#METABOLOMICS WORKBENCH Jung_DNLI_20250623_151403 DATATRACK_ID:6083 STUDY_ID:ST004058 ANALYSIS_ID:AN006707 PROJECT_ID:PR002548
VERSION             	1
CREATED_ON             	July 22, 2025, 11:13 am
#PROJECT
PR:PROJECT_TITLE                 	Lysosomal polyamine storage upon ATP13A2 loss impairs β-glucocerebrosidase via
PR:PROJECT_TITLE                 	altered lysosomal pH and electrostatic hydrolase-lipid interactions
PR:PROJECT_TYPE                  	Preclinical Mouse and cellular studies
PR:PROJECT_SUMMARY               	ATP13A2 is an endolysosomal polyamine transporter mutated in several
PR:PROJECT_SUMMARY               	neurodegenerative conditions involving lysosomal defects, including
PR:PROJECT_SUMMARY               	Parkinson’s disease (PD). While polyamines are polybasic and polycationic
PR:PROJECT_SUMMARY               	molecules that play pleiotropic cellular roles, their specific impact on
PR:PROJECT_SUMMARY               	lysosomal health is unknown. Here, we demonstrate lysosomal polyamine
PR:PROJECT_SUMMARY               	accumulation in ATP13A2 knockout (KO) cell lines. Primary polyamine storage
PR:PROJECT_SUMMARY               	caused secondary storage of lysosomal anionic phospholipid
PR:PROJECT_SUMMARY               	bis(monoacylglycero)phosphate (BMP) and age-dependent increase in the
PR:PROJECT_SUMMARY               	β-glucocerebrosidase (GCase) substrate, glucosylsphingosine, in Atp13a2 KO
PR:PROJECT_SUMMARY               	brains. Polyamine accumulation inhibited lysosomal GCase activity in cells and
PR:PROJECT_SUMMARY               	this was reversed by lysosome reacidification or BMP supplementation. A
PR:PROJECT_SUMMARY               	liposome-based GCase assay utilizing physiological substrates demonstrated
PR:PROJECT_SUMMARY               	dose-dependent inhibition of BMP-stimulated GCase activity by polyamines, in
PR:PROJECT_SUMMARY               	part via a pH-independent, electrostatics-based mechanism. Therefore, excess
PR:PROJECT_SUMMARY               	polyamine compromises lysosomes by disrupting pH and electrostatic interactions
PR:PROJECT_SUMMARY               	between GCase and BMP enabling efficient substrate hydrolysis, potentially
PR:PROJECT_SUMMARY               	clarifying their pathogenic mechanisms, and suggesting convergence on
PR:PROJECT_SUMMARY               	PD-relevant pathways.
PR:INSTITUTE                     	Denali Therapeutics
PR:LAST_NAME                     	Suh
PR:FIRST_NAME                    	Jung
PR:ADDRESS                       	161 Oyster Point Blvd, South San Francisco, California, 94080, USA
PR:EMAIL                         	suh@dnli.com
PR:PHONE                         	+1 6507973837
#STUDY
ST:STUDY_TITLE                   	Targeted Lipid and Metabolite Profiling in ATP13A2 knockout (KO) in HAP1 cells
ST:STUDY_SUMMARY                 	Targeted profiling of lipids and metabolites was performed in ATP13A2 knockout
ST:STUDY_SUMMARY                 	(KO) HAP1 cells with and without polyamine (Spermine) and lipid (DOPC or PG
ST:STUDY_SUMMARY                 	22:6) treatments.
ST:INSTITUTE                     	Denali Therapeutics
ST:LAST_NAME                     	Suh
ST:FIRST_NAME                    	Jung
ST:ADDRESS                       	161 Oyster Point Blvd
ST:EMAIL                         	suh@dnli.com
ST:PHONE                         	+1 6507973837
#SUBJECT
SU:SUBJECT_TYPE                  	Cultured cells
SU:SUBJECT_SPECIES               	Homo sapiens
SU:TAXONOMY_ID                   	9606
#SUBJECT_SAMPLE_FACTORS:         	SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data
SUBJECT_SAMPLE_FACTORS           	Pool_001	HSA-000043722	Genotype:NA | Treatment:NA | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=-; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000956_HALO_Pos_002.mzML
SUBJECT_SAMPLE_FACTORS           	KO_b	HSA-000043633	Genotype:ATP13A2 KO | Treatment:none | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=-; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000956_HALO_Pos_003.mzML
SUBJECT_SAMPLE_FACTORS           	WT_b	HSA-000043625	Genotype:WT | Treatment:none | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=-; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000956_HALO_Pos_007.mzML
SUBJECT_SAMPLE_FACTORS           	WT_a	HSA-000043624	Genotype:WT | Treatment:none | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=-; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000956_HALO_Pos_009.mzML
SUBJECT_SAMPLE_FACTORS           	WT_c	HSA-000043626	Genotype:WT | Treatment:none | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=-; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000956_HALO_Pos_010.mzML
SUBJECT_SAMPLE_FACTORS           	Pool_002	HSA-000043812	Genotype:NA | Treatment:NA | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=-; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000956_HALO_Pos_011.mzML
SUBJECT_SAMPLE_FACTORS           	WT_d	HSA-000043627	Genotype:WT | Treatment:none | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=-; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000956_HALO_Pos_014.mzML
SUBJECT_SAMPLE_FACTORS           	KO_a	HSA-000043632	Genotype:ATP13A2 KO | Treatment:none | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=-; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000956_HALO_Pos_015.mzML
SUBJECT_SAMPLE_FACTORS           	KO_c	HSA-000043634	Genotype:ATP13A2 KO | Treatment:none | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=-; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000956_HALO_Pos_016.mzML
