#METABOLOMICS WORKBENCH boryana_ptrva_20210915_065709_mwtab.txt DATATRACK_ID:2841 STUDY_ID:ST001979 ANALYSIS_ID:AN003229 PROJECT_ID:000000 VERSION 1 CREATED_ON September 17, 2021, 9:59 am #PROJECT PR:PROJECT_TITLE Gene-therapy enhances CSF’s anti-oxidative activity to mitigate chemotherapy PR:PROJECT_TITLE side effects PR:PROJECT_TYPE Anti-oxidative Metabolism Measurement in CSF of MTX-treated mice under gene PR:PROJECT_TYPE therapy by quantitative LC/MS method (part VI) PR:PROJECT_SUMMARY In order to test the protective activity of SOD3 levels on the redox state of PR:PROJECT_SUMMARY the CSF of MTX-treated mice, targeted metabolomics on CSF was employed at PR:PROJECT_SUMMARY different timepoints after treatment, on mice of both sexes, at various levels PR:PROJECT_SUMMARY of impacted hSOD3 expression. PR:INSTITUTE Boston Childrens Hospital PR:DEPARTMENT Pathology PR:LABORATORY Naama Kanarek PR:LAST_NAME Petrova PR:FIRST_NAME Boryana PR:ADDRESS 300 Longwood Av, Boston, MA, 2115, USA PR:EMAIL boryana.petrova@childrens.harvard.edu PR:PHONE 6173557433 #STUDY ST:STUDY_TITLE Anti-oxidation metabolism measurement in mammalian cells and tissues by ST:STUDY_TITLE quantitative LC/MS method (VI) ST:STUDY_SUMMARY Anti-oxidation metabolism measurement in mammalian cells and tissues by ST:STUDY_SUMMARY quantitative LC/MS method of mouse ctrl CSF. ST:INSTITUTE Boston Children's Hospital, Harvard Medical School ST:LAST_NAME Petrova ST:FIRST_NAME Boryana ST:ADDRESS 300 Longwood Ave ST:EMAIL boryana.petrova@childrens.harvard.edu ST:PHONE 6173557433 #SUBJECT SU:SUBJECT_TYPE Mammal SU:SUBJECT_SPECIES Mus musculus SU:TAXONOMY_ID 10090 SU:GENDER Male and female #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 - Mouse CSF Ctrl 1 Factor:PBS-1 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ441_20210403144300; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 2 Factor:PBS-2 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ442_20210403134529; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 3 Factor:PBS-3 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ443_20210402205911; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 4 Factor:PBS-4 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ444_20210403080025; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 5 Factor:PBS-5 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ445_20210403060526; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 6 Factor:PBS-6 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ446_20210403102412; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 7 Factor:PBS-7 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ447_20210403193036; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 8 Factor:PBS-8 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ448_20210403011757; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 9 Factor:PBS-9 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ449_20210402151403; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 10 Factor:PBS+MTX-1 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ450_20210403131645; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 11 Factor:PBS+MTX-2 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ451_20210403115029; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 12 Factor:PBS+MTX-3 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ452_20210402134749; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 13 Factor:PBS+MTX-4 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ453_20210403212538; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 14 Factor:PBS+MTX-5 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ454_20210402203026; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 15 Factor:PBS+MTX-6 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ455_20210403195922; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 16 Factor:PBS+MTX-7 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ456_20210403154031; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 17 Factor:PBS+MTX-8 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ457_20210403085756; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 18 Factor:PBS+MTX-9 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ458_20210402232257; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 19 Factor:Null GFP-1 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ459_20210403105257; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 20 Factor:Null GFP-2 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ460_20210403151146; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 21 Factor:Null GFP-3 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ461_20210403190151; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 22 Factor:Null GFP-4 