#METABOLOMICS WORKBENCH Codreags00_20211013_124924 DATATRACK_ID:2884 STUDY_ID:ST001957 ANALYSIS_ID:AN003191 VERSION 1 CREATED_ON 02-08-2024 #PROJECT PR:PROJECT_TITLE Untargeted Mass Spectrometry Metabolomic Profiles of iPSC-derived Dopaminergic PR:PROJECT_TITLE Neurons from Clinically Discordant Brothers with Identical PRKN Deletions PR:PROJECT_TYPE Untargeted Metabolomics analysis PR:PROJECT_SUMMARY We have previously reported on two brothers, PM and SM, who carry identical PR:PROJECT_SUMMARY compound heterozygous PRKN mutations but present with very different clinical PR:PROJECT_SUMMARY Parkinson’s disease (PD) phenotypes, with PM, but not SM having been diagnosed PR:PROJECT_SUMMARY with early onset disease. The occurrence of juvenile cases demonstrates that PD PR:PROJECT_SUMMARY is not necessarily an age-associated disease, indeed evidence is accumulating PR:PROJECT_SUMMARY that there is a developmental component to PD pathogenesis. We hypothesize that PR:PROJECT_SUMMARY additional genetic modifiers, potentially including genetic loci relevant to PR:PROJECT_SUMMARY mesencephalic dopamine neuron development may play a role. We differentiated PR:PROJECT_SUMMARY human-induced pluripotent stem cells (hiPSCs) derived from SM and PM into PR:PROJECT_SUMMARY mitotically active mesencephalic neural precursor cells and early post mitotic PR:PROJECT_SUMMARY dopaminergic neurons and performed whole exome sequencing, transcriptomic- and PR:PROJECT_SUMMARY metabolomic analyses. No significant differences in canonical markers of PR:PROJECT_SUMMARY differentiation were observed between SM and PM. Yet our transcriptomic analysis PR:PROJECT_SUMMARY revealed a significant down regulation of three neurodevelopmentally relevant PR:PROJECT_SUMMARY cell adhesion molecules, CNTN6, CNTN4 and CHL1 in PM - compared to SM cultures PR:PROJECT_SUMMARY on days 11 and 25 of differentiation. In addition, several HLA genes, known to PR:PROJECT_SUMMARY play a role in neurodevelopment, independent of their well-established function PR:PROJECT_SUMMARY in immunity, were differentially regulated in PM and SM developing dopamine PR:PROJECT_SUMMARY neurons. EN2, a transcription factor crucial for mesencephalic dopamine neuron PR:PROJECT_SUMMARY development, was also differentially regulated. We further observed differences PR:PROJECT_SUMMARY in cellular processes relevant to dopamine homeostasis. Lastly, our whole exome PR:PROJECT_SUMMARY sequencing, transcriptomics and metabolomics data of SM and PM neurons revealed PR:PROJECT_SUMMARY differences in GSH homeostasis, the dysregulation of which has been associated PR:PROJECT_SUMMARY with PD. PR:INSTITUTE VANDERBILT UNIVERSITY PR:DEPARTMENT Chemistry PR:LABORATORY Center for Innovative Technology PR:LAST_NAME CODREANU PR:FIRST_NAME SIMONA PR:ADDRESS 1234 STEVENSON CENTER LANE, NASHVILLE, TN, 37235, USA PR:EMAIL SIMONA.CODREANU@VANDERBILT.EDU PR:PHONE 6158758422 PR:DOI http://dx.doi.org/10.21228/M8X40N #STUDY ST:STUDY_TITLE Untargeted Mass Spectrometry Metabolomic Profiles of iPSC-derived Dopaminergic ST:STUDY_TITLE Neurons from Clinically Discordant Brothers with Identical PRKN Deletions ST:STUDY_TYPE untargeted metabolomics analysis ST:STUDY_SUMMARY We have previously reported on two brothers, PM and SM, who carry identical ST:STUDY_SUMMARY compound heterozygous PRKN mutations but present with very different clinical ST:STUDY_SUMMARY Parkinson’s disease (PD) phenotypes, with PM, but not SM having been diagnosed ST:STUDY_SUMMARY with early onset disease. The occurrence of juvenile cases demonstrates that PD ST:STUDY_SUMMARY is not necessarily an age-associated disease, indeed evidence is accumulating ST:STUDY_SUMMARY that there is a developmental component to PD pathogenesis. We hypothesize that ST:STUDY_SUMMARY additional genetic modifiers, potentially including genetic loci relevant to ST:STUDY_SUMMARY mesencephalic dopamine neuron development may play a role. We differentiated ST:STUDY_SUMMARY human-induced pluripotent stem cells (hiPSCs) derived from SM and PM into ST:STUDY_SUMMARY mitotically active mesencephalic neural precursor cells and early postmitotic ST:STUDY_SUMMARY dopaminergic neurons and performed whole exome sequencing, transcriptomic- and ST:STUDY_SUMMARY metabolomic analyses. No significant differences in canonical markers of ST:STUDY_SUMMARY differentiation were observed between SM and PM. Yet our transcriptomic analysis ST:STUDY_SUMMARY revealed a significant down regulation of three neurodevelopmentally relevant ST:STUDY_SUMMARY cell adhesion molecules, CNTN6, CNTN4 and CHL1 in PM- compared to SM cultures on ST:STUDY_SUMMARY days 11 and 25 of differentiation. In addition, several HLA genes, known to play ST:STUDY_SUMMARY a role in neurodevelopment, independent of their well-established function in ST:STUDY_SUMMARY immunity, were differentially regulated in PM and SM developing dopamine ST:STUDY_SUMMARY neurons. EN2, a transcription factor crucial for mesencephalic dopamine neuron ST:STUDY_SUMMARY development, was also differentially regulated. We further observed differences ST:STUDY_SUMMARY in cellular processes relevant to dopamine homeostasis. Lastly, our whole exome ST:STUDY_SUMMARY sequencing, transcriptomics and metabolomics data of SM and PM neurons revealed ST:STUDY_SUMMARY differences in GSH homeostasis, the dysregulation of which has been associated ST:STUDY_SUMMARY with PD. ST:INSTITUTE Vanderbilt University ST:DEPARTMENT Chemistry ST:LABORATORY Center for Innovative Technology ST:LAST_NAME CODREANU ST:FIRST_NAME SIMONA ST:ADDRESS 1234 STEVENSON CENTER LANE ST:EMAIL SIMONA.CODREANU@VANDERBILT.EDU ST:PHONE 6158758422 ST:SUBMIT_DATE 2021-10-13 #SUBJECT SU:SUBJECT_TYPE Cultured cells SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 SU:GENOTYPE_STRAIN