#METABOLOMICS WORKBENCH jburre_20240119_103013 DATATRACK_ID:4598 STUDY_ID:ST003052 ANALYSIS_ID:AN005005 PROJECT_ID:PR001901
VERSION             	1
CREATED_ON             	January 23, 2024, 7:49 am
#PROJECT
PR:PROJECT_TITLE                 	Synaptic vesicle lipidomics captures signatures of aging and synucleinopathy
PR:PROJECT_TYPE                  	MS quantitative analysis
PR:PROJECT_SUMMARY               	Untargeted synaptic vesicle lipidomics analysis: Synaptic vesicles were isolated
PR:PROJECT_SUMMARY               	from six animals each of 1-month, 3-month, and 10-month old wild-type mice (JAX
PR:PROJECT_SUMMARY               	strain #: 000664), α-synuclein knockout mice (JAX strain #: 023837), and
PR:PROJECT_SUMMARY               	α-synuclein BAC mice (JAX strain #: 023837) using subcellular fractionation.
PR:PROJECT_SUMMARY               	Vesicles were concentrated using 3 kDa cutoff Amicon ultra centrifugal devices
PR:PROJECT_SUMMARY               	(Millipore). Pellets were resuspended in 100 µl water and homogenized. Protein
PR:PROJECT_SUMMARY               	concentration was determined using absorption at 280 nm. Samples were adjusted
PR:PROJECT_SUMMARY               	to the same concentration to a final volume of 200 µl in 50% methanol. All
PR:PROJECT_SUMMARY               	samples were mixed with a panel of 15 lipid internal standards (Splash LipidMix
PR:PROJECT_SUMMARY               	lot#330707), followed by lipid extraction as previously reported.1 Lipids were
PR:PROJECT_SUMMARY               	analyzed by LC-MS/MS on an Accucore C30 column (2.1 mm id x 150mm) under both
PR:PROJECT_SUMMARY               	positive and negative ion modes. Raw data files were searched and processed
PR:PROJECT_SUMMARY               	using LipidSearch 5.1 (Thermo Scientific) and normalized against the known
PR:PROJECT_SUMMARY               	amount of internal standard lipids for each sample, allowing for reliably
PR:PROJECT_SUMMARY               	quantitative measurements of all 15 categories of lipids.1 1 Bhawal, R., Fu, Q.,
PR:PROJECT_SUMMARY               	Anderson, E.T., Gibson, G.E., and Zhang, S. (2021). Serum Metabolomic and
PR:PROJECT_SUMMARY               	Lipidomic Profiling Reveals Novel Biomarkers of Efficacy for Benfotiamine in
PR:PROJECT_SUMMARY               	Alzheimer's Disease. Int J Mol Sci 22.
PR:INSTITUTE                     	Weill Cornell Medicine
PR:DEPARTMENT                    	Brain and Mind Research Institute
PR:LABORATORY                    	Burré lab
PR:LAST_NAME                     	Burré
PR:FIRST_NAME                    	Jacqueline
PR:ADDRESS                       	413 East 69th Street, BB-1024, New York, NY, 10021, USA
PR:EMAIL                         	jab2058@med.cornell.edu
PR:PHONE                         	6469626155
#STUDY
ST:STUDY_TITLE                   	Synaptic vesicle lipidomics captures signatures of aging and synucleinopathy
ST:STUDY_SUMMARY                 	Untargeted synaptic vesicle lipidomics analysis: Synaptic vesicles were isolated
ST:STUDY_SUMMARY                 	from six animals each of 1-month, 3-month, and 10-month old wild-type mice (JAX
ST:STUDY_SUMMARY                 	strain #: 000664), α-synuclein knockout mice (JAX strain #: 023837), and
ST:STUDY_SUMMARY                 	α-synuclein BAC mice (JAX strain #: 023837) using subcellular fractionation.