SUBJECT_SAMPLE_FACTORS           	KO_d	HSA-000043635	Genotype:ATP13A2 KO | Treatment:none | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=-; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000956_HALO_Pos_018.mzML
SUBJECT_SAMPLE_FACTORS           	Pool_003	HSA-000043813	Genotype:NA | Treatment:NA | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=-; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000956_HALO_Pos_020.mzML
SUBJECT_SAMPLE_FACTORS           	Pool1_001	HSA-000043814	Genotype:NA | Treatment:NA | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_002.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_002.mzML
SUBJECT_SAMPLE_FACTORS           	pH_KO_c	HSA-000043739	Genotype:ATP13A2 KO | Treatment:PBS | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_003.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_003.mzML
SUBJECT_SAMPLE_FACTORS           	pH_WT_b	HSA-000043726	Genotype:WT | Treatment:PBS | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_004.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_004.mzML
SUBJECT_SAMPLE_FACTORS           	pH_WT_SPM_b	HSA-000043729	Genotype:WT | Treatment:SPM | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_005.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_005.mzML
SUBJECT_SAMPLE_FACTORS           	pH_KO_Rim_a	HSA-000043743	Genotype:ATP13A2 KO | Treatment:Rim | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_006.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_006.mzML
SUBJECT_SAMPLE_FACTORS           	pH_WT_SPM_Rim_c	HSA-000043736	Genotype:WT | Treatment:SPM + Rim | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_007.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_007.mzML
SUBJECT_SAMPLE_FACTORS           	pH_KO_SPM_Rim_b	HSA-000043747	Genotype:ATP13A2 KO | Treatment:SPM + Rim | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_008.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_008.mzML
SUBJECT_SAMPLE_FACTORS           	pH_WT_Rim_a	HSA-000043731	Genotype:WT | Treatment:Rim | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_009.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_009.mzML
SUBJECT_SAMPLE_FACTORS           	pH_WT_Rim_b	HSA-000043732	Genotype:WT | Treatment:Rim | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_010.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_010.mzML
SUBJECT_SAMPLE_FACTORS           	pH_WT_SPM_Rim_b	HSA-000043735	Genotype:WT | Treatment:SPM + Rim | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_011.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_011.mzML
SUBJECT_SAMPLE_FACTORS           	pH_KO_SPM_c	HSA-000043742	Genotype:ATP13A2 KO | Treatment:SPM | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_012.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_012.mzML
SUBJECT_SAMPLE_FACTORS           	pH_KO_SPM_Rim_a	HSA-000043746	Genotype:ATP13A2 KO | Treatment:SPM + Rim | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_013.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_013.mzML
SUBJECT_SAMPLE_FACTORS           	pH_KO_a	HSA-000043737	Genotype:ATP13A2 KO | Treatment:PBS | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_014.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_014.mzML
SUBJECT_SAMPLE_FACTORS           	Pool1_002	HSA-000043815	Genotype:NA | Treatment:NA | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_015.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_015.mzML
SUBJECT_SAMPLE_FACTORS           	pH_WT_Rim_c	HSA-000043733	Genotype:WT | Treatment:Rim | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_016.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_016.mzML
SUBJECT_SAMPLE_FACTORS           	pH_KO_SPM_a	HSA-000043740	Genotype:ATP13A2 KO | Treatment:SPM | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_017.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_017.mzML
SUBJECT_SAMPLE_FACTORS           	pH_WT_SPM_a	HSA-000043728	Genotype:WT | Treatment:SPM | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_018.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_018.mzML
SUBJECT_SAMPLE_FACTORS           	pH_WT_SPM_c	HSA-000043730	Genotype:WT | Treatment:SPM | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_019.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_019.mzML
SUBJECT_SAMPLE_FACTORS           	pH_KO_SPM_Rim_c	HSA-000043748	Genotype:ATP13A2 KO | Treatment:SPM + Rim | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_020.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_020.mzML
SUBJECT_SAMPLE_FACTORS           	pH_KO_Rim_b	HSA-000043744	Genotype:ATP13A2 KO | Treatment:Rim | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_021.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_021.mzML
SUBJECT_SAMPLE_FACTORS           	pH_WT_a	HSA-000043725	Genotype:WT | Treatment:PBS | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_022.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_022.mzML
SUBJECT_SAMPLE_FACTORS           	pH_WT_c	HSA-000043727	Genotype:WT | Treatment:PBS | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_023.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_023.mzML
SUBJECT_SAMPLE_FACTORS           	pH_WT_SPM_Rim_a	HSA-000043734	Genotype:WT | Treatment:SPM + Rim | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_024.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_024.mzML
SUBJECT_SAMPLE_FACTORS           	pH_KO_SPM_b	HSA-000043741	Genotype:ATP13A2 KO | Treatment:SPM | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_025.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_025.mzML