PRKN mutations (PD) SU:GENDER Male #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS SM3 HILICn_43_SM3_200_1 genotype:PRKN_no_PD | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190423_HILICn_PRM_43_SM3_200_1; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS SM3 HILICn_44_SM3_200_2 genotype:PRKN_no_PD | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190423_HILICn_PRM_44_SM3_200_2; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS SM3 HILICn_45_SM3_200_3 genotype:PRKN_no_PD | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190423_HILICn_PRM_45_SM3_200_3; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS SM5 HILICn_52_SM5_200_1 genotype:PRKN_no_PD | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190423_HILICn_PRM_52_SM5_200_1; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS SM5 HILICn_53_SM5_200_2 genotype:PRKN_no_PD | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190423_HILICn_PRM_53_SM5_200_2; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS SM5 HILICn_54_SM5_200_3 genotype:PRKN_no_PD | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190423_HILICn_PRM_54_SM5_200_3; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS SM14 HILICp_18_SM14_200 genotype:PRKN_no_PD | Mn treatment (uM):200 RAW_FILE_NAME=SC_20160524_ND_HILICp_FMS_SM14_200; MS Method=Method#1_HILIC_Pos SUBJECT_SAMPLE_FACTORS SM15 HILICp_21_SM15_200 genotype:PRKN_no_PD | Mn treatment (uM):200 RAW_FILE_NAME=SC_20160524_ND_HILICp_FMS_SM15_200; MS Method=Method#1_HILIC_Pos SUBJECT_SAMPLE_FACTORS SM3 HILICp_43_SM3_200_1 genotype:PRKN_no_PD | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190410_HILICp_PRM_43_SM3_200_1; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS SM3 HILICp_44_SM3_200_2 genotype:PRKN_no_PD | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190410_HILICp_PRM_44_SM3_200_2; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS SM3 HILICp_45_SM3_200_3 genotype:PRKN_no_PD | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190410_HILICp_PRM_45_SM3_200_3; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS SM5 HILICp_52_SM5_200_1 genotype:PRKN_no_PD | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190410_HILICp_PRM_52_SM5_200_1; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS SM5 HILICp_53_SM5_200_2 genotype:PRKN_no_PD | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190410_HILICp_PRM_53_SM5_200_2; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS SM5 HILICp_54_SM5_200_3 genotype:PRKN_no_PD | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190410_HILICp_PRM_54_SM5_200_3; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS SM14 RPLCp_35_SM14_200_TH1 genotype:PRKN_no_PD | Mn treatment (uM):200 RAW_FILE_NAME=sgc_021516r_ND_SM14_200_TH1.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS SM14 RPLCp_36_SM14_200_TH2 genotype:PRKN_no_PD | Mn treatment (uM):200 RAW_FILE_NAME=sgc_021516r_ND_SM14_200_TH2.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS SM15 RPLCp_41_SM15_200_TH1 genotype:PRKN_no_PD | Mn treatment (uM):200 RAW_FILE_NAME=sgc_021516r_ND_SM15_200_TH1.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS SM15 RPLCp_42_SM15_200_TH2 genotype:PRKN_no_PD | Mn treatment (uM):200 RAW_FILE_NAME=sgc_021516r_ND_SM15_200_TH2.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS SM3 HILICn_40_SM3_50_1 genotype:PRKN_no_PD | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190423_HILICn_PRM_40_SM3_50_1; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS SM3 HILICn_41_SM3_50_2 genotype:PRKN_no_PD | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190423_HILICn_PRM_41_SM3_50_2; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS SM3 HILICn_42_SM3_50_3 genotype:PRKN_no_PD | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190423_HILICn_PRM_42_SM3_50_3; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS SM5 HILICn_49_SM5_50_1 genotype:PRKN_no_PD | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190423_HILICn_PRM_49_SM5_50_1; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS SM5 HILICn_50_SM5_50_2 genotype:PRKN_no_PD | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190423_HILICn_PRM_50_SM5_50_2; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS SM5 HILICn_51_SM5_50_3 genotype:PRKN_no_PD | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190423_HILICn_PRM_51_SM5_50_3; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS SM14 HILICp_17_SM14_50 genotype:PRKN_no_PD | Mn treatment (uM):50 RAW_FILE_NAME=SC_20160524_ND_HILICp_FMS_SM14_50; MS Method=Method#1_HILIC_Pos SUBJECT_SAMPLE_FACTORS SM15 HILICp_20_SM15_50 genotype:PRKN_no_PD | Mn treatment (uM):50 RAW_FILE_NAME=SC_20160524_ND_HILICp_FMS_SM15_50; MS Method=Method#1_HILIC_Pos SUBJECT_SAMPLE_FACTORS SM3 HILICp_40_SM3_50_1 genotype:PRKN_no_PD | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190410_HILICp_PRM_40_SM3_50_1; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS SM3 HILICp_41_SM3_50_2 genotype:PRKN_no_PD | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190410_HILICp_PRM_41_SM3_50_2; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS SM3 HILICp_42_SM3_50_3 genotype:PRKN_no_PD | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190410_HILICp_PRM_42_SM3_50_3; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS SM5 HILICp_49_SM5_50_1 genotype:PRKN_no_PD | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190410_HILICp_PRM_49_SM5_50_1; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS SM5 HILICp_50_SM5_50_2 genotype:PRKN_no_PD | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190410_HILICp_PRM_50_SM5_50_2; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS SM5 HILICp_51_SM5_50_3 genotype:PRKN_no_PD | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190410_HILICp_PRM_51_SM5_50_3; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS SM14 RPLCp_33_SM14_50_TH1 genotype:PRKN_no_PD | Mn treatment (uM):50 RAW_FILE_NAME=sgc_021516r_ND_SM14_50_TH1.