ST:STUDY_SUMMARY                 	Vesicles were concentrated using 3 kDa cutoff Amicon ultra centrifugal devices
ST:STUDY_SUMMARY                 	(Millipore). Pellets were resuspended in 100 µl water and homogenized. Protein
ST:STUDY_SUMMARY                 	concentration was determined using absorption at 280 nm. Samples were adjusted
ST:STUDY_SUMMARY                 	to the same concentration to a final volume of 200 µl in 50% methanol. All
ST:STUDY_SUMMARY                 	samples were mixed with a panel of 15 lipid internal standards (Splash LipidMix
ST:STUDY_SUMMARY                 	lot#330707), followed by lipid extraction as previously reported.1 Lipids were
ST:STUDY_SUMMARY                 	analyzed by LC-MS/MS on an Accucore C30 column (2.1 mm id x 150mm) under both
ST:STUDY_SUMMARY                 	positive and negative ion modes. Raw data files were searched and processed
ST:STUDY_SUMMARY                 	using LipidSearch 5.1 (Thermo Scientific) and normalized against the known
ST:STUDY_SUMMARY                 	amount of internal standard lipids for each sample, allowing for reliably
ST:STUDY_SUMMARY                 	quantitative measurements of all 15 categories of lipids.1 1 Bhawal, R., Fu, Q.,
ST:STUDY_SUMMARY                 	Anderson, E.T., Gibson, G.E., and Zhang, S. (2021). Serum Metabolomic and
ST:STUDY_SUMMARY                 	Lipidomic Profiling Reveals Novel Biomarkers of Efficacy for Benfotiamine in
ST:STUDY_SUMMARY                 	Alzheimer's Disease. Int J Mol Sci 22.
ST:INSTITUTE                     	Weill Cornell Medicine
ST:DEPARTMENT                    	Brain and Mind Research Institute
ST:LABORATORY                    	Burré lab
ST:LAST_NAME                     	Burré
ST:FIRST_NAME                    	Jacqueline
ST:ADDRESS                       	413 East 69th Street, BB-1024, New York, NY, 10021, USA
ST:EMAIL                         	jab2058@med.cornell.edu
ST:PHONE                         	6469626155
ST:NUM_GROUPS                    	3
ST:TOTAL_SUBJECTS                	54
#SUBJECT
SU:SUBJECT_TYPE                  	Mammal
SU:SUBJECT_SPECIES               	Mus musculus
SU:TAXONOMY_ID                   	10090
#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           	-	aKO1mo neg1	Genotype:alpha-synuclein knockout | Age:1  month	RAW_FILE_NAME=NEG_aKO1A_37.raw; Sample number=1; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	aKO1mo neg2	Genotype:alpha-synuclein knockout | Age:1  month	RAW_FILE_NAME=NEG_aKO1B_38.raw; Sample number=2; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	aKO1mo neg3	Genotype:alpha-synuclein knockout | Age:1  month	RAW_FILE_NAME=NEG_aKO1C_39.raw; Sample number=3; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	aKO1mo neg4	Genotype:alpha-synuclein knockout | Age:1  month	RAW_FILE_NAME=NEG_aKO1D_40.raw; Sample number=4; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	aKO1mo neg5	Genotype:alpha-synuclein knockout | Age:1  month	RAW_FILE_NAME=NEG_aKO1E_41.raw; Sample number=5; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	aKO1mo neg6	Genotype:alpha-synuclein knockout | Age:1  month	RAW_FILE_NAME=NEG_aKO1F_42.raw; Sample number=6; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	aKO3mo neg1	Genotype:alpha-synuclein knockout | Age:3 months	RAW_FILE_NAME=NEG_aKO3A_43.raw; Sample number=1; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	aKO3mo neg2	Genotype:alpha-synuclein knockout | Age:3 months	RAW_FILE_NAME=NEG_aKO3B_44.raw; Sample number=2; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	aKO3mo neg3	Genotype:alpha-synuclein knockout | Age:3 months	RAW_FILE_NAME=NEG_aKO3C_45.raw; Sample number=3; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	aKO3mo neg4	Genotype:alpha-synuclein knockout | Age:3 months	RAW_FILE_NAME=NEG_aKO3D_46.raw; Sample number=4; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	aKO3mo neg5	Genotype:alpha-synuclein knockout | Age:3 months	RAW_FILE_NAME=NEG_aKO3E_47.raw; Sample number=5; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	aKO3mo neg6	Genotype:alpha-synuclein knockout | Age:3 