SUBJECT_SAMPLE_FACTORS           	pH_KO_Rim_c	HSA-000043745	Genotype:ATP13A2 KO | Treatment:Rim | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_026.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_026.mzML
SUBJECT_SAMPLE_FACTORS           	pH_KO_b	HSA-000043738	Genotype:ATP13A2 KO | Treatment:PBS | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_027.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_027.mzML
SUBJECT_SAMPLE_FACTORS           	Pool1_003	HSA-000043816	Genotype:NA | Treatment:NA | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_028.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_028.mzML
SUBJECT_SAMPLE_FACTORS           	Pool2_001	HSA-000043817	Genotype:NA | Treatment:NA | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_030.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_030.mzML
SUBJECT_SAMPLE_FACTORS           	PG_WT_c	HSA-000043754	Genotype:WT | Treatment:PBS | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_031.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_031.mzML
SUBJECT_SAMPLE_FACTORS           	PG_WT_SPM_DOPC_b	HSA-000043759	Genotype:WT | Treatment:SPM + DOPC | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_033.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_033.mzML
SUBJECT_SAMPLE_FACTORS           	PG_KO_22 6 PG_b	HSA-000043798	Genotype:ATP13A2 KO | Treatment:22 6 PG | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_034.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_034.mzML
SUBJECT_SAMPLE_FACTORS           	PG_WT_DOPC_c	HSA-000043769	Genotype:WT | Treatment:DOPC | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_035.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_035.mzML
SUBJECT_SAMPLE_FACTORS           	PG_KO_c	HSA-000043778	Genotype:ATP13A2 KO | Treatment:PBS | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_036.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_036.mzML
SUBJECT_SAMPLE_FACTORS           	PG_KO_22 6 PG_a	HSA-000043797	Genotype:ATP13A2 KO | Treatment:22 6 PG | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_037.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_037.mzML
SUBJECT_SAMPLE_FACTORS           	PG_KO_SPM_22 6 PG_b	HSA-000043789	Genotype:ATP13A2 KO | Treatment:SPM + 22 6 PG | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_038.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_038.mzML
SUBJECT_SAMPLE_FACTORS           	PG_WT_SPM_c	HSA-000043757	Genotype:WT | Treatment:SPM | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_039.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_039.mzML
SUBJECT_SAMPLE_FACTORS           	PG_WT_SPM_DOPC_c	HSA-000043760	Genotype:WT | Treatment:SPM + DOPC | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_040.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_040.mzML
SUBJECT_SAMPLE_FACTORS           	PG_KO_a	HSA-000043776	Genotype:ATP13A2 KO | Treatment:PBS | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_041.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_041.mzML
SUBJECT_SAMPLE_FACTORS           	PG_WT_22 6 PG_c	HSA-000043775	Genotype:WT | Treatment:22 6 PG | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_042.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_042.mzML
SUBJECT_SAMPLE_FACTORS           	PG_WT_SPM_a	HSA-000043755	Genotype:WT | Treatment:SPM | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_043.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_043.mzML
SUBJECT_SAMPLE_FACTORS           	PG_WT_b	HSA-000043753	Genotype:WT | Treatment:PBS | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_044.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_044.mzML
SUBJECT_SAMPLE_FACTORS           	PG_KO_22 6 PG_c	HSA-000043799	Genotype:ATP13A2 KO | Treatment:22 6 PG | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_045.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_045.mzML
SUBJECT_SAMPLE_FACTORS           	PG_KO_SPM_DOPC_a	HSA-000043782	Genotype:ATP13A2 KO | Treatment:SPM + DOPC | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_046.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_046.mzML
SUBJECT_SAMPLE_FACTORS           	PG_WT_DOPC_b	HSA-000043768	Genotype:WT | Treatment:DOPC | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_049.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_049.mzML
SUBJECT_SAMPLE_FACTORS           	PG_WT_SPM_22 6 PG_c	HSA-000043766	Genotype:WT | Treatment:SPM + 22 6 PG | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_051.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_051.mzML
SUBJECT_SAMPLE_FACTORS           	PG_WT_SPM_DOPC_a	HSA-000043758	Genotype:WT | Treatment:SPM + DOPC | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_054.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_054.mzML
SUBJECT_SAMPLE_FACTORS           	Pool2_002	HSA-000043818	Genotype:NA | Treatment:NA | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_055.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_055.mzML
SUBJECT_SAMPLE_FACTORS           	PG_WT_SPM_22 6 PG_a	HSA-000043764	Genotype:WT | Treatment:SPM + 22 6 PG | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_057.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_057.mzML
SUBJECT_SAMPLE_FACTORS           	PG_KO_SPM_22 6 PG_c	HSA-000043790	Genotype:ATP13A2 KO | Treatment:SPM + 22 6 PG | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_059.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_059.mzML
SUBJECT_SAMPLE_FACTORS           	PG_KO_SPM_DOPC_c	HSA-000043784	Genotype:ATP13A2 KO | Treatment:SPM + DOPC | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_060.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_060.mzML