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS SM14 RPLCp_34_SM14_50_TH2 genotype:PRKN_no_PD | Mn treatment (uM):50 RAW_FILE_NAME=sgc_021516r_ND_SM14_50_TH2.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS SM15 RPLCp_39_SM15_50_TH1 genotype:PRKN_no_PD | Mn treatment (uM):50 RAW_FILE_NAME=sgc_021516r_ND_SM15_50_TH1.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS SM15 RPLCp_40_SM15_50_TH2 genotype:PRKN_no_PD | Mn treatment (uM):50 RAW_FILE_NAME=sgc_021516r_ND_SM15_50_TH2.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS SM3 HILICn_37_SM3_0_1 genotype:PRKN_no_PD | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190423_HILICn_PRM_37_SM3_0_1; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS SM3 HILICn_38_SM3_0_2 genotype:PRKN_no_PD | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190423_HILICn_PRM_38_SM3_0_2; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS SM3 HILICn_39_SM3_0_3 genotype:PRKN_no_PD | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190423_HILICn_PRM_39_SM3_0_3; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS SM5 HILICn_46_SM5_0_1 genotype:PRKN_no_PD | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190423_HILICn_PRM_46_SM5_0_1; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS SM5 HILICn_47_SM5_0_2 genotype:PRKN_no_PD | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190423_HILICn_PRM_47_SM5_0_2; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS SM5 HILICn_48_SM5_0_3 genotype:PRKN_no_PD | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190423_HILICn_PRM_48_SM5_0_3; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS SM14 HILICp_16_SM14_0 genotype:PRKN_no_PD | Mn treatment (uM):Control RAW_FILE_NAME=SC_20160524_ND_HILICp_FMS_SM14_0; MS Method=Method#1_HILIC_Pos SUBJECT_SAMPLE_FACTORS SM15 HILICp_19_SM15_0 genotype:PRKN_no_PD | Mn treatment (uM):Control RAW_FILE_NAME=SC_20160524_ND_HILICp_FMS_SM15_0; MS Method=Method#1_HILIC_Pos SUBJECT_SAMPLE_FACTORS SM3 HILICp_37_SM3_0_1 genotype:PRKN_no_PD | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190410_HILICp_PRM_37_SM3_0_1; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS SM3 HILICp_38_SM3_0_2 genotype:PRKN_no_PD | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190410_HILICp_PRM_38_SM3_0_2; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS SM3 HILICp_39_SM3_0_3 genotype:PRKN_no_PD | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190410_HILICp_PRM_39_SM3_0_3; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS SM5 HILICp_46_SM5_0_1 genotype:PRKN_no_PD | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190410_HILICp_PRM_46_SM5_0_1; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS SM5 HILICp_47_SM5_0_2 genotype:PRKN_no_PD | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190410_HILICp_PRM_47_SM5_0_2; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS SM5 HILICp_48_SM5_0_3 genotype:PRKN_no_PD | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190410_HILICp_PRM_48_SM5_0_3; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS SM14 RPLCp_31_SM14_0_TH1 genotype:PRKN_no_PD | Mn treatment (uM):Control RAW_FILE_NAME=sgc_021516r_ND_SM14_0_TH1.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS SM14 RPLCp_32_SM14_0_TH2 genotype:PRKN_no_PD | Mn treatment (uM):Control RAW_FILE_NAME=sgc_021516r_ND_SM14_0_TH2.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS SM15 RPLCp_37_SM15_0_TH1 genotype:PRKN_no_PD | Mn treatment (uM):Control RAW_FILE_NAME=sgc_021516r_ND_SM15_0_TH1.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS SM15 RPLCp_38_SM15_0_TH2 genotype:PRKN_no_PD | Mn treatment (uM):Control RAW_FILE_NAME=sgc_021516r_ND_SM15_0_TH2.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS PM1 HILICn_61_PM1_200_1 genotype:PRKN_PD | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190423_HILICn_PRM_61_PM1_200_1; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS PM1 HILICn_62_PM1_200_2 genotype:PRKN_PD | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190423_HILICn_PRM_62_PM1_200_2; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS PM1 HILICn_63_PM1_200_3 genotype:PRKN_PD | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190423_HILICn_PRM_63_PM1_200_3; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS PM18 HILICn_70_PM18_200_1 genotype:PRKN_PD | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190423_HILICn_PRM_70_PM18_200_1; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS PM18 HILICn_71_PM18_200_2 genotype:PRKN_PD | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190423_HILICn_PRM_71_PM18_200_2; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS PM18 HILICn_72_PM18_200_3 genotype:PRKN_PD | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190423_HILICn_PRM_72_PM18_200_3; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS PM12 HILICp_12_PM12_200 genotype:PRKN_PD | Mn treatment (uM):200 RAW_FILE_NAME=SC_20160524_ND_HILICp_FMS_PM12_200; MS Method=Method#1_HILIC_Pos SUBJECT_SAMPLE_FACTORS PM17 HILICp_15_PM17_200 genotype:PRKN_PD | Mn treatment (uM):200 RAW_FILE_NAME=SC_20160524_ND_HILICp_FMS_PM17_200; MS Method=Method#1_HILIC_Pos SUBJECT_SAMPLE_FACTORS PM1 HILICp_61_PM1_200_1 genotype:PRKN_PD | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190410_HILICp_PRM_61_PM1_200_1; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS PM1 HILICp_62_PM1_200_2 genotype:PRKN_PD | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190410_HILICp_PRM_62_PM1_200_2; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS PM1 HILICp_63_PM1_200_3 genotype:PRKN_PD | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190410_HILICp_PRM_63_PM1_200_3; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS PM18 HILICp_70_PM18_200_1 genotype:PRKN_PD | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190410_HILICp_PRM_70_PM18_200_1; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS PM18 HILICp_71_PM18_200_2 genotype:PRKN_PD | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190410_HILICp_PRM_71_PM18_200_2; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS PM18 HILICp_72_PM18_200_3 genotype:PRKN_PD | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190410_HILICp_PRM_72_PM18_200_3; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS PM12 RPLCp_23_PM12_200_TH1 genotype:PRKN_PD | Mn treatment (uM):200 RAW_FILE_NAME=sgc_021516r_ND_PM12_200_TH1.