months	RAW_FILE_NAME=NEG_aKO3F_48.raw; Sample number=6; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	aKO10mo neg1	Genotype:alpha-synuclein knockout | Age:10 months	RAW_FILE_NAME=NEG_aKO10A_49.raw; Sample number=1; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	aKO10mo neg2	Genotype:alpha-synuclein knockout | Age:10 months	RAW_FILE_NAME=NEG_aKO10B_50.raw; Sample number=2; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	aKO10mo neg3	Genotype:alpha-synuclein knockout | Age:10 months	RAW_FILE_NAME=NEG_aKO10C_51.raw; Sample number=3; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	aKO10mo neg4	Genotype:alpha-synuclein knockout | Age:10 months	RAW_FILE_NAME=NEG_aKO10D_52.raw; Sample number=4; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	aKO10mo neg5	Genotype:alpha-synuclein knockout | Age:10 months	RAW_FILE_NAME=NEG_aKO10E_53.raw; Sample number=5; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	aKO10mo neg6	Genotype:alpha-synuclein knockout | Age:10 months	RAW_FILE_NAME=NEG_aKO10F_54.raw; Sample number=6; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	Blank neg1	Genotype:NA | Age:NA	RAW_FILE_NAME=NEG_blank2.raw; Sample number=NA; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	Blank neg2	Genotype:NA | Age:NA	RAW_FILE_NAME=NEG_BLANK3.raw; Sample number=NA; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	SKB1mo neg1	Genotype:alpha-synuclein BAC | Age:1  month	RAW_FILE_NAME=NEG_SKB1A_19.raw; Sample number=1; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	SKB1mo neg2	Genotype:alpha-synuclein BAC | Age:1  month	RAW_FILE_NAME=NEG_SKB1B_20.raw; Sample number=2; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	SKB1mo neg3	Genotype:alpha-synuclein BAC | Age:1  month	RAW_FILE_NAME=NEG_SKB1C_21.raw; Sample number=3; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	SKB1mo neg4	Genotype:alpha-synuclein BAC | Age:1  month	RAW_FILE_NAME=NEG_SKB1D_22.raw; Sample number=4; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	SKB1mo neg5	Genotype:alpha-synuclein BAC | Age:1  month	RAW_FILE_NAME=NEG_SKB1E_23.raw; Sample number=5; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	SKB1mo neg6	Genotype:alpha-synuclein BAC | Age:1  month	RAW_FILE_NAME=NEG_SKB1F_24.raw; Sample number=6; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	SKB3mo neg1	Genotype:alpha-synuclein BAC | Age:3 months	RAW_FILE_NAME=NEG_SKB3A_25.raw; Sample number=1; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	SKB3mo neg2	Genotype:alpha-synuclein BAC | Age:3 months	RAW_FILE_NAME=NEG_SKB3B_26.raw; Sample number=2; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	SKB3mo neg3	Genotype:alpha-synuclein BAC | Age:3 months	RAW_FILE_NAME=NEG_SKB3C_27.raw; Sample number=3; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	SKB3mo neg4	Genotype:alpha-synuclein BAC | Age:3 months	RAW_FILE_NAME=NEG_SKB3D_28.raw; Sample number=4; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	SKB3mo neg5	Genotype:alpha-synuclein BAC | Age:3 months	RAW_FILE_NAME=NEG_SKB3E_29.raw; Sample number=5; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	SKB3mo neg6	Genotype:alpha-synuclein BAC | Age:3 months	RAW_FILE_NAME=NEG_SKB3F_30.raw; Sample number=6; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	SKB10mo neg1	Genotype:alpha-synuclein BAC | Age:10 months	RAW_FILE_NAME=NEG_SKB10A_31.raw; Sample number=1; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	SKB10mo neg1re	Genotype:alpha-synuclein BAC | Age:10 months	RAW_FILE_NAME=NEG_SKB10A_31re.raw; Sample number=1re; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	SKB10mo neg2	Genotype:alpha-synuclein BAC | Age:10 months	RAW_FILE_NAME=NEG_SKB10B_32.raw; Sample number=2; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	SKB10mo neg3	Genotype:alpha-synuclein BAC | Age:10 months	RAW_FILE_NAME=NEG_SKB10C_33.raw; Sample number=3; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	SKB10mo neg4	Genotype:alpha-synuclein BAC | Age:10 months	RAW_FILE_NAME=NEG_SKB10D_34.raw; Sample number=4; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	SKB10mo neg5	