SUBJECT_SAMPLE_FACTORS           	PG_KO_DOPC_c	HSA-000043793	Genotype:ATP13A2 KO | Treatment:DOPC | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_062.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_062.mzML
SUBJECT_SAMPLE_FACTORS           	PG_WT_SPM_b	HSA-000043756	Genotype:WT | Treatment:SPM | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_063.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_063.mzML
SUBJECT_SAMPLE_FACTORS           	PG_WT_22 6 PG_a	HSA-000043773	Genotype:WT | Treatment:22 6 PG | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_064.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_064.mzML
SUBJECT_SAMPLE_FACTORS           	PG_KO_DOPC_b	HSA-000043792	Genotype:ATP13A2 KO | Treatment:DOPC | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_065.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_065.mzML
SUBJECT_SAMPLE_FACTORS           	PG_KO_DOPC_a	HSA-000043791	Genotype:ATP13A2 KO | Treatment:DOPC | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_066.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_066.mzML
SUBJECT_SAMPLE_FACTORS           	PG_WT_a	HSA-000043752	Genotype:WT | Treatment:PBS | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_067.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_067.mzML
SUBJECT_SAMPLE_FACTORS           	PG_KO_b	HSA-000043777	Genotype:ATP13A2 KO | Treatment:PBS | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_069.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_069.mzML
SUBJECT_SAMPLE_FACTORS           	PG_KO_SPM_DOPC_b	HSA-000043783	Genotype:ATP13A2 KO | Treatment:SPM + DOPC | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_070.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_070.mzML
SUBJECT_SAMPLE_FACTORS           	PG_KO_SPM_c	HSA-000043781	Genotype:ATP13A2 KO | Treatment:SPM | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_071.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_071.mzML
SUBJECT_SAMPLE_FACTORS           	PG_WT_DOPC_a	HSA-000043767	Genotype:WT | Treatment:DOPC | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_072.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_072.mzML
SUBJECT_SAMPLE_FACTORS           	PG_WT_22 6 PG_b	HSA-000043774	Genotype:WT | Treatment:22 6 PG | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_075.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_075.mzML
SUBJECT_SAMPLE_FACTORS           	PG_WT_SPM_22 6 PG_b	HSA-000043765	Genotype:WT | Treatment:SPM + 22 6 PG | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_076.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_076.mzML
SUBJECT_SAMPLE_FACTORS           	PG_KO_SPM_a	HSA-000043779	Genotype:ATP13A2 KO | Treatment:SPM | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_077.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_077.mzML
SUBJECT_SAMPLE_FACTORS           	PG_KO_SPM_b	HSA-000043780	Genotype:ATP13A2 KO | Treatment:SPM | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_078.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_078.mzML
SUBJECT_SAMPLE_FACTORS           	PG_KO_SPM_22 6 PG_a	HSA-000043788	Genotype:ATP13A2 KO | Treatment:SPM + 22 6 PG | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_079.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_079.mzML
SUBJECT_SAMPLE_FACTORS           	Pool2_003	HSA-000043819	Genotype:NA | Treatment:NA | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=-; RAW_FILE_NAME(Raw Source Name.LN)=20250124_MS_HEX-000957_Lipid_Neg_080.mzML; RAW_FILE_NAME(Raw Source Name.MP)=-; RAW_FILE_NAME(Raw Source Name.MN)=-; RAW_FILE_NAME(Raw Source Name.HALO)=20250122_MS_HEX-000957_HALO_Pos_080.mzML
SUBJECT_SAMPLE_FACTORS           	Pool_Lyso_001	HSA-000038939	Genotype:NA | Treatment:NA | Sample source:HAP1 | Sample Type:lysosome	RAW_FILE_NAME(Raw Source Name.BZC)=20240905_MS_HEX-000820_PolyA_BzC_Pos_002.mzML; RAW_FILE_NAME(Raw Source Name.LN)=-; RAW_FILE_NAME(Raw Source Name.MP)=20240904_MS_HEX-000820_Met_Pos_002.mzML; RAW_FILE_NAME(Raw Source Name.MN)=20240905_MS_HEX-000820_Met_Neg_002.mzML; RAW_FILE_NAME(Raw Source Name.HALO)=-
SUBJECT_SAMPLE_FACTORS           	WT #1 Lyso	HSA-000038932	Genotype:WT | Treatment:none | Sample source:HAP1 | Sample Type:lysosome	RAW_FILE_NAME(Raw Source Name.BZC)=20240905_MS_HEX-000820_PolyA_BzC_Pos_003.mzML; RAW_FILE_NAME(Raw Source Name.LN)=-; RAW_FILE_NAME(Raw Source Name.MP)=20240904_MS_HEX-000820_Met_Pos_003.mzML; RAW_FILE_NAME(Raw Source Name.MN)=20240905_MS_HEX-000820_Met_Neg_003.mzML; RAW_FILE_NAME(Raw Source Name.HALO)=-
SUBJECT_SAMPLE_FACTORS           	WT #2 Lyso	HSA-000038933	Genotype:WT | Treatment:none | Sample source:HAP1 | Sample Type:lysosome	RAW_FILE_NAME(Raw Source Name.BZC)=20240905_MS_HEX-000820_PolyA_BzC_Pos_007.mzML; RAW_FILE_NAME(Raw Source Name.LN)=-; RAW_FILE_NAME(Raw Source Name.MP)=20240904_MS_HEX-000820_Met_Pos_007.mzML; RAW_FILE_NAME(Raw Source Name.MN)=20240905_MS_HEX-000820_Met_Neg_007.mzML; RAW_FILE_NAME(Raw Source Name.HALO)=-
SUBJECT_SAMPLE_FACTORS           	Pool_Lyso_002	HSA-000040325	Genotype:NA | Treatment:NA | Sample source:HAP1 | Sample Type:lysosome	RAW_FILE_NAME(Raw Source Name.BZC)=20240905_MS_HEX-000820_PolyA_BzC_Pos_008.mzML; RAW_FILE_NAME(Raw Source Name.LN)=-; RAW_FILE_NAME(Raw Source Name.MP)=20240904_MS_HEX-000820_Met_Pos_008.mzML; RAW_FILE_NAME(Raw Source Name.MN)=20240905_MS_HEX-000820_Met_Neg_008.mzML; RAW_FILE_NAME(Raw Source Name.HALO)=-