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ462_20210403041027; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 23 Factor:Null GFP-5 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ463_20210402225413; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 24 Factor:Null GFP-6 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ464_20210403050755; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 25 Factor:Null GFP-7 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ465_20210402222527; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 26 Factor:Null GFP+MTX-1 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ466_20210403021527; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 27 Factor:Null GFP+MTX-2 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ467_20210403095526; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 28 Factor:Null GFP+MTX-3 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ468_20210402235142; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 29 Factor:Null GFP+MTX-4 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ469_20210403053641; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 30 Factor:Null GFP+MTX-5 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ470_20210403031257; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 31 Factor:Null GFP+MTX-6 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ471_20210402200142; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 32 Factor:Null GFP+MTX-7 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ472_20210402164022; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 33 Factor:Null GFP+MTX-8 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ473_20210403180419; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 34 Factor:CAG-GFP-1 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ474_20210402125018; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 35 Factor:CAG-GFP-2 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ475_20210402180641; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 36 Factor:CAG-GFP-3 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ476_20210402212756; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 37 Factor:CAG-GFP-4 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ477_20210402161138; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 38 Factor:CAG-GFP-5 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ478_20210403043912; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 39 Factor:CAG-GFP-6 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ479_20210403014642; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 40 Factor:CAG-GFP-7 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ480_20210402190411; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 41 Factor:CAG-GFP-8 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ481_20210403092641; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 42 Factor:CAG-GFP+MTX-1 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ482_20210403063410; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 43 Factor:CAG-GFP+MTX-2 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ483_20210402183527; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 44 Factor:CAG-GFP+MTX-3 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ484_20210402131904; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 45 Factor:CAG-GFP+MTX-4 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ485_20210402154249; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 46 Factor:CAG-GFP+MTX-5 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ486_20210403160917; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 47 Factor:CAG-GFP+MTX-6 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ487_20210402144519; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 48 Factor:CAG-GFP+MTX-7 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ488_20210403202807; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 49 Factor:CMV-GFP-1 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ489_20210403082911; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 50 Factor:CMV-GFP-2 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ490_20210403163805; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 51 Factor:CMV-GFP-3 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ491_20210403173535; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 52 Factor:CMV-GFP-4 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ492_20210403034141; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 53 Factor:CMV-GFP-5 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ493_20210403070255; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 54 Factor:CMV-GFP-6 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ494_20210403205651; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 55 