Genotype:alpha-synuclein BAC | Age:10 months	RAW_FILE_NAME=NEG_SKB10E_35.raw; Sample number=5; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	SKB10mo neg6	Genotype:alpha-synuclein BAC | Age:10 months	RAW_FILE_NAME=NEG_SKB10F_36.raw; Sample number=6; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	Std neg1	Genotype:NA | Age:NA	RAW_FILE_NAME=NEG_splash1.raw; Sample number=NA; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	Std neg2	Genotype:NA | Age:NA	RAW_FILE_NAME=NEG_splash2.raw; Sample number=NA; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	Std neg3	Genotype:NA | Age:NA	RAW_FILE_NAME=NEG_splash3.raw; Sample number=NA; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	Std neg4	Genotype:NA | Age:NA	RAW_FILE_NAME=NEG_splash4.raw; Sample number=NA; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	WT1mo neg1	Genotype:Wild-type | Age:1  month	RAW_FILE_NAME=NEG_WT1A_1.raw; Sample number=1; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	WT1mo neg2	Genotype:Wild-type | Age:1  month	RAW_FILE_NAME=NEG_WT1B_2.raw; Sample number=2; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	WT1mo neg3	Genotype:Wild-type | Age:1  month	RAW_FILE_NAME=NEG_WT1C_3.raw; Sample number=3; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	WT1mo neg4	Genotype:Wild-type | Age:1  month	RAW_FILE_NAME=NEG_WT1D_4.raw; Sample number=4; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	WT1mo neg5	Genotype:Wild-type | Age:1  month	RAW_FILE_NAME=NEG_WT1E_5.raw; Sample number=5; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	WT1mo neg6	Genotype:Wild-type | Age:1  month	RAW_FILE_NAME=NEG_WT1F_6.raw; Sample number=6; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	WT3mo neg1	Genotype:Wild-type | Age:3 months	RAW_FILE_NAME=NEG_WT3A_7.raw; Sample number=1; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	WT3mo neg2	Genotype:Wild-type | Age:3 months	RAW_FILE_NAME=NEG_WT3B_8.raw; Sample number=2; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	WT3mo neg3	Genotype:Wild-type | Age:3 months	RAW_FILE_NAME=NEG_WT3C_9.raw; Sample number=3; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	WT3mo neg4	Genotype:Wild-type | Age:3 months	RAW_FILE_NAME=NEG_WT3D_10.raw; Sample number=4; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	WT3mo neg4re	Genotype:Wild-type | Age:3 months	RAW_FILE_NAME=NEG_WT3D_10re.raw; Sample number=4re; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	WT3mo neg5	Genotype:Wild-type | Age:3 months	RAW_FILE_NAME=NEG_WT3E_11.raw; Sample number=5; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	WT3mo neg6	Genotype:Wild-type | Age:3 months	RAW_FILE_NAME=NEG_WT3F_12.raw; Sample number=6; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	WT10mo neg1	Genotype:Wild-type | Age:10 months	RAW_FILE_NAME=NEG_WT10A_13.raw; Sample number=1; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	WT10mo neg2	Genotype:Wild-type | Age:10 months	RAW_FILE_NAME=NEG_WT10B_14.raw; Sample number=2; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	WT10mo neg3	Genotype:Wild-type | Age:10 months	RAW_FILE_NAME=NEG_WT10C_15.raw; Sample number=3; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	WT10mo neg4	Genotype:Wild-type | Age:10 months	RAW_FILE_NAME=NEG_WT10D_16.raw; Sample number=4; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	WT10mo neg5	Genotype:Wild-type | Age:10 months	RAW_FILE_NAME=NEG_WT10E_17.raw; Sample number=5; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	WT10mo neg6	Genotype:Wild-type | Age:10 months	RAW_FILE_NAME=NEG_WT10F_18.raw; Sample number=6; Polarity=negative mode