SUBJECT_SAMPLE_FACTORS           	WT #3 Lyso	HSA-000038934	Genotype:WT | Treatment:none | Sample source:HAP1 | Sample Type:lysosome	RAW_FILE_NAME(Raw Source Name.BZC)=20240905_MS_HEX-000820_PolyA_BzC_Pos_009.mzML; RAW_FILE_NAME(Raw Source Name.LN)=-; RAW_FILE_NAME(Raw Source Name.MP)=20240904_MS_HEX-000820_Met_Pos_009.mzML; RAW_FILE_NAME(Raw Source Name.MN)=20240905_MS_HEX-000820_Met_Neg_009.mzML; RAW_FILE_NAME(Raw Source Name.HALO)=-
SUBJECT_SAMPLE_FACTORS           	KO #2 Lyso	HSA-000038936	Genotype:ATP13A2 KO | Treatment:none | Sample source:HAP1 | Sample Type:lysosome	RAW_FILE_NAME(Raw Source Name.BZC)=20240905_MS_HEX-000820_PolyA_BzC_Pos_011.mzML; RAW_FILE_NAME(Raw Source Name.LN)=-; RAW_FILE_NAME(Raw Source Name.MP)=20240904_MS_HEX-000820_Met_Pos_011.mzML; RAW_FILE_NAME(Raw Source Name.MN)=20240905_MS_HEX-000820_Met_Neg_011.mzML; RAW_FILE_NAME(Raw Source Name.HALO)=-
SUBJECT_SAMPLE_FACTORS           	Pool_Lyso_003	HSA-000040326	Genotype:NA | Treatment:NA | Sample source:HAP1 | Sample Type:lysosome	RAW_FILE_NAME(Raw Source Name.BZC)=20240905_MS_HEX-000820_PolyA_BzC_Pos_016.mzML; RAW_FILE_NAME(Raw Source Name.LN)=-; RAW_FILE_NAME(Raw Source Name.MP)=20240904_MS_HEX-000820_Met_Pos_016.mzML; RAW_FILE_NAME(Raw Source Name.MN)=20240905_MS_HEX-000820_Met_Neg_016.mzML; RAW_FILE_NAME(Raw Source Name.HALO)=-
SUBJECT_SAMPLE_FACTORS           	KO #1 Lyso	HSA-000038935	Genotype:ATP13A2 KO | Treatment:none | Sample source:HAP1 | Sample Type:lysosome	RAW_FILE_NAME(Raw Source Name.BZC)=20240905_MS_HEX-000820_PolyA_BzC_Pos_019.mzML; RAW_FILE_NAME(Raw Source Name.LN)=-; RAW_FILE_NAME(Raw Source Name.MP)=20240904_MS_HEX-000820_Met_Pos_019.mzML; RAW_FILE_NAME(Raw Source Name.MN)=20240905_MS_HEX-000820_Met_Neg_019.mzML; RAW_FILE_NAME(Raw Source Name.HALO)=-
SUBJECT_SAMPLE_FACTORS           	KO #3 Lyso	HSA-000038937	Genotype:ATP13A2 KO | Treatment:none | Sample source:HAP1 | Sample Type:lysosome	RAW_FILE_NAME(Raw Source Name.BZC)=20240905_MS_HEX-000820_PolyA_BzC_Pos_022.mzML; RAW_FILE_NAME(Raw Source Name.LN)=-; RAW_FILE_NAME(Raw Source Name.MP)=20240904_MS_HEX-000820_Met_Pos_022.mzML; RAW_FILE_NAME(Raw Source Name.MN)=20240905_MS_HEX-000820_Met_Neg_022.mzML; RAW_FILE_NAME(Raw Source Name.HALO)=-
SUBJECT_SAMPLE_FACTORS           	Pool_Lyso_004	HSA-000040327	Genotype:NA | Treatment:NA | Sample source:HAP1 | Sample Type:lysosome	RAW_FILE_NAME(Raw Source Name.BZC)=20240905_MS_HEX-000820_PolyA_BzC_Pos_023.mzML; RAW_FILE_NAME(Raw Source Name.LN)=-; RAW_FILE_NAME(Raw Source Name.MP)=20240904_MS_HEX-000820_Met_Pos_023.mzML; RAW_FILE_NAME(Raw Source Name.MN)=20240905_MS_HEX-000820_Met_Neg_023.mzML; RAW_FILE_NAME(Raw Source Name.HALO)=-
SUBJECT_SAMPLE_FACTORS           	Pool_WCL_001	HSA-000038938	Genotype:NA | Treatment:NA | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=20240905_MS_HEX-000820_PolyA_BzC_Pos_024.mzML; RAW_FILE_NAME(Raw Source Name.LN)=-; RAW_FILE_NAME(Raw Source Name.MP)=20240904_MS_HEX-000820_Met_Pos_024.mzML; RAW_FILE_NAME(Raw Source Name.MN)=20240905_MS_HEX-000820_Met_Neg_024.mzML; RAW_FILE_NAME(Raw Source Name.HALO)=-
SUBJECT_SAMPLE_FACTORS           	KO #1 WCL	HSA-000038929	Genotype:ATP13A2 KO | Treatment:none | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=20240905_MS_HEX-000820_PolyA_BzC_Pos_028.mzML; RAW_FILE_NAME(Raw Source Name.LN)=-; RAW_FILE_NAME(Raw Source Name.MP)=20240904_MS_HEX-000820_Met_Pos_028.mzML; RAW_FILE_NAME(Raw Source Name.MN)=20240905_MS_HEX-000820_Met_Neg_028.mzML; RAW_FILE_NAME(Raw Source Name.HALO)=-
SUBJECT_SAMPLE_FACTORS           	KO #2 WCL	HSA-000038930	Genotype:ATP13A2 KO | Treatment:none | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=20240905_MS_HEX-000820_PolyA_BzC_Pos_029.mzML; RAW_FILE_NAME(Raw Source Name.LN)=-; RAW_FILE_NAME(Raw Source Name.MP)=20240904_MS_HEX-000820_Met_Pos_029.mzML; RAW_FILE_NAME(Raw Source Name.MN)=20240905_MS_HEX-000820_Met_Neg_029.mzML; RAW_FILE_NAME(Raw Source Name.HALO)=-
SUBJECT_SAMPLE_FACTORS           	KO #3 WCL	HSA-000038931	Genotype:ATP13A2 KO | Treatment:none | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=20240905_MS_HEX-000820_PolyA_BzC_Pos_030.mzML; RAW_FILE_NAME(Raw Source Name.LN)=-; RAW_FILE_NAME(Raw Source Name.MP)=20240904_MS_HEX-000820_Met_Pos_030.mzML; RAW_FILE_NAME(Raw Source Name.MN)=20240905_MS_HEX-000820_Met_Neg_030.mzML; RAW_FILE_NAME(Raw Source Name.HALO)=-
SUBJECT_SAMPLE_FACTORS           	Pool_WCL_002	HSA-000040322	Genotype:NA | Treatment:NA | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=20240905_MS_HEX-000820_PolyA_BzC_Pos_031.mzML; RAW_FILE_NAME(Raw Source Name.LN)=-; RAW_FILE_NAME(Raw Source Name.MP)=20240904_MS_HEX-000820_Met_Pos_031.mzML; RAW_FILE_NAME(Raw Source Name.MN)=20240905_MS_HEX-000820_Met_Neg_031.mzML; RAW_FILE_NAME(Raw Source Name.HALO)=-
SUBJECT_SAMPLE_FACTORS           	WT #2 WCL	HSA-000038927	Genotype:WT | Treatment:none | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=20240905_MS_HEX-000820_PolyA_BzC_Pos_036.mzML; RAW_FILE_NAME(Raw Source Name.LN)=-; RAW_FILE_NAME(Raw Source Name.MP)=20240904_MS_HEX-000820_Met_Pos_036.mzML; RAW_FILE_NAME(Raw Source Name.MN)=20240905_MS_HEX-000820_Met_Neg_036.mzML; RAW_FILE_NAME(Raw Source Name.HALO)=-
SUBJECT_SAMPLE_FACTORS           	WT #1 WCL	HSA-000038926	Genotype:WT | Treatment:none | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=20240905_MS_HEX-000820_PolyA_BzC_Pos_037.mzML; RAW_FILE_NAME(Raw Source Name.LN)=-; RAW_FILE_NAME(Raw Source Name.MP)=20240904_MS_HEX-000820_Met_Pos_037.mzML; RAW_FILE_NAME(Raw Source Name.MN)=20240905_MS_HEX-000820_Met_Neg_037.mzML; RAW_FILE_NAME(Raw Source Name.HALO)=-