Factor:CMV-GFP+MTX-1 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ495_20210403004912; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 56 Factor:CMV-GFP+MTX-2 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ496_20210403112143; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 57 Factor:CMV-GFP+MTX-3 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ497_20210402193255; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 58 Factor:CMV-GFP+MTX-4 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ498_20210403183305; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 59 Factor:CMV-GFP+MTX-5 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ499_20210403002026; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 60 Factor:CMV-GFP+MTX-6 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ500_20210402141633; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 61 Factor:CMV-GFP+MTX-7 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ501_20210403141414; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 62 Factor:CMV-GFP+MTX-8 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ502_20210402173755; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - Mouse CSF Ctrl 63 Factor:CMV-GFP+MTX-9 RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ503_20210403124800; other=3ul CSF 200 FB reconstituted in 25ul water with QReSS; other=folate buffer isoAAs GSH aminopterin; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - pooled sample QC 1a Factor:- RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ504_pool1x_a_20210402112359; other=-; other=-; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - pooled sample QC 1b Factor:- RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ504_pool1x_b_20210402170909; other=-; other=-; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - pooled sample QC 1c Factor:- RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ504_pool1x_c_20210402215641; other=-; other=-; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - pooled sample QC 1d Factor:- RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ504_pool1x_d_20210403024411; other=-; other=-; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - pooled sample QC 1e Factor:- RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ504_pool1x_e_20210403073139; other=-; other=-; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - pooled sample QC 1f Factor:- RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ504_pool1x_f_20210403121915; other=-; other=-; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - pooled sample QC 1g Factor:- RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ504_pool1x_g_20210403170649; other=-; other=-; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - pooled sample QC 1h Factor:- RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ504_pool1x_h_20210403215423; other=-; other=-; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - pooled sample QC 1/3 dilution Factor:- RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ505_pool03x_20210403222310; other=-; other=-; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - pooled sample QC 1/10 dilution a-2x Factor:- RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ506_pool01x_2x_20210402122129; other=-; other=-; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - pooled sample QC 1/10 dilution a Factor:- RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ506_pool01x_a_20210402115245; other=-; other=-; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - pooled sample QC 1/10 dilution b Factor:- RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_AJ506_pool01x_b_20210403225154; other=-; other=-; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - blank 1 Factor:- RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_blank1_20210402095740; other=-; other=-; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - blank 2 Factor:- RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_blank2_20210402102630; other=-; other=-; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - blank 3 Factor:- RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_blank3_20210402105515; other=-; other=-; chromatography=HILIC SUBJECT_SAMPLE_FACTORS - blank 4 Factor:- RAW_FILE_NAME=20210331_QEF1_HILIC_Aram_newGFPcontrols_MTX_blank4_20210403232038; other=-; other=-; chromatography=HILIC #COLLECTION CO:COLLECTION_SUMMARY All animal studies were performed under the protocol approved by the CO:COLLECTION_SUMMARY Institutional Animal Care and Use Committee (IACUC) of Boston Children’s CO:COLLECTION_SUMMARY Hospital (BCH). CD-1 mice (timed pregnant and 6-8 weeks) and Sprague Dawley rats CO:COLLECTION_SUMMARY (6-8 weeks) were purchased (Charles River Laboratories). Male and female animals CO:COLLECTION_SUMMARY were used equally for all studies. All