant_b4_01 Strain:- | Sample type:pool_mutant RAW_FILE_NAME=b4_pool_mutant_b4_01.mzML; Batch=4; Set=2 SUBJECT_SAMPLE_FACTORS - b4_pool_mutant_b4_02 Strain:- | Sample type:pool_mutant RAW_FILE_NAME=b4_pool_mutant_b4_02.mzML; Batch=4; Set=2 SUBJECT_SAMPLE_FACTORS - b5_pool_mutant_b5_01 Strain:- | Sample type:pool_mutant RAW_FILE_NAME=b5_pool_mutant_b5_01.mzML; Batch=5; Set=3 SUBJECT_SAMPLE_FACTORS - b5_pool_mutant_b5_02 Strain:- | Sample type:pool_mutant RAW_FILE_NAME=b5_pool_mutant_b5_02.mzML; Batch=5; Set=3 SUBJECT_SAMPLE_FACTORS - b6_pool_mutant_b6_01 Strain:- | Sample type:pool_mutant RAW_FILE_NAME=b6_pool_mutant_b6_01.mzML; Batch=6; Set=3 SUBJECT_SAMPLE_FACTORS - b6_pool_mutant_b6_02 Strain:- | Sample type:pool_mutant RAW_FILE_NAME=b6_pool_mutant_b6_02.mzML; Batch=6; Set=3 SUBJECT_SAMPLE_FACTORS - b1_pool_natural_b1_01 Strain:- | Sample type:pool_natural RAW_FILE_NAME=b1_pool_natural_b1_01.mzML; Batch=1; Set=1 SUBJECT_SAMPLE_FACTORS - b1_pool_natural_b1_02 Strain:- | Sample type:pool_natural RAW_FILE_NAME=b1_pool_natural_b1_02.mzML; Batch=1; Set=1 SUBJECT_SAMPLE_FACTORS - b2_pool_natural_b2_01 Strain:- | Sample type:pool_natural RAW_FILE_NAME=b2_pool_natural_b2_01.mzML; Batch=2; Set=1 SUBJECT_SAMPLE_FACTORS - b2_pool_natural_b2_02 Strain:- | Sample type:pool_natural RAW_FILE_NAME=b2_pool_natural_b2_02.mzML; Batch=2; Set=1 SUBJECT_SAMPLE_FACTORS - b1_pool_pd1074_b1_01 Strain:- | Sample type:pool_pd1074 RAW_FILE_NAME=b1_pool_pd1074_b1_01.mzML; Batch=1; Set=1 SUBJECT_SAMPLE_FACTORS - b1_pool_pd1074_b1_02 Strain:- | Sample type:pool_pd1074 RAW_FILE_NAME=b1_pool_pd1074_b1_02.mzML; Batch=1; Set=1 SUBJECT_SAMPLE_FACTORS - b2_pool_pd1074_b2_01 Strain:- | Sample type:pool_pd1074 RAW_FILE_NAME=b2_pool_pd1074_b2_01.mzML; Batch=2; Set=1 SUBJECT_SAMPLE_FACTORS - b2_pool_pd1074_b2_02 Strain:- | Sample type:pool_pd1074 RAW_FILE_NAME=b2_pool_pd1074_b2_02.mzML; Batch=2; Set=1 SUBJECT_SAMPLE_FACTORS - b3_pool_pd1074_b3_01 Strain:- | Sample type:pool_pd1074 RAW_FILE_NAME=b3_pool_pd1074_b3_01.mzML; Batch=3; Set=2 SUBJECT_SAMPLE_FACTORS - b3_pool_pd1074_b3_02 Strain:- | Sample type:pool_pd1074 RAW_FILE_NAME=b3_pool_pd1074_b3_02.mzML; Batch=3; Set=2 SUBJECT_SAMPLE_FACTORS - b4_pool_pd1074_b4_01 Strain:- | Sample type:pool_pd1074 RAW_FILE_NAME=b4_pool_pd1074_b4_01.mzML; Batch=4; Set=2 SUBJECT_SAMPLE_FACTORS - b4_pool_pd1074_b4_02 Strain:- | Sample type:pool_pd1074 RAW_FILE_NAME=b4_pool_pd1074_b4_02.mzML; Batch=4; Set=2 SUBJECT_SAMPLE_FACTORS - b5_pool_pd1074_b5_01 Strain:- | Sample type:pool_pd1074 RAW_FILE_NAME=b5_pool_pd1074_b5_01.mzML; Batch=5; Set=3 SUBJECT_SAMPLE_FACTORS - b5_pool_pd1074_b5_02 Strain:- | Sample type:pool_pd1074 RAW_FILE_NAME=b5_pool_pd1074_b5_02.mzML; Batch=5; Set=3 SUBJECT_SAMPLE_FACTORS - b6_pool_pd1074_b6_01 Strain:- | Sample type:pool_pd1074 RAW_FILE_NAME=b6_pool_pd1074_b6_01.mzML; Batch=6; Set=3 SUBJECT_SAMPLE_FACTORS - b6_pool_pd1074_b6_02 Strain:- | Sample type:pool_pd1074 RAW_FILE_NAME=b6_pool_pd1074_b6_02.mzML; Batch=6; Set=3 SUBJECT_SAMPLE_FACTORS - b3_aos_184 Strain:VC1265 | Sample type:sample RAW_FILE_NAME=b3_aos_184.mzML; Batch=3; Set=2 SUBJECT_SAMPLE_FACTORS - b3_aos_42 Strain:VC1265 | Sample type:sample RAW_FILE_NAME=b3_aos_42.mzML; Batch=3; Set=2 SUBJECT_SAMPLE_FACTORS - b3_aos_98 Strain:VC1265 | Sample type:sample