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS PM12 RPLCp_24_PM12_200_TH2 genotype:PRKN_PD | Mn treatment (uM):200 RAW_FILE_NAME=sgc_021516r_ND_PM12_200_TH2.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS PM17 RPLCp_29_PM17_200_TH1 genotype:PRKN_PD | Mn treatment (uM):200 RAW_FILE_NAME=sgc_021516r_ND_PM17_200_TH1.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS PM17 RPLCp_30_PM17_200_TH2 genotype:PRKN_PD | Mn treatment (uM):200 RAW_FILE_NAME=sgc_021516r_ND_PM17_200_TH2.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS PM1 HILICn_58_PM1_50_1 genotype:PRKN_PD | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190423_HILICn_PRM_58_PM1_50_1; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS PM1 HILICn_59_PM1_50_2 genotype:PRKN_PD | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190423_HILICn_PRM_59_PM1_50_2; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS PM1 HILICn_60_PM1_50_3 genotype:PRKN_PD | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190423_HILICn_PRM_60_PM1_50_3; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS PM18 HILICn_67_PM18_50_1 genotype:PRKN_PD | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190423_HILICn_PRM_67_PM18_50_1; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS PM18 HILICn_68_PM18_50_2 genotype:PRKN_PD | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190423_HILICn_PRM_68_PM18_50_2; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS PM18 HILICn_69_PM18_50_3 genotype:PRKN_PD | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190423_HILICn_PRM_69_PM18_50_3; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS PM12 HILICp_11_PM12_50 genotype:PRKN_PD | Mn treatment (uM):50 RAW_FILE_NAME=SC_20160524_ND_HILICp_FMS_PM12_50; MS Method=Method#1_HILIC_Pos SUBJECT_SAMPLE_FACTORS PM17 HILICp_14_PM17_50 genotype:PRKN_PD | Mn treatment (uM):50 RAW_FILE_NAME=SC_20160524_ND_HILICp_FMS_PM17_50; MS Method=Method#1_HILIC_Pos SUBJECT_SAMPLE_FACTORS PM1 HILICp_58_PM1_50_1 genotype:PRKN_PD | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190410_HILICp_PRM_58_PM1_50_1; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS PM1 HILICp_59_PM1_50_2 genotype:PRKN_PD | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190410_HILICp_PRM_59_PM1_50_2; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS PM1 HILICp_60_PM1_50_3 genotype:PRKN_PD | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190410_HILICp_PRM_60_PM1_50_3; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS PM18 HILICp_67_PM18_50_1 genotype:PRKN_PD | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190410_HILICp_PRM_67_PM18_50_1; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS PM18 HILICp_68_PM18_50_2 genotype:PRKN_PD | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190410_HILICp_PRM_68_PM18_50_2; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS PM18 HILICp_69_PM18_50_3 genotype:PRKN_PD | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190410_HILICp_PRM_69_PM18_50_3; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS PM12 RPLCp_21_PM12_50_TH1 genotype:PRKN_PD | Mn treatment (uM):50 RAW_FILE_NAME=sgc_021516r_ND_PM12_50_TH1.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS PM12 RPLCp_22_PM12_50_TH2 genotype:PRKN_PD | Mn treatment (uM):50 RAW_FILE_NAME=sgc_021516r_ND_PM12_50_TH2.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS PM17 RPLCp_27_PM17_50_TH1 genotype:PRKN_PD | Mn treatment (uM):50 RAW_FILE_NAME=sgc_021516r_ND_PM17_50_TH1.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS PM17 RPLCp_28_PM17_50_TH2 genotype:PRKN_PD | Mn treatment (uM):50 RAW_FILE_NAME=sgc_021516r_ND_PM17_50_TH2.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS PM1 HILICn_55_PM1_0_1 genotype:PRKN_PD | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190423_HILICn_PRM_55_PM1_0_1; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS PM1 HILICn_56_PM1_0_2 genotype:PRKN_PD | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190423_HILICn_PRM_56_PM1_0_2; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS PM1 HILICn_57_PM1_0_3 genotype:PRKN_PD | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190423_HILICn_PRM_57_PM1_0_3; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS PM18 HILICn_64_PM18_0_1 genotype:PRKN_PD | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190423_HILICn_PRM_64_PM18_0_1; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS PM18 HILICn_65_PM18_0_2 genotype:PRKN_PD | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190423_HILICn_PRM_65_PM18_0_2; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS PM18 HILICn_66_PM18_0_3 genotype:PRKN_PD | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190423_HILICn_PRM_66_PM18_0_3; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS PM12 HILICp_10_PM12_0 genotype:PRKN_PD | Mn treatment (uM):Control RAW_FILE_NAME=SC_20160524_ND_HILICp_FMS_PM12_0; MS Method=Method#1_HILIC_Pos SUBJECT_SAMPLE_FACTORS PM17 HILICp_13_PM17_0 genotype:PRKN_PD | Mn treatment (uM):Control RAW_FILE_NAME=SC_20160524_ND_HILICp_FMS_PM17_0; MS Method=Method#1_HILIC_Pos SUBJECT_SAMPLE_FACTORS PM1 