SUBJECT_SAMPLE_FACTORS           	Pool_WCL_003	HSA-000040323	Genotype:NA | Treatment:NA | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=20240905_MS_HEX-000820_PolyA_BzC_Pos_038.mzML; RAW_FILE_NAME(Raw Source Name.LN)=-; RAW_FILE_NAME(Raw Source Name.MP)=20240904_MS_HEX-000820_Met_Pos_038.mzML; RAW_FILE_NAME(Raw Source Name.MN)=20240905_MS_HEX-000820_Met_Neg_038.mzML; RAW_FILE_NAME(Raw Source Name.HALO)=-
SUBJECT_SAMPLE_FACTORS           	WT #3 WCL	HSA-000038928	Genotype:WT | Treatment:none | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=20240905_MS_HEX-000820_PolyA_BzC_Pos_043.mzML; RAW_FILE_NAME(Raw Source Name.LN)=-; RAW_FILE_NAME(Raw Source Name.MP)=20240904_MS_HEX-000820_Met_Pos_043.mzML; RAW_FILE_NAME(Raw Source Name.MN)=20240905_MS_HEX-000820_Met_Neg_043.mzML; RAW_FILE_NAME(Raw Source Name.HALO)=-
SUBJECT_SAMPLE_FACTORS           	Pool_WCL_004	HSA-000040324	Genotype:NA | Treatment:NA | Sample source:HAP1 | Sample Type:whole cell lysate	RAW_FILE_NAME(Raw Source Name.BZC)=20240905_MS_HEX-000820_PolyA_BzC_Pos_045.mzML; RAW_FILE_NAME(Raw Source Name.LN)=-; RAW_FILE_NAME(Raw Source Name.MP)=20240904_MS_HEX-000820_Met_Pos_045.mzML; RAW_FILE_NAME(Raw Source Name.MN)=20240905_MS_HEX-000820_Met_Neg_045.mzML; RAW_FILE_NAME(Raw Source Name.HALO)=-
#COLLECTION
CO:COLLECTION_SUMMARY            	Human HAP1 parental WT and ATP13A2 KO cells (~25,000) were washed 1x with 0.9%
CO:COLLECTION_SUMMARY            	sodium chloride and harvested for metabolite and lipid extraction. Lysosomal
CO:COLLECTION_SUMMARY            	fractions were isolated from HAP1 parental WT and ATP13A2 KO cells following
CO:COLLECTION_SUMMARY            	endocytosis-mediated labeling using superparamagnetic iron oxide nanoparticles
CO:COLLECTION_SUMMARY            	(SPION). HAP1 cells were seeded in 3X 10cm tissue culture dishes and allowed to
CO:COLLECTION_SUMMARY            	grow till ~75% confluency at which time they were treated for 24 h with 10%
CO:COLLECTION_SUMMARY            	(v/v) dextran-magnetite solution (DexoMAG40, Liquids Research Ltd.). The cells
CO:COLLECTION_SUMMARY            	were rinsed with warmed 1X PBS, pH 7.4 (Gibco; # 10010023) to remove residual
CO:COLLECTION_SUMMARY            	extracellular dextran-magnetite and re-supplemented with fresh culture medium
CO:COLLECTION_SUMMARY            	for at least 4 h to allow for specific labeling of lysosomes and late endosomes.
CO:COLLECTION_SUMMARY            	Cells were harvested by scraping with ice cold 1X PBS and centrifugation at 300
CO:COLLECTION_SUMMARY            	x g for 5 min at 4°C; resuspended in isolation buffer (250mM sucrose, 10 mM
CO:COLLECTION_SUMMARY            	HEPES, 1 mM CaCl2, 1 mM MgCl2, 1 mM DTT, cOmplete Protease Inhibitor (Roche;
CO:COLLECTION_SUMMARY            	#04693132001)), and replicates pooled by centrifugation into 1 mL lysis buffer.
CO:COLLECTION_SUMMARY            	Cells were lysed using a 27G needle for 20 strokes, followed by centrifugation
CO:COLLECTION_SUMMARY            	of the cell lysate at 600 x g for 10 min at 4°C. Post-nuclear supernatant (PNS)
CO:COLLECTION_SUMMARY            	was collected, and pellet was resuspended in 1 mL isolation buffer followed by
CO:COLLECTION_SUMMARY            	another round of needle lysis and PNS collection to capture maximum lysosomes.
CO:COLLECTION_SUMMARY            	Pooled supernatants from both rounds of needle lysis were then loaded onto LS
CO:COLLECTION_SUMMARY            	columns (Miltenyi Biotec; #130-042-401), attached to Quadro MACS magnet, that
CO:COLLECTION_SUMMARY            	were already pre equilibrated with chilled isolation buffer. Flowthrough was
CO:COLLECTION_SUMMARY            	collected after passing the PNS through the column by gravity flow and passed
CO:COLLECTION_SUMMARY            	through the column again to increase retention of unbound labeled lysosomes.
CO:COLLECTION_SUMMARY            	Finally, the columns were washed three times with isolation buffer to eliminate
CO:COLLECTION_SUMMARY            	other membrane-bound organelle contaminants, and magnetically bound lysosomes
CO:COLLECTION_SUMMARY            	eluted twice into 0.5 mL isolation buffer. The elutes were diluted with 1 mL 1X
CO:COLLECTION_SUMMARY            	PBS, centrifuged at 21,000 x g for 40 min at 4°C. The lysosomal pellet was
CO:COLLECTION_SUMMARY            	resuspended in 200 µL isolation buffer and harvested for metabolite and lipid
CO:COLLECTION_SUMMARY            	extraction.
CO:SAMPLE_TYPE                   	HAP1 cells
CO:STORAGE_CONDITIONS            	-80℃
CO:COLLECTION_VIALS              	Lobind 1.5 mL Eppendorf tubes
CO:STORAGE_VIALS                 	Lobind 1.5 mL Eppendorf tubes
#TREATMENT
TR:TREATMENT_SUMMARY             	Human HAP1 parental WT and ATP13A2 KO cells (Horizon Discovery; WT: C631;
TR:TREATMENT_SUMMARY             	ATP13A2 KO: HZGHC003547c002) were cultured in Iscove’s Modified Dulbecco’s
TR:TREATMENT_SUMMARY             	Medium (IMDM, Gibco; #12440053) supplemented with 10% fetal bovine serum (VWR
TR:TREATMENT_SUMMARY             	Seradigm; #97068-085) and 1% Penicillin/Streptomycin (Gibco; #15140122). No
TR:TREATMENT_SUMMARY             	treatment.Cells were treated for 20 hours with PBS, Rimeporide(Rim), Spermine
TR:TREATMENT_SUMMARY             	(SPM), or a combination of Spermine (SPM) + Rimeporide(Rim), followed by
TR:TREATMENT_SUMMARY             	metabolite extraction. Cells were treated for 20 hours with PBS , Spermine
TR:TREATMENT_SUMMARY             	(SPM), 18:1 (Δ9-Cis) PC (DOPC), 22:6 PG, a combination of Spermine(SPM) + DOPC,
TR:TREATMENT_SUMMARY             	or a combination of Spermine (SPM) + 22:6 PG,followed by metabolite extraction.