RAW_FILE_NAME=b3_aos_98.mzML; Batch=3; Set=2 SUBJECT_SAMPLE_FACTORS - b4_aos_125 Strain:VC1265 | Sample type:sample RAW_FILE_NAME=b4_aos_125.mzML; Batch=4; Set=2 SUBJECT_SAMPLE_FACTORS - b4_aos_73 Strain:VC1265 | Sample type:sample RAW_FILE_NAME=b4_aos_73.mzML; Batch=4; Set=2 SUBJECT_SAMPLE_FACTORS - b4_aos_84 Strain:VC1265 | Sample type:sample RAW_FILE_NAME=b4_aos_84.mzML; Batch=4; Set=2 SUBJECT_SAMPLE_FACTORS - b4_aos_93 Strain:VC1265 | Sample type:sample RAW_FILE_NAME=b4_aos_93.mzML; Batch=4; Set=2 SUBJECT_SAMPLE_FACTORS - b5_aos_187 Strain:VC2512 | Sample type:sample RAW_FILE_NAME=b5_aos_187.mzML; Batch=5; Set=3 SUBJECT_SAMPLE_FACTORS - b5_aos_33 Strain:VC2512 | Sample type:sample RAW_FILE_NAME=b5_aos_33.mzML; Batch=5; Set=3 SUBJECT_SAMPLE_FACTORS - b5_aos_66 Strain:VC2512 | Sample type:sample RAW_FILE_NAME=b5_aos_66.mzML; Batch=5; Set=3 SUBJECT_SAMPLE_FACTORS - b6_aos_193 Strain:VC2512 | Sample type:sample RAW_FILE_NAME=b6_aos_193.mzML; Batch=6; Set=3 SUBJECT_SAMPLE_FACTORS - b5_aos_179 Strain:VC2524 | Sample type:sample RAW_FILE_NAME=b5_aos_179.mzML; Batch=5; Set=3 SUBJECT_SAMPLE_FACTORS - b5_aos_47 Strain:VC2524 | Sample type:sample RAW_FILE_NAME=b5_aos_47.mzML; Batch=5; Set=3 SUBJECT_SAMPLE_FACTORS - b5_aos_70 Strain:VC2524 | Sample type:sample RAW_FILE_NAME=b5_aos_70.mzML; Batch=5; Set=3 SUBJECT_SAMPLE_FACTORS - b6_aos_105 Strain:VC2524 | Sample type:sample RAW_FILE_NAME=b6_aos_105.mzML; Batch=6; Set=3 SUBJECT_SAMPLE_FACTORS - b6_aos_85 Strain:VC2524 | Sample type:sample RAW_FILE_NAME=b6_aos_85.mzML; Batch=6; Set=3 SUBJECT_SAMPLE_FACTORS - b6_aos_94 Strain:VC2524 | Sample type:sample RAW_FILE_NAME=b6_aos_94.mzML; Batch=6; Set=3 #COLLECTION CO:COLLECTION_SUMMARY Escherichia coli (E. coli) IBAT (iterative batch average method) reference CO:COLLECTION_SUMMARY material and food source used throughout this experiment. Briefly, for each CO:COLLECTION_SUMMARY biological sample, a large-scale culture plate (LSCP) was used to generate a CO:COLLECTION_SUMMARY large mixed-stage population of worms (four to seven LSCP replicates per test CO:COLLECTION_SUMMARY strain). For each LSCP, worms were collected, population size estimated, and CO:COLLECTION_SUMMARY subsequently divided into at least 12 identical aliquots of 200,000 worms in CO:COLLECTION_SUMMARY ddH2O and flash-frozen in liquid nitrogen and stored at -80°C 8. As a quality CO:COLLECTION_SUMMARY control sample, C. elegans IBAT reference material was generated and saved in CO:COLLECTION_SUMMARY 200,000 worm aliquots. CO:SAMPLE_TYPE Worms CO:VOLUMEORAMOUNT_COLLECTED 200,000 worms CO:STORAGE_CONDITIONS -80℃ #TREATMENT TR:TREATMENT_SUMMARY No treatments. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Frozen aliquots of 200,000 C. elegans worms were retrieved from -80°C and SP:SAMPLEPREP_SUMMARY lyophilized in a VirTis® BenchTop™ “K” Series Freeze Dryer (SP SP:SAMPLEPREP_SUMMARY Industries, Inc.). After lyophilization, each aliquot was weighed and stored at SP:SAMPLEPREP_SUMMARY -80°C until homogenization. Aliquots were homogenized for three minutes in a SP:SAMPLEPREP_SUMMARY Qiagen Tissuelyser 2, using glass beads. Homogenized worms were extracted with SP:SAMPLEPREP_SUMMARY 1.5 mL of isopropanol (IPA) at -20°C overnight (approximately 12 hours), then SP:SAMPLEPREP_SUMMARY pelleted and the