HILICp_55_PM1_0_1 genotype:PRKN_PD | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190410_HILICp_PRM_55_PM1_0_1; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS PM1 HILICp_56_PM1_0_2 genotype:PRKN_PD | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190410_HILICp_PRM_56_PM1_0_2; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS PM1 HILICp_57_PM1_0_3 genotype:PRKN_PD | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190410_HILICp_PRM_57_PM1_0_3; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS PM18 HILICp_64_PM18_0_1 genotype:PRKN_PD | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190410_HILICp_PRM_64_PM18_0_1; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS PM18 HILICp_65_PM18_0_2 genotype:PRKN_PD | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190410_HILICp_PRM_65_PM18_0_2; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS PM18 HILICp_66_PM18_0_3 genotype:PRKN_PD | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190410_HILICp_PRM_66_PM18_0_3; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS PM12 RPLCp_19_PM12_0_TH1 genotype:PRKN_PD | Mn treatment (uM):Control RAW_FILE_NAME=sgc_021516r_ND_PM12_0_TH1.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS PM12 RPLCp_20_PM12_0_TH2 genotype:PRKN_PD | Mn treatment (uM):Control RAW_FILE_NAME=sgc_021516r_ND_PM12_0_TH2.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS PM17 RPLCp_25_PM17_0_TH1 genotype:PRKN_PD | Mn treatment (uM):Control RAW_FILE_NAME=sgc_021516r_ND_PM17_0_TH1.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS PM17 RPLCp_26_PM17_0_TH2 genotype:PRKN_PD | Mn treatment (uM):Control RAW_FILE_NAME=sgc_021516r_ND_PM17_0_TH2.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS CA30 HILICn_16_CA30_200_1 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190423_HILICn_PRM_16_CA30_200_1; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CA30 HILICn_17_CA30_200_2 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190423_HILICn_PRM_17_CA30_200_2; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CA30 HILICn_18_CA30_200_3 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190423_HILICn_PRM_18_CA30_200_3; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CD10 HILICn_25_CD10_200_1 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190423_HILICn_PRM_25_CD10_200_1; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CD10 HILICn_26_CD10_200_2 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190423_HILICn_PRM_26_CD10_200_2; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CD10 HILICn_27_CD10_200_3 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190423_HILICn_PRM_27_CD10_200_3; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CD12 HILICn_34_CD12_200_1 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190423_HILICn_PRM_34_CD12_200_1; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CD12 HILICn_35_CD12_200_2 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190423_HILICn_PRM_35_CD12_200_2; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CD12 HILICn_36_CD12_200_3 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190423_HILICn_PRM_36_CD12_200_3; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CA11 HILICn_7_CA11_200_1 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190423_HILICn_PRM_7_CA11_200_1; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CA11 HILICn_8_CA11_200_2 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190423_HILICn_PRM_8_CA11_200_2; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CA11 HILICn_9_CA11_200_3 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190423_HILICn_PRM_9_CA11_200_3; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CA30 HILICp_16_CA30_200_1 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190410_HILICp_PRM_16_CA30_200_1; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CA30 HILICp_17_CA30_200_2 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190410_HILICp_PRM_17_CA30_200_2; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CA30 HILICp_18_CA30_200_3 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190410_HILICp_PRM_18_CA30_200_3; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CD10 HILICp_25_CD10_200_1 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190410_HILICp_PRM_25_CD10_200_1; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CD10 HILICp_26_CD10_200_2 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190410_HILICp_PRM_26_CD10_200_2; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CD10 HILICp_27_CD10_200_3 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190410_HILICp_PRM_27_CD10_200_3; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CD12 HILICp_34_CD12_200_1 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190410_HILICp_PRM_34_CD12_200_1; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CD12 HILICp_35_CD12_200_2 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190410_HILICp_PRM_35_CD12_200_2; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CD12 HILICp_36_CD12_200_3 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190410_HILICp_PRM_36_CD12_200_3; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CC3 HILICp_3_CC3_200 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=SC_20160524_ND_HILICp_FMS_CC3_200; MS Method=Method#1_HILIC_Pos SUBJECT_SAMPLE_FACTORS CD12 HILICp_6_CD12_200 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=SC_20160524_ND_HILICp_FMS_CD12_200; MS Method=Method#1_HILIC_Pos SUBJECT_SAMPLE_FACTORS CA11 HILICp_7_CA11_200_1 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190410_HILICp_PRM_7_CA11_200_1; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CA11 HILICp_8_CA11_200_2 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190410_HILICp_PRM_8_CA11_200_2; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CA11 HILICp_9_CA11_200_3 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=SC_20190410_HILICp_PRM_9_CA11_200_3; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CE6 HILICp_9_CE6_200 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=SC_20160524_ND_HILICp_FMS_CE6_200; MS Method=Method#1_HILIC_Pos SUBJECT_SAMPLE_FACTORS CD12 RPLCp_11_CD12_200_TH1 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=sgc_021516r_ND_CD12_200_TH1.