SUBJECT_SAMPLE_FACTORS           	-	aKO1mo pos1	Genotype:alpha-synuclein knockout | Age:1  month	RAW_FILE_NAME=POS_aKO1A_37.raw; Sample number=1; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	aKO1mo pos2	Genotype:alpha-synuclein knockout | Age:1  month	RAW_FILE_NAME=POS_aKO1B_38.raw; Sample number=2; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	aKO1mo pos3	Genotype:alpha-synuclein knockout | Age:1  month	RAW_FILE_NAME=POS_aKO1C_39.raw; Sample number=3; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	aKO1mo pos4	Genotype:alpha-synuclein knockout | Age:1  month	RAW_FILE_NAME=POS_aKO1D_40.raw; Sample number=4; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	aKO1mo pos5	Genotype:alpha-synuclein knockout | Age:1  month	RAW_FILE_NAME=POS_aKO1E_41.raw; Sample number=5; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	aKO1mo pos6	Genotype:alpha-synuclein knockout | Age:1  month	RAW_FILE_NAME=POS_aKO1F_42.raw; Sample number=6; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	aKO3mo pos1	Genotype:alpha-synuclein knockout | Age:3 months	RAW_FILE_NAME=POS_aKO3A_43.raw; Sample number=1; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	aKO3mo pos2	Genotype:alpha-synuclein knockout | Age:3 months	RAW_FILE_NAME=POS_aKO3B_44.raw; Sample number=2; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	aKO3mo pos3	Genotype:alpha-synuclein knockout | Age:3 months	RAW_FILE_NAME=POS_aKO3C_45.raw; Sample number=3; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	aKO3mo pos4	Genotype:alpha-synuclein knockout | Age:3 months	RAW_FILE_NAME=POS_aKO3D_46.raw; Sample number=4; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	aKO3mo pos5	Genotype:alpha-synuclein knockout | Age:3 months	RAW_FILE_NAME=POS_aKO3E_47.raw; Sample number=5; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	aKO3mo pos6	Genotype:alpha-synuclein knockout | Age:3 months	RAW_FILE_NAME=POS_aKO3F_48.raw; Sample number=6; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	aKO10mo pos1	Genotype:alpha-synuclein knockout | Age:10 months	RAW_FILE_NAME=POS_aKO10A_49.raw; Sample number=1; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	aKO10mo pos2	Genotype:alpha-synuclein knockout | Age:10 months	RAW_FILE_NAME=POS_aKO10B_50.raw; Sample number=2; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	aKO10mo pos3	Genotype:alpha-synuclein knockout | Age:10 months	RAW_FILE_NAME=POS_aKO10C_51.raw; Sample number=3; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	aKO10mo pos4	Genotype:alpha-synuclein knockout | Age:10 months	RAW_FILE_NAME=POS_aKO10D_52.raw; Sample number=4; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	aKO10mo pos5	Genotype:alpha-synuclein knockout | Age:10 months	RAW_FILE_NAME=POS_aKO10E_53.raw; Sample number=5; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	aKO10mo pos6	Genotype:alpha-synuclein knockout | Age:10 months	RAW_FILE_NAME=POS_aKO10F_54.raw; Sample number=6; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	Blank pos1	Genotype:NA | Age:NA	RAW_FILE_NAME=POS_BLANK2.raw; Sample number=NA; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	Blank pos2	Genotype:NA | Age:NA	RAW_FILE_NAME=POS_BLANK3.raw; Sample number=NA; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	SKB1mo pos1	Genotype:alpha-synuclein BAC | Age:1  month	RAW_FILE_NAME=POS_SKB1A_19.raw; Sample number=1; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	SKB1mo pos2	Genotype:alpha-synuclein BAC | Age:1  month	RAW_FILE_NAME=POS_SKB1B_20.raw; Sample number=2; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	SKB1mo pos3	Genotype:alpha-synuclein BAC | Age:1  month	RAW_FILE_NAME=POS_SKB1C_21.raw; Sample number=3; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	SKB1mo pos4	Genotype:alpha-synuclein BAC | Age:1  month	RAW_FILE_NAME=POS_SKB1D_22.raw; Sample number=4; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	SKB1mo pos5	Genotype:alpha-synuclein BAC | Age:1  month	RAW_FILE_NAME=POS_SKB1E_23.raw; Sample number=5; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	SKB1mo pos6	Genotype:alpha-synuclein BAC | Age:1  month	RAW_FILE_NAME=POS_SKB1F_24.raw; Sample number=6; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	SKB3mo pos1	Genotype:alpha-synuclein BAC | Age:3 months	RAW_FILE_NAME=POS_SKB3A_25.raw; Sample number=1; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	SKB3mo pos2	Genotype:alpha-synuclein BAC | Age:3 months	RAW_FILE_NAME=POS_SKB3B_26.raw; Sample number=2; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	SKB3mo pos3	Genotype:alpha-synuclein BAC | Age:3 months	RAW_FILE_NAME=POS_SKB3C_27.raw; Sample