#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