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS CD12 RPLCp_12_CD12_200_TH2 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=sgc_021516r_ND_CD12_200_TH2.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS CE6 RPLCp_17_CE6_200_TH1 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=sgc_021516r_ND_CE6_200_TH1.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS CE6 RPLCp_18_CE6_200_TH2 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=sgc_021516r_ND_CE6_200_TH2.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS CC3 RPLCp_5_CC3_200_TH1 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=sgc_021516r_ND_CC3_200_TH1.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS CC3 RPLCp_6_CC3_200_TH2 genotype:Wild-type | Mn treatment (uM):200 RAW_FILE_NAME=sgc_021516r_ND_CC3_200_TH2.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS CA30 HILICn_13_CA30_50_1 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190423_HILICn_PRM_13_CA30_50_1; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CA30 HILICn_14_CA30_50_2 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190423_HILICn_PRM_14_CA30_50_2; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CA30 HILICn_15_CA30_50_3 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190423_HILICn_PRM_15_CA30_50_3; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CD10 HILICn_22_CD10_50_1 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190423_HILICn_PRM_22_CD10_50_1; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CD10 HILICn_23_CD10_50_2 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190423_HILICn_PRM_23_CD10_50_2; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CD10 HILICn_24_CD10_50_3 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190423_HILICn_PRM_24_CD10_50_3; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CD12 HILICn_31_CD12_50_1 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190423_HILICn_PRM_31_CD12_50_1; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CD12 HILICn_32_CD12_50_2 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190423_HILICn_PRM_32_CD12_50_2; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CD12 HILICn_33_CD12_50_3 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190423_HILICn_PRM_33_CD12_50_3; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CA11 HILICn_4_CA11_50_1 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190423_HILICn_PRM_4_CA11_50_1; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CA11 HILICn_5_CA11_50_2 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190423_HILICn_PRM_5_CA11_50_2; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CA11 HILICn_6_CA11_50_3 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190423_HILICn_PRM_6_CA11_50_3; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CA30 HILICp_13_CA30_50_1 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190410_HILICp_PRM_13_CA30_50_1; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CA30 HILICp_14_CA30_50_2 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190410_HILICp_PRM_14_CA30_50_2; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CA30 HILICp_15_CA30_50_3 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190410_HILICp_PRM_15_CA30_50_3; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CD10 HILICp_22_CD10_50_1 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190410_HILICp_PRM_22_CD10_50_1; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CD10 HILICp_23_CD10_50_2 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190410_HILICp_PRM_23_CD10_50_2; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CD10 HILICp_24_CD10_50_3 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190410_HILICp_PRM_24_CD10_50_3; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CC3 HILICp_2_CC3_50 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=SC_20160524_ND_HILICp_FMS_CC3_50; MS Method=Method#1_HILIC_Pos SUBJECT_SAMPLE_FACTORS CD12 HILICp_31_CD12_50_1 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190410_HILICp_PRM_31_CD12_50_1; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CD12 HILICp_32_CD12_50_2 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190410_HILICp_PRM_32_CD12_50_2; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CD12 HILICp_33_CD12_50_3 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190410_HILICp_PRM_33_CD12_50_3; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CA11 HILICp_4_CA11_50_1 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190410_HILICp_PRM_4_CA11_50_1; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CA11 HILICp_5_CA11_50_2 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190410_HILICp_PRM_5_CA11_50_2; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CD12 HILICp_5_CD12_50 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=SC_20160524_ND_HILICp_FMS_CD12_50; MS Method=Method#1_HILIC_Pos SUBJECT_SAMPLE_FACTORS CA11 HILICp_6_CA11_50_3 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=SC_20190410_HILICp_PRM_6_CA11_50_3; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CE6 HILICp_8_CE6_50 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=SC_20160524_ND_HILICp_FMS_CE6_50; MS Method=Method#1_HILIC_Pos SUBJECT_SAMPLE_FACTORS CD12 RPLCp_10_CD12_50_TH2 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=sgc_021516r_ND_CD12_50_TH2.