TR:TREATMENT_SUMMARY             	NOTE: To evaluate whether BMP can rescue spermine-dependent inhibition, WT HAP1
TR:TREATMENT_SUMMARY             	cells were treated with spermine and supplemented with PG(22:6/22:6), a
TR:TREATMENT_SUMMARY             	structural isomer and precursor of BMP(22:6/22:6). PG (22:6/22:6) was
TR:TREATMENT_SUMMARY             	supplemented due to its lower cost and greater availability, relying on its
TR:TREATMENT_SUMMARY             	established rapid conversion to BMP in lysosomes (see
TR:TREATMENT_SUMMARY             	10.1016/j.bbalip.2021.158916).
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	Cells (~25,000) and lysosomal fractions (100 µg) were directly lysed and
SP:SAMPLEPREP_SUMMARY            	extracted in 150 µL methanol containing stable-isotope internal standards for
SP:SAMPLEPREP_SUMMARY            	20 min at 4°C with shaking. The supernatant fraction was transferred to a
SP:SAMPLEPREP_SUMMARY            	96-well sample collection plate (Waters; #186005837) following a 14,000 x g spin
SP:SAMPLEPREP_SUMMARY            	at 4°C for 20 min from which the supernatant was distributed for the LC-MS/MS
SP:SAMPLEPREP_SUMMARY            	analyses.
SP:PROCESSING_STORAGE_CONDITIONS 	On ice
SP:EXTRACT_STORAGE               	-20℃
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_TYPE           	Ion exchange
CH:INSTRUMENT_NAME               	Agilent 1290 Infinity II
CH:COLUMN_NAME                   	Imtakt Intrada Organic Acid (150 × 2 mm, 3 um)
CH:SOLVENT_A                     	10% acetonitrile/90% water; 0.1% formic acid
CH:SOLVENT_B                     	10% acetonitrile/90% water; 100mM ammonium formate
CH:FLOW_GRADIENT                 	0.0-1.0 min at 0% B; 1.0-7.0 min to 100% B; 7.1 at 0% B; and 7.1-10 min at 0% B.
CH:FLOW_RATE                     	0.20 mL/min
CH:COLUMN_TEMPERATURE            	60
CH:SAMPLE_INJECTION              	5
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:INSTRUMENT_NAME               	ABI Sciex 6500+ QTrap
MS:INSTRUMENT_TYPE               	Triple quadrupole
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	NEGATIVE
MS:MS_COMMENTS                   	curtain gas at 30 psi; collision gas was set at medium; ion spray voltage at
MS:MS_COMMENTS                   	-4,500 V; temperature at 600°C; ion source Gas 1 at 50 psi; ion source Gas 2 at
MS:MS_COMMENTS                   	60 psi
#MS_METABOLITE_DATA
MS_METABOLITE_DATA:UNITS	normalized peak area
MS_METABOLITE_DATA_START
Samples	HSA-000038939	HSA-000038932	HSA-000038933	HSA-000040325	HSA-000038934	HSA-000038936	HSA-000040326	HSA-000038935	HSA-000038937	HSA-000040327	HSA-000038938	HSA-000038929	HSA-000038930	HSA-000038931	HSA-000040322	HSA-000038927	HSA-000038926	HSA-000040323	HSA-000038928	HSA-000040324
Factors	Genotype:NA | Treatment:NA | Sample source:HAP1 | Sample Type:lysosome	Genotype:WT | Treatment:none | Sample source:HAP1 | Sample Type:lysosome	Genotype:WT | Treatment:none | Sample source:HAP1 | Sample Type:lysosome	Genotype:NA | Treatment:NA | Sample source:HAP1 | Sample Type:lysosome	Genotype:WT | Treatment:none | Sample source:HAP1 | Sample Type:lysosome	Genotype:ATP13A2 KO | Treatment:none | Sample source:HAP1 | Sample Type:lysosome	Genotype:NA | Treatment:NA | Sample source:HAP1 | Sample Type:lysosome	Genotype:ATP13A2 KO | Treatment:none | Sample source:HAP1 | Sample Type:lysosome	Genotype:ATP13A2 KO | Treatment:none | Sample source:HAP1 | Sample Type:lysosome	Genotype:NA | Treatment:NA | Sample source:HAP1 | Sample Type:lysosome	Genotype:NA | Treatment:NA | Sample source:HAP1 | Sample Type:whole cell lysate	Genotype:ATP13A2 KO | Treatment:none | Sample source:HAP1 | Sample Type:whole cell lysate	Genotype:ATP13A2 KO | Treatment:none | Sample source:HAP1 | Sample Type:whole cell lysate	Genotype:ATP13A2 KO | Treatment:none | Sample source:HAP1 | Sample Type:whole cell lysate	Genotype:NA | Treatment:NA | Sample source:HAP1 | Sample Type:whole cell lysate	Genotype:WT | Treatment:none | Sample source:HAP1 | Sample Type:whole cell lysate	Genotype:WT | Treatment:none | Sample source:HAP1 | Sample Type:whole cell lysate	Genotype:NA | Treatment:NA | Sample source:HAP1 | Sample Type:whole cell lysate	Genotype:WT | Treatment:none | Sample source:HAP1 | Sample Type:whole cell lysate	Genotype:NA | Treatment:NA | Sample source:HAP1 | Sample Type:whole cell lysate
13C3-Citric acid	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
13C4-Fumaric acid	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
13C4-Malic acid	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
13C4-Succinic acid	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
13C5-Itaconic acid	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
13C5-Oxoglutaric acid	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
15N5-ADP	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
2-Hydroxyglutarate	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
2-Phosphoglyceric acid	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
3-Hydroxybutyric acid	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
3-Phosphoglyceric acid	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
6-Phosphogluconic acid	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
ADP	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	1.779	7.14	3.536	26.44	3.377	30.925	69.12	3.962	56.329	4.217
Acetoacetic acid	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Adenosine monophosphate	0.093	0.006	0.03	0.094	0.035	0.75	0.105	0.006	0.35	0.1	1.959	75.78	10.127	48.59	1.894	55.969	106.618	1.973	68.753	1.883