number=3; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	SKB3mo pos4	Genotype:alpha-synuclein BAC | Age:3 months	RAW_FILE_NAME=POS_SKB3D_28.raw; Sample number=4; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	SKB3mo pos5	Genotype:alpha-synuclein BAC | Age:3 months	RAW_FILE_NAME=POS_SKB3E_29.raw; Sample number=5; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	SKB3mo pos6	Genotype:alpha-synuclein BAC | Age:3 months	RAW_FILE_NAME=POS_SKB3F_30.raw; Sample number=6; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	SKB10mo pos1	Genotype:alpha-synuclein BAC | Age:10 months	RAW_FILE_NAME=POS_SKB10A_31.raw; Sample number=1; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	SKB10mo pos2	Genotype:alpha-synuclein BAC | Age:10 months	RAW_FILE_NAME=POS_SKB10B_32.raw; Sample number=2; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	SKB10mo pos3	Genotype:alpha-synuclein BAC | Age:10 months	RAW_FILE_NAME=POS_SKB10C_33.raw; Sample number=3; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	SKB10mo pos4	Genotype:alpha-synuclein BAC | Age:10 months	RAW_FILE_NAME=POS_SKB10D_34.raw; Sample number=4; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	SKB10mo pos5	Genotype:alpha-synuclein BAC | Age:10 months	RAW_FILE_NAME=POS_SKB10E_35.raw; Sample number=5; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	SKB10mo pos6	Genotype:alpha-synuclein BAC | Age:10 months	RAW_FILE_NAME=POS_SKB10F_36.raw; Sample number=6; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	Std pos1	Genotype:NA | Age:NA	RAW_FILE_NAME=POS_SPLASH1.raw; Sample number=NA; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	Std pos2	Genotype:NA | Age:NA	RAW_FILE_NAME=POS_SPLASH2.raw; Sample number=NA; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	Std pos3	Genotype:NA | Age:NA	RAW_FILE_NAME=POS_SPLASH3.raw; Sample number=NA; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	Std pos4	Genotype:NA | Age:NA	RAW_FILE_NAME=POS_SPLASH4.raw; Sample number=NA; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	WT1mo pos1	Genotype:Wild-type | Age:1  month	RAW_FILE_NAME=POS_WT1A_1.raw; Sample number=1; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	WT1mo pos2	Genotype:Wild-type | Age:1  month	RAW_FILE_NAME=POS_WT1B_2.raw; Sample number=2; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	WT1mo pos3	Genotype:Wild-type | Age:1  month	RAW_FILE_NAME=POS_WT1C_3.raw; Sample number=3; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	WT1mo pos4	Genotype:Wild-type | Age:1  month	RAW_FILE_NAME=POS_WT1D_4.raw; Sample number=4; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	WT1mo pos5	Genotype:Wild-type | Age:1  month	RAW_FILE_NAME=POS_WT1E_5.raw; Sample number=5; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	WT1mo pos6	Genotype:Wild-type | Age:1  month	RAW_FILE_NAME=POS_WT1F_6.raw; Sample number=6; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	WT3mo pos1	Genotype:Wild-type | Age:3 months	RAW_FILE_NAME=POS_WT3A_7.raw; Sample number=1; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	WT3mo pos2	Genotype:Wild-type | Age:3 months	RAW_FILE_NAME=POS_WT3B_8.raw; Sample number=2; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	WT3mo pos3	Genotype:Wild-type | Age:3 months	RAW_FILE_NAME=POS_WT3C_9.raw; Sample number=3; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	WT3mo pos4	Genotype:Wild-type | Age:3 months	RAW_FILE_NAME=POS_WT3D_10.raw; Sample number=4; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	WT3mo pos5	Genotype:Wild-type | Age:3 months	RAW_FILE_NAME=POS_WT3E_11.raw; Sample number=5; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	WT3mo pos6	Genotype:Wild-type | Age:3 months	RAW_FILE_NAME=POS_WT3F_12.raw; Sample number=6; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	WT10mo pos1	Genotype:Wild-type | Age:10 months	RAW_FILE_NAME=POS_WT10A_13.raw; Sample number=1; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	WT10mo pos2	Genotype:Wild-type | Age:10 months	RAW_FILE_NAME=POS_WT10B_14.raw; Sample number=2; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	WT10mo pos3	Genotype:Wild-type | Age:10 months	RAW_FILE_NAME=POS_WT10C_15.raw; Sample number=3; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	WT10mo pos4	Genotype:Wild-type | Age:10 months	RAW_FILE_NAME=POS_WT10D_16.raw; Sample number=4; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	WT10mo pos5	Genotype:Wild-type | Age:10 months	RAW_FILE_NAME=POS_WT10E_17.raw; Sample number=5; Polarity=positive mode