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS CE6 RPLCp_15_CE6_50_TH1 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=sgc_021516r_ND_CE6_50_TH1.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS CE6 RPLCp_16_CE6_50_TH2 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=sgc_021516r_ND_CE6_50_TH2.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS CC3 RPLCp_3_CC3_50_TH1 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=sgc_021516r_ND_CC3_50_TH1.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS CC3 RPLCp_4_CC3_50_TH2 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=sgc_021516r_ND_CC3_50_TH2.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS CD12 RPLCp_9_CD12_50_TH1 genotype:Wild-type | Mn treatment (uM):50 RAW_FILE_NAME=sgc_021516r_ND_CD12_50_TH1.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS CA30 HILICn_10_CA30_0_1 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190423_HILICn_PRM_10_CA30_0_1; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CA30 HILICn_11_CA30_0_2 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190423_HILICn_PRM_11_CA30_0_2; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CA30 HILICn_12_CA30_0_3 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190423_HILICn_PRM_12_CA30_0_3; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CD10 HILICn_19_CD10_0_1 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190423_HILICn_PRM_19_CD10_0_1; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CA11 HILICn_1_CA11_0_1 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190423_HILICn_PRM_1_CA11_0_1; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CD10 HILICn_20_CD10_0_2 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190423_HILICn_PRM_20_CD10_0_2; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CD10 HILICn_21_CD10_0_3 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190423_HILICn_PRM_21_CD10_0_3; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CD12 HILICn_28_CD12_0_1 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190423_HILICn_PRM_28_CD12_0_1; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CD12 HILICn_29_CD12_0_2 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190423_HILICn_PRM_29_CD12_0_2; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CA11 HILICn_2_CA11_0_2 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190423_HILICn_PRM_2_CA11_0_2; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CD12 HILICn_30_CD12_0_3 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190423_HILICn_PRM_30_CD12_0_3; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CA11 HILICn_3_CA11_0_3 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190423_HILICn_PRM_3_CA11_0_3; MS Method=Method#2_HILIC_neg SUBJECT_SAMPLE_FACTORS CA30 HILICp_10_CA30_0_1 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190410_HILICp_PRM_10_CA30_0_1; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CA30 HILICp_11_CA30_0_2 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190410_HILICp_PRM_11_CA30_0_2; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CA30 HILICp_12_CA30_0_3 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190410_HILICp_PRM_12_CA30_0_3; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CD10 HILICp_19_CD10_0_1 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190410_HILICp_PRM_19_CD10_0_1; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CA11 HILICp_1_CA11_0_1 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190410_HILICp_PRM_1_CA11_0_1; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CC3 HILICp_1_CC3_0 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=SC_20160524_ND_HILICp_FMS_CC3_0; MS Method=Method#1_HILIC_Pos SUBJECT_SAMPLE_FACTORS CD10 HILICp_20_CD10_0_2 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190410_HILICp_PRM_20_CD10_0_2; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CD10 HILICp_21_CD10_0_3 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190410_HILICp_PRM_21_CD10_0_3; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CD12 HILICp_28_CD12_0_1 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190410_HILICp_PRM_28_CD12_0_1; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CD12 HILICp_29_CD12_0_2 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190410_HILICp_PRM_29_CD12_0_2; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CA11 HILICp_2_CA11_0_2 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190410_HILICp_PRM_2_CA11_0_2; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CD12 HILICp_30_CD12_0_3 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190410_HILICp_PRM_30_CD12_0_3; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CA11 HILICp_3_CA11_0_3 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=SC_20190410_HILICp_PRM_3_CA11_0_3; MS Method=Method#2_HILIC_pos SUBJECT_SAMPLE_FACTORS CD12 HILICp_4_CD12_0 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=SC_20160524_ND_HILICp_FMS_CD12_0; MS Method=Method#1_HILIC_Pos SUBJECT_SAMPLE_FACTORS CE6 HILICp_7_CE6_0 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=SC_20160524_ND_HILICp_FMS_CE6_0; MS Method=Method#1_HILIC_Pos SUBJECT_SAMPLE_FACTORS CE6 RPLCp_13_CE6_0_TH1 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=sgc_021516r_ND_CE6_0_TH1.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS CE6 RPLCp_14_CE6_0_TH2 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=sgc_021516r_ND_CE6_0_TH2.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS CC3 RPLCp_1_CC3_0_TH1 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=sgc_021516r_ND_CC3_0_TH1.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS CC3 RPLCp_2_CC3_0_TH2 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=sgc_021516r_ND_CC3_0_TH2.