supernatant transferred to separate 2 mL centrifuge tubes. SP:SAMPLEPREP_SUMMARY Supernatants were then dried down to completion in a Labconco Centrivap and SP:SAMPLEPREP_SUMMARY stored at -80°C for non-polar LC-MS analysis. The pellet was extracted a second SP:SAMPLEPREP_SUMMARY time using 80:20 methanol:water (MeOH:H2O) (v:v) for 20 minutes at room SP:SAMPLEPREP_SUMMARY temperature (RT) while shaking at 1500 rpm. Samples were again pelleted to SP:SAMPLEPREP_SUMMARY separate proteins, and the supernatant was transferred to separate 2 mL SP:SAMPLEPREP_SUMMARY centrifuge tubes, dried down to completion, and stored at -80°C for polar LC-MS SP:SAMPLEPREP_SUMMARY analysis SP:SAMPLEPREP_PROTOCOL_FILENAME lcms_sequential_extraction_method.pdf SP:PROCESSING_STORAGE_CONDITIONS -80℃ SP:EXTRACTION_METHOD IPA for non-polar; 80/20 MeOH/H2O for polar SP:EXTRACT_STORAGE -80℃ SP:SAMPLE_RESUSPENSION 75 µL of IPA containing isotopically labeled lipid standards; 75 µL of 80:20 SP:SAMPLE_RESUSPENSION MeOH: H2O containing isotopically labeled arginine, hypoxanthine, hippuric acid, SP:SAMPLE_RESUSPENSION and methionine #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY Polar extracts were separated using a Vanquish (ThermoFisher Scientific), fitted CH:CHROMATOGRAPHY_SUMMARY with a Waters Acquity UPLC BEH Amide column (2.1 x 150 mm, 1.7 µm particle CH:CHROMATOGRAPHY_SUMMARY size). The compounds were eluted with the following gradient: 80:20 CH:CHROMATOGRAPHY_SUMMARY water:acetonitrile (H2O:ACN) with 10 mM ammonium formate and 0.1% formic acid CH:CHROMATOGRAPHY_SUMMARY (mobile phase A) and 100% ACN with 0.1% formic acid (mobile phase B) using the CH:CHROMATOGRAPHY_SUMMARY following gradient program: 0.0-0.5 min 95% B; 8.0-9.4 min 40% B; 9.5-11.0 min CH:CHROMATOGRAPHY_SUMMARY 95% B. A curve 5 value was set for 0.0 minutes, a curve 6 at 0.5 min, curve 7 at CH:CHROMATOGRAPHY_SUMMARY 8.0 min, and a curve 6 for the remainder of the gradient. The flow rate was set CH:CHROMATOGRAPHY_SUMMARY at 0.400 mL min-1. The column temperature was set to 40°C, and the injection CH:CHROMATOGRAPHY_SUMMARY volume was 2 µL. CH:INSTRUMENT_NAME Thermo Vanquish CH:COLUMN_NAME Waters Acquity BEH Amide (150 x 2.1mm,1.7um) CH:COLUMN_TEMPERATURE 40 CH:SOLVENT_A 80% water/20% acetonitrile; 0.1% formic acid; 10 mM ammonium formate CH:SOLVENT_B 100% acetonitrile; 0.1% formic acid CH:CHROMATOGRAPHY_TYPE HILIC #ANALYSIS AN:LABORATORY_NAME Fernandez Lab - Georgia Tech University AN:ANALYSIS_TYPE MS AN:ACQUISITION_DATE 7/28/20-08/07/20 AN:OPERATOR_NAME Carter Asef AN:DETECTOR_TYPE Orbitrap AN:DATA_FORMAT .raw #MS MS:INSTRUMENT_NAME Thermo Orbitrap ID-X tribrid MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:MS_COMMENTS LC-MS data was collected using a Thermo Orbitrap ID-X tribrid in full profile MS:MS_COMMENTS mode at 240,000 resolution. A m/z range of 70-1050 was used. Data was centroided MS:MS_COMMENTS using Proteowizard and processed using open source software SLAW for peak MS:MS_COMMENTS picking, alignment, and feature assignment. MS:ION_MODE POSITIVE MS:CAPILLARY_TEMPERATURE 275 MS:DRY_GAS_FLOW 40 MS:DRY_GAS_TEMP 320 MS:SPRAY_VOLTAGE 3500 MS:DATAFORMAT .raw Profile MS:MS_RESULTS_FILE ST002092_AN003418_Results.txt UNITS:Ranked Peak Height Has m/z:Yes Has RT:Yes RT units:Minutes #END