SUBJECT_SAMPLE_FACTORS           	-	WT10mo pos6	Genotype:Wild-type | Age:10 months	RAW_FILE_NAME=POS_WT10F_18.raw; Sample number=6; Polarity=positive mode
#COLLECTION
CO:COLLECTION_SUMMARY            	Synaptic vesicle were isolated by subcellular fractionation and concentrated
CO:SAMPLE_TYPE                   	Brain
#TREATMENT
TR:TREATMENT_SUMMARY             	No treatments
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	Synaptic vesicles were isolated from six animals each of 1-month, 3-month, and
SP:SAMPLEPREP_SUMMARY            	10-month old wild-type mice (JAX strain #: 000664), α-synuclein knockout mice
SP:SAMPLEPREP_SUMMARY            	(JAX strain #: 023837), and α-synuclein BAC mice (JAX strain #: 023837) using
SP:SAMPLEPREP_SUMMARY            	subcellular fractionation. Vesicles were concentrated using 3 kDa cutoff Amicon
SP:SAMPLEPREP_SUMMARY            	ultra centrifugal devices (Millipore). Pellets were resuspended in 100 µl water
SP:SAMPLEPREP_SUMMARY            	and homogenized. Protein concentration was determined using absorption at 280
SP:SAMPLEPREP_SUMMARY            	nm. Samples were adjusted to the same concentration to a final volume of 200 µl
SP:SAMPLEPREP_SUMMARY            	in 50% methanol. All samples were mixed with a panel of 15 lipid internal
SP:SAMPLEPREP_SUMMARY            	standards (Splash LipidMix lot#330707), followed by lipid extraction as
SP:SAMPLEPREP_SUMMARY            	previously reported.1 Lipids were analyzed by LC-MS/MS on an Accucore C30 column
SP:SAMPLEPREP_SUMMARY            	(2.1 mm id x 150mm) under both positive and negative ion modes. Raw data files
SP:SAMPLEPREP_SUMMARY            	were searched and processed using LipidSearch 5.1 (Thermo Scientific) and
SP:SAMPLEPREP_SUMMARY            	normalized against the known amount of internal standard lipids for each sample,
SP:SAMPLEPREP_SUMMARY            	allowing for reliably quantitative measurements of all 15 categories of lipids.1
SP:SAMPLEPREP_SUMMARY            	1 Bhawal, R., Fu, Q., Anderson, E.T., Gibson, G.E., and Zhang, S. (2021). Serum
SP:SAMPLEPREP_SUMMARY            	Metabolomic and Lipidomic Profiling Reveals Novel Biomarkers of Efficacy for
SP:SAMPLEPREP_SUMMARY            	Benfotiamine in Alzheimer's Disease. Int J Mol Sci 22.
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_TYPE           	Other
CH:INSTRUMENT_NAME               	Q Exactive HF Hybrid Quadrupole-Orbitrap Mass Spectrometer
CH:COLUMN_NAME                   	Thermo Accucore C30 (150 x 2.1mm,2.6um)
CH:SOLVENT_A                     	60% ACN, 40% H2O, 10 mM ammonium formate with 0.1% formic acid
CH:SOLVENT_B                     	90% IPA, 10% ACN, 10 mM ammonium formate with 0.1% formic acid
CH:FLOW_GRADIENT                 	0-4 min: 32% B; 4-5 min: 45% B; 5-8 min: 52% B; 8-11 min: 66% B; 11-14 min: 66%
CH:FLOW_GRADIENT                 	B; 14-18 min: 70% B, 18-21 min: 75% B; 21-25.01 min, 97% B; 21.01-30 min: 32% B
CH:FLOW_RATE                     	0.26 ml/min
CH:COLUMN_TEMPERATURE            	55
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:INSTRUMENT_NAME               	Thermo Q Exactive HF Hybrid Quadrupole-Orbitrap Mass Spectrometer
MS:INSTRUMENT_TYPE               	Orbitrap
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	NEGATIVE
MS:MS_COMMENTS                   	ESI voltage: 4kV Sheath gas flow rate: 50 (AU) Aux gas flow rate: 5 Sweep gas
MS:MS_COMMENTS                   	flow rate: 1 capillary temperature: 320°C S-Lens RF level: 60 Aux gas heater
MS:MS_COMMENTS                   	temperature: 350°C
MS:MS_RESULTS_FILE               	ST003052_AN005005_Results.txt	UNITS:area	Has m/z:Yes	Has RT:Yes	RT units:Minutes
#END