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS CD12 RPLCp_7_CD12_0_TH1 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=sgc_021516r_ND_CD12_0_TH1.raw; MS Method=Method#1_RPLC_Pos SUBJECT_SAMPLE_FACTORS CD12 RPLCp_8_CD12_0_TH2 genotype:Wild-type | Mn treatment (uM):Control RAW_FILE_NAME=sgc_021516r_ND_CD12_0_TH2.raw; MS Method=Method#1_RPLC_Pos #COLLECTION CO:COLLECTION_SUMMARY iPSC lines were derived from dermal fibroblasts from two human subjects, PM and CO:COLLECTION_SUMMARY SM, and four independent clones from each patient were used in this study (PM1, CO:COLLECTION_SUMMARY PM12, PM17 and PM18; SM3, SM5, SM14 and SM15).Fibroblasts were obtained by skin CO:COLLECTION_SUMMARY biopsy after the appropriate patient consent/assent under the guidelines of an CO:COLLECTION_SUMMARY approved Internal Review Board (IRB) protocol at Vanderbilt University CO:COLLECTION_SUMMARY (#080369). Three of the iPSC lines (PM1, SM3, SM5) were generated by transducing CO:COLLECTION_SUMMARY the fibroblasts with a lentivirus as previously described. The other five lines CO:COLLECTION_SUMMARY (PM12, PM17, PM18, SM14, SM15) were reprogrammed by electroporation with CXLE CO:COLLECTION_SUMMARY plasmid vectors (Addgene) using the Neon Transfection System (Life Technologies) CO:COLLECTION_SUMMARY following published methods. CO:SAMPLE_TYPE Skin Biopsy CO:STORAGE_CONDITIONS -80℃ #TREATMENT TR:TREATMENT_SUMMARY Differentiation of the iPSCs to a mesencephalic dopaminergic lineage was TR:TREATMENT_SUMMARY performed as previously described 39,40,126. In brief, iPSCs were differentiated TR:TREATMENT_SUMMARY in a first stage into floor plate cells (mesencephalic neural precursors) (days TR:TREATMENT_SUMMARY 0-11) via dual SMAD inhibition combined with ventral midbrain patterning. In a TR:TREATMENT_SUMMARY second stage, these floor plate cells were further differentiated (days 11-25) TR:TREATMENT_SUMMARY into early post mitotic mesencephalic dopamine neurons. Cells were treated in TR:TREATMENT_SUMMARY culture with either 0, 50uM or 200uM Mn. TR:TREATMENT_COMPOUND Mn TR:TREATMENT_DOSE 0uM, 50uM, 200uM #SAMPLEPREP SP:SAMPLEPREP_SUMMARY For method #1 (RPLC pos/ HILIC pos) day 11 neural dopaminergic precursor cells SP:SAMPLEPREP_SUMMARY (floor plate cells of one well of a 6 well plate) were harvested into 500 µl of SP:SAMPLEPREP_SUMMARY ice-cold methanol, flash frozen and then stored at -80oC. To extract the SP:SAMPLEPREP_SUMMARY metabolites, the 500 µl methanol cell suspensions were thawed and 100 µl of SP:SAMPLEPREP_SUMMARY H2O added. Then the samples were frozen on dry ice for 3 min, defrosted in ice SP:SAMPLEPREP_SUMMARY over a 10 min period, and sonicated with 10 pulses using a probe sonicator at SP:SAMPLEPREP_SUMMARY 30% power. The freeze-thaw-sonication sequence was repeated three times. The SP:SAMPLEPREP_SUMMARY proteins were precipitated by placing the lysates at -80°C overnight and then SP:SAMPLEPREP_SUMMARY pelleted by centrifugation at 15,000 rpm for 15 minutes. Cleared supernatants SP:SAMPLEPREP_SUMMARY containing the metabolites were placed in clean Eppendorf tubes, dried in a SP:SAMPLEPREP_SUMMARY vacuum concentrator and stored frozen at -80°C. For reverse phase liquid SP:SAMPLEPREP_SUMMARY chromatography (RPLC)-positive (pos) mode mass spectrometry analysis the dried SP:SAMPLEPREP_SUMMARY extracts were reconstituted in 60 μl of RPLC buffer (acetonitrile/water with SP:SAMPLEPREP_SUMMARY 0.1% formic acid, 2:98, v/v). Samples were vortexed rigorously to solubilize the SP:SAMPLEPREP_SUMMARY metabolites, cleared by centrifugation for 5 min at 15,000 rpm, and the SP:SAMPLEPREP_SUMMARY supernatants were injected twice (5μl/injection) randomly. For method #2 (HILIC SP:SAMPLEPREP_SUMMARY pos/neg) the cells were washed three times with 2.5 ml of an ammonium formate SP:SAMPLEPREP_SUMMARY buffer (50 mM, pH 6.8), scraped into the same buffer, centrifugated at 200 x for SP:SAMPLEPREP_SUMMARY 5 min, the cell pellets flash frozen in liquid nitrogen and stored at -80o C. To SP:SAMPLEPREP_SUMMARY extract the metabolites, cell pellets were lysed in 200 µl ice-cold lysis SP:SAMPLEPREP_SUMMARY buffer (1:1:2, Acetonitrile:MeOH:Ammonium Bicarbonate 0.1M, pH 8.0, LC-MS grade) SP:SAMPLEPREP_SUMMARY and sonicated once as described above. The protein concentration was determined SP:SAMPLEPREP_SUMMARY (BCA assay, Thermo Fisher Scientific) and adjusted to 1 mg/ml. Isotopically SP:SAMPLEPREP_SUMMARY labeled standard molecules, Phenylalanine-D8 and Biotin-D2 were added to the 200 SP:SAMPLEPREP_SUMMARY µl cell lysates, the protein precipitated by addition of 800 µl of ice-cold SP:SAMPLEPREP_SUMMARY methanol and stored at -80°C overnight. Upon thawing, the precipitated proteins SP:SAMPLEPREP_SUMMARY were pelleted by centrifugation at 9300 x g for 10 min, the supernatants SP:SAMPLEPREP_SUMMARY transferred into two clean Eppendorf tubes, dried down in vacuo and stored at SP:SAMPLEPREP_SUMMARY -80°C. SP:SAMPLEPREP_PROTOCOL_FILENAME Materials_and_Methods_DN.pdf SP:PROCESSING_STORAGE_CONDITIONS -80℃ SP:EXTRACT_STORAGE On ice #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY Method#2_HILIC_positive CH:METHODS_FILENAME Materials_and_Methods_DN.pdf CH:INSTRUMENT_NAME Thermo Vanquish CH:COLUMN_NAME EMD Millipore ZIC-HILIC (100 x 2.1mm,3.5um) CH:COLUMN_TEMPERATURE 40 CH:FLOW_RATE 0.20 mL/min CH:INJECTION_TEMPERATURE 8 CH:SOLVENT_A 90% acetonitrile/10% water; 5 mM ammonium formate CH:SOLVENT_B 10% water/90% acetonitrile; 5 mM ammonium formate CH:CHROMATOGRAPHY_TYPE HILIC #ANALYSIS AN:ANALYSIS_TYPE MS AN:ANALYSIS_PROTOCOL_FILE Materials_and_Methods_DN.pdf #MS MS:INSTRUMENT_NAME Thermo Q Exactive HF hybrid Orbitrap MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:MS_COMMENTS Progenesis QI MS:ION_MODE NEGATIVE MS:MS_RESULTS_FILE ST001957_AN003191_Results.txt UNITS:peak area Has m/z:Yes Has RT:Yes RT units:Minutes #END