Adenosine triphosphate	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Adenosine triphosphate-d4	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Alanine	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Alanine-d4	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Arginine	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Arginine-d4C13	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Asparagine	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Aspartic acid	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Aspartic acid-d3	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Dihydroxyacetone phosphate	0.22	0.119	0.071	0.553	0.075	0.747	0.308	0.124	1.15	0.455	61.764	873.38	93.22	2209.636	62.338	886.991	1563.334	55.938	1374.108	58.052
Erythose 4-phosphate	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Fructose 1,6-bisphosphate	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Fructose 1-phosphate	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Fructose 6-phosphate	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Fumaric acid	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Glucose 1-phosphate	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Glucose 6-phosphate	3.619	5.715	3.55	3.928	5.09	13.127	3.838	3.173	11.898	3.826	45.563	345.098	305.388	563.029	43.533	411.679	449.954	45.701	399.789	45.261
Glutamic acid	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Glutamic acid-d3	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Glutamine	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Glyceraldehyde 3-phosphate	0.688	0.156	0.271	0.279	0.201	0.578	0.638	0.094	1.479	0.657	82.927	1160.502	116.723	2895.919	85.038	1161.41	2063.026	74.168	1809.27	75.576
Itaconic acid	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Lactic acid	4.9	5.454	2.685	5.029	3.639	7.034	4.94	4.948	4.552	4.649	29.495	170.59	248.929	323.79	27.884	143.01	188.927	26.454	265.511	28.066
Malic acid	0.933	1.564	0.79	0.767	0.982	1.776	0.729	0.684	1.704	0.681	20.37	594.055	583.58	511.734	18.273	456.212	653.822	19.608	575.571	19.6
NAD	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
NADH	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
NADP	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
NADPH	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Oxalacetic acid	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Oxoglutaric acid	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Phosphocreatine	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Phosphoenolpyruvic acid	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Pyruvic acid	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Ribose 5-phosphate	0.193	0.597	0.128	0.18	0.851	3.853	0.161	0.142	3.594	0.161	25.923	259.558	287.061	316.553	26.42	170.818	354.643	25.42	206.452	26.237
Ribulose 5-phosphate	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Sedoheptulose 7-phosphate	0.447	0.292	0.266	0.415	0.355	2.351	0.44	0.141	0.93	0.459	8.862	141.955	147.634	200.164	8.487	82.558	311.76	7.796	141.665	8.677
Serine	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Succinic acid	7.438	10.499	11.985	8.387	11.819	13.489	7.976	7.27	9.983	7.057	14.979	156.882	285.391	118.081	14.531	155.753	265.752	14.888	168.34	14.901
Sum of Citric acid and Isocitric acid	20.575	33.082	16.986	14.489	19.688	13.915	10.198	10.413	14.63	6.954	13.641	155.221	190.452	169.771	22.322	151.018	242.748	27.33	195.701	29.56
U-13C10,U-15N5-Adenosine monophosphate	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
U-13C3-Pyruvic acid	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
U-13C6-Glucose 6-phosphate	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
UDP-Glucose	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Xylulose 5-phosphate	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
cis-Aconitic acid	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
MS_METABOLITE_DATA_END
#METABOLITES
METABOLITES_START
metabolite_name	Expected RT	MS1_mz	MS2_mz
13C3-Citric acid	4.61	194.2	113
13C4-Fumaric acid	4.48	119.2	74.3
13C5-Itaconic acid	2.67	134	89.2
13C4-Malic acid	3.37	137.2	119.2
13C4-Succinic acid	2.32	121.3	76
13C5-Oxoglutaric acid	4.7	150.2	105.3
15N5-ADP	5.95	431.1	79
2-Hydroxyglutarate	2.9	145	101
2-Phosphoglyceric acid	5.66	185.5	97.1
3-Hydroxybutyric acid	2.17	103.2	59.2
3-Phosphoglyceric acid	5.67	185.5	97
6-Phosphogluconic acid	5.3	275	97
Acetoacetic acid	0.31	101	101
Adenosine monophosphate	3.9	346	79
Adenosine triphosphate	7	506.1	158.9
Adenosine triphosphate-d4	7	510	158.9
ADP	5.97	426.1	79
Alanine	2.18	88	88
Alanine-d4	2.07	92	92
Arginine	1.24	173	131
Arginine-d4C13	1.24	178	136
Asparagine	1.78	131	114
Aspartic acid	2.25	132	88
Aspartic acid-d3	2.25	135	91
cis-Aconitic acid	5.33	173	129
Sum of Citric acid and Isocitric acid	4.54	191.2	111
Dihydroxyacetone phosphate	4.55	169.1	79
Erythose 4-phosphate	4.36	199	97
Fructose 1,6-bisphosphate	5.51	339.1	79
Fructose 6-phosphate	4.5	259	97.1
Fumaric acid	4.7	115.2	71.3
Glucose 1-phosphate	4.5	259	241
Glucose 6-phosphate	4.5	259	97
Glutamic acid	1.9	146	128
Glutamic acid-d3	1.91	149	131
Glutamine	1.78	145	127
Glyceraldehyde 3-phosphate	4.55	169.1	97
Itaconic acid	2.67	129.2	85
Lactic acid	2.5	89.2	43.2
Malic acid	3.36	133.2	115.2
NAD	3.77	662.1	540.3
NADH	2.87	664.1	408.1
NADP	5.97	742.1	620
NADPH	4.73	744.1	408
Oxalacetic acid	3.63	131	131
Oxoglutaric acid	4.87	145.2	101.3
Phosphocreatine	3.53	210	79
Phosphoenolpyruvic acid	5.78	167	79
Pyruvic acid	4.64	87.2	43.2
Ribose 5-phosphate	4.54	229	97
Ribulose 5-phosphate	4.42	229	97.1
Sedoheptulose 7-phosphate	4.41	289	97
Serine	1.77	104	74
Succinic acid	2.28	117.2	73.2
U-13C10,U-15N5-Adenosine monophosphate	3.9	361	79
U-13C3-Pyruvic acid	4.64	90.2	45.2
U-13C6-Glucose 6-phosphate	4.4	265	97
Xylulose 5-phosphate	4.5	229.1	97
Fructose 1-phosphate	4.5	259.1	79
UDP-Glucose	5.19	565.2	323.4
METABOLITES_END
#END