animals were housed in a 12h light-dark CO:COLLECTION_SUMMARY cycle with ad libitum access to food and water. CSF was collected from the CO:COLLECTION_SUMMARY cisterna magna and centrifuged at 10,000g for 10 min. at 4 °C to remove any CO:COLLECTION_SUMMARY tissue debris (38). CSF samples were flash frozen and stored at −80°C until CO:COLLECTION_SUMMARY use. CO:SAMPLE_TYPE CSF #TREATMENT TR:TREATMENT_SUMMARY Mice were treated with PBS, PBS+ MTX, Null GFP with and without MTX, CAG-GFP TR:TREATMENT_SUMMARY with and without MTX, and CMV-GFP with and without MTX. buffers from study TR:TREATMENT_SUMMARY design were used for all respective samples. CD-1 mice (6-8 weeks) or Sprague TR:TREATMENT_SUMMARY Dawley rats (8 weeks) were given a single intravenous injection of 75 mg/kg MTX TR:TREATMENT_SUMMARY (Fisher Scientific, AAJ66364MD) dissolved in 0.9 % NaCl (Mountainside Medical, TR:TREATMENT_SUMMARY 0409-4888-10). MTX was freshly prepared for each experiment. MTX in mouse serum TR:TREATMENT_SUMMARY or CSF was assessed by MTX ELISA according to the manufacturer's instructions TR:TREATMENT_SUMMARY (Enzo Life Sciences, 142-0001). #SAMPLEPREP SP:SAMPLEPREP_SUMMARY For characterization by mass spectrometry, CSF was acquired 4h, 24h, and 48h SP:SAMPLEPREP_SUMMARY following a single 75 mg/kg MTX injection from 6-8 mice and flash frozen for SP:SAMPLEPREP_SUMMARY further analysis. Per condition, 3 μl of CSF were extracted by brief sonication SP:SAMPLEPREP_SUMMARY in 240 μl 100% methanol, supplemented with isotopically labeled internal SP:SAMPLEPREP_SUMMARY standards (17 amino acids and reduced glutathione, Cambridge Isotope SP:SAMPLEPREP_SUMMARY Laboratories, MSK-A2-1.2 and CNLM-6245-10) and 60 μl 20 mM Ellman’s reagent SP:SAMPLEPREP_SUMMARY in water (Sigma-Aldrich, D8130). After centrifugation for 10min. at maximum SP:SAMPLEPREP_SUMMARY speed on a benchtop centrifuge (Eppendorf) the cleared supernatant was dried SP:SAMPLEPREP_SUMMARY using a nitrogen dryer and reconstituted in 30 µl water by brief sonication. SP:SAMPLEPREP_SUMMARY Extracted metabolites were spun again and cleared supernatant was transferred in SP:SAMPLEPREP_SUMMARY LC-MS microvials. A small amount of each sample was pooled and serially diluted SP:SAMPLEPREP_SUMMARY 3 and 10-fold to be used as quality controls throughout the batch run. SP:SAMPLEPREP_SUMMARY Two microliters (equivalent to 0.2 ul of CSF) of reconstituted sample were SP:SAMPLEPREP_SUMMARY injected into a ZIC-pHILIC 150 × 2.1 mm (5 µm particle size) column SP:SAMPLEPREP_SUMMARY (EMD Millipore) operated on a Dionex UltiMate 3000 UPLC system (Thermo Fisher SP:SAMPLEPREP_SUMMARY Scientific). Chromatographic separation was achieved using the following SP:SAMPLEPREP_SUMMARY conditions: buffer A was acetonitrile; buffer B was 20 mM ammonium carbonate, SP:SAMPLEPREP_SUMMARY 0.1% ammonium hydroxide. Gradient conditions were: linear gradient from 20% to SP:SAMPLEPREP_SUMMARY 80% B; 20–20.5 min: from 80% to 20% B; 20.5–28 min: hold at 20% B. The SP:SAMPLEPREP_SUMMARY column oven and autosampler tray were held at 25 °C and 4 °C, SP:SAMPLEPREP_SUMMARY respectively. The MS data acquisition was on a QExactive benchtop orbitrap mass SP:SAMPLEPREP_SUMMARY spectrometer equipped with an Ion Max source and a HESI II probe and was SP:SAMPLEPREP_SUMMARY performed in a range of m/z= 70–1000, with the resolution set at 70,000, the SP:SAMPLEPREP_SUMMARY AGC target at 1x106, and the maximum injection time (Max IT) at 20 msec. For SP:SAMPLEPREP_SUMMARY tSIM scans, the resolution was set at 70,000, the AGC target was 1x105, and the SP:SAMPLEPREP_SUMMARY max IT was 100 msec. Relative quantitation of polar metabolites was performed SP:SAMPLEPREP_SUMMARY with TraceFinder 4.1 (Thermo Fisher Scientific) using a 5 ppm mass tolerance and SP:SAMPLEPREP_SUMMARY referencing an in-house library of chemical standards. Pooled samples and SP:SAMPLEPREP_SUMMARY fractional dilutions were prepared as quality controls and only those SP:SAMPLEPREP_SUMMARY metabolites were taken for further analysis, for which the correlation between SP:SAMPLEPREP_SUMMARY the dilution factor and the peak area was >0.95 (high confidence metabolites). SP:SAMPLEPREP_SUMMARY Normalization for biological material amounts was based on the total integrated SP:SAMPLEPREP_SUMMARY peak area values of high-confidence metabolites within an experimental batch SP:SAMPLEPREP_SUMMARY after normalizing to the averaged factor from all mean-centered chromatographic SP:SAMPLEPREP_SUMMARY peak areas of isotopically labeled amino acids internal standards (Cambridge SP:SAMPLEPREP_SUMMARY Isotope Laboratories). The data were Log transformed and Pareto scaled for SP:SAMPLEPREP_SUMMARY MetaboAnalyst-based statistical or pathway analysis (41). We profiled 200 SP:SAMPLEPREP_SUMMARY metabolites, 85 of which were detected in CSF and passed our quality control SP:SAMPLEPREP_SUMMARY protocol. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE HILIC CH:INSTRUMENT_NAME Thermo Q Exactive Orbitrap CH:COLUMN_NAME EMD Millipore ZIC-HILIC (100 x 2.1 mm, 3.5 um) #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo Exactive Plus Orbitrap MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:ION_MODE UNSPECIFIED MS:MS_COMMENTS Xcalibur + Tracefinder #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS ppm MS_METABOLITE_DATA_START Samples Mouse CSF Ctrl 1 Mouse CSF Ctrl 2 Mouse CSF Ctrl 3 Mouse CSF Ctrl 4 Mouse CSF Ctrl 5 Mouse CSF Ctrl 6 Mouse CSF Ctrl 7 Mouse CSF Ctrl 8 Mouse CSF Ctrl 9 Mouse CSF Ctrl 10 Mouse CSF Ctrl 11 Mouse CSF Ctrl 12 Mouse CSF Ctrl 13 Mouse CSF Ctrl 14 Mouse CSF Ctrl 15 Mouse CSF Ctrl 16 Mouse CSF Ctrl 17 Mouse CSF Ctrl 18 Mouse CSF Ctrl 19 Mouse CSF Ctrl 20 Mouse CSF Ctrl 21 Mouse CSF Ctrl 22 Mouse CSF Ctrl 23 Mouse CSF Ctrl 24 Mouse CSF Ctrl 25 Mouse CSF Ctrl 26 Mouse CSF Ctrl 27 Mouse CSF Ctrl 28 Mouse CSF Ctrl 29 Mouse CSF Ctrl 30 Mouse CSF Ctrl 31 Mouse CSF Ctrl 32 Mouse CSF Ctrl 33 Mouse CSF Ctrl 34 Mouse CSF Ctrl 35 Mouse CSF Ctrl 36 Mouse CSF Ctrl 37 Mouse CSF Ctrl 38 Mouse CSF Ctrl 39 Mouse CSF Ctrl 40 Mouse CSF Ctrl 41 Mouse CSF Ctrl 42 Mouse CSF Ctrl 43 Mouse CSF Ctrl 44 Mouse CSF Ctrl 45 Mouse CSF Ctrl 46 Mouse CSF Ctrl 47 Mouse CSF Ctrl 48 Mouse CSF Ctrl 49 Mouse CSF Ctrl 50 Mouse CSF Ctrl 51 Mouse CSF Ctrl 52 Mouse CSF Ctrl 53 Mouse CSF Ctrl 54 Mouse CSF Ctrl 55 Mouse CSF Ctrl 56 Mouse CSF Ctrl 57 Mouse CSF Ctrl 58 Mouse CSF Ctrl 59 Mouse CSF Ctrl 60 Mouse CSF Ctrl 61 Mouse CSF Ctrl 62 Mouse CSF Ctrl 63 pooled sample QC 1a pooled sample QC 1b pooled sample QC 1c pooled sample QC 1d pooled sample QC 1e pooled sample QC 1f pooled sample QC 1g pooled sample QC 1h pooled sample QC 1/3 dilution pooled sample QC 1/10 dilution a-2x pooled sample QC 1/10 dilution a pooled sample QC 1/10 dilution b blank 1 blank 2 blank 3 blank 4 Factors Factor:PBS-1 Factor:PBS-2 Factor:PBS-3 Factor:PBS-4 Factor:PBS-5 Factor:PBS-6 Factor:PBS-7 Factor:PBS-8 Factor:PBS-9 Factor:PBS+MTX-1 Factor:PBS+MTX-2 Factor:PBS+MTX-3 Factor:PBS+MTX-4 Factor:PBS+MTX-5 Factor:PBS+MTX-6 Factor:PBS+MTX-7 Factor:PBS+MTX-8 Factor:PBS+MTX-9 Factor:Null GFP-1 Factor:Null GFP-2 Factor:Null GFP-3 Factor:Null GFP-4 Factor:Null GFP-5 Factor:Null GFP-6 Factor:Null GFP-7 Factor:Null GFP+MTX-1 Factor:Null GFP+MTX-2 Factor:Null GFP+MTX-3 Factor:Null GFP+MTX-4 Factor:Null GFP+MTX-5 Factor:Null GFP+MTX-6 Factor:Null GFP+MTX-7 Factor:Null GFP+MTX-8 Factor:CAG-GFP-1 Factor:CAG-GFP-2 Factor:CAG-GFP-3 Factor:CAG-GFP-4 Factor:CAG-GFP-5 Factor:CAG-GFP-6 Factor:CAG-GFP-7 Factor:CAG-GFP-8 Factor:CAG-GFP+MTX-1 Factor:CAG-GFP+MTX-2 Factor:CAG-GFP+MTX-3 Factor:CAG-GFP+MTX-4 Factor:CAG-GFP+MTX-5 Factor:CAG-GFP+MTX-6 Factor:CAG-GFP+MTX-7 Factor:CMV-GFP-1 Factor:CMV-GFP-2 Factor:CMV-GFP-3 Factor:CMV-GFP-4 Factor:CMV-GFP-5 Factor:CMV-GFP-6 Factor:CMV-GFP+MTX-1 Factor:CMV-GFP+MTX-2 Factor:CMV-GFP+MTX-3 Factor:CMV-GFP+MTX-4 Factor:CMV-GFP+MTX-5 Factor:CMV-GFP+MTX-6 Factor:CMV-GFP+MTX-7 Factor:CMV-GFP+MTX-8 Factor:CMV-GFP+MTX-9 Factor:- Factor:- Factor:- Factor:- Factor:- Factor:- Factor:- Factor:- Factor:- Factor:- Factor:- Factor:- Factor:- Factor:- Factor:- Factor:- GSH-13C2_15N N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F GSH_13C2-15N-Ellmans 3897674 3272502 2729500 4164179 4820161 3135990 5686300 2028539 1219497 5228198 5027629 1152474 4541579 1571656 4137268 4363462 3500808 1427368 3015480 4233792 4218514 3309275 859423 3651052 2339991 3142175 3177320 2462337 3638004 3742328 2353480 1569429 4070432 1646532 2665204 1825613 1071052 N/F 2262529 2120100 2902911 2935680 2075585 835563 859150 3443460 476765 3044060 2723376 2705087 3872250 2475790 1728059 3960959 1955687 3874866 422190 4184859 2127612 397549 3548800 464502 3518810 736850 1602170 2289267 2980622 3490771 4264756 4808487 5354530 90076 N/F N/F N/F N/F N/F N/F N/F GSH N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F N/F GSH_Ellmans 6898851 5423822 6749206 6646625 7995875 6351669 7877775 4843969 6652754 7475234 5496072 4650239 5892392 5130672 5588014 6304254 6049682 4178156 6003332 8170794 6349209 6335427 4417419 5445032 5848691 5270008 6656141 7437871 4692011 6925128 6411101 5492854 6448555 6777372 6654649 4223337 5112654 N/F 3924535 4656071 6149663 4020700 4297600 3513616 4496361 6938294 5198853 5371741 5562049 5223523 5614047 4976717 3425087 5788723 5652503 6534721 4975471 7446529 4708694 4737949 6801780 2459185 5118587 4629087 5697865 5813477 5471953 5462121 5652985 5876195 6557403 847453 104028 38093 32482 N/F N/F N/F N/F GSSG 1386203 512592 280972 547984 961886 616787 394794 259915 798700 1052816 255075 586997 642472 1133217 405983 892042 722967 915403 504196 649253 744868 73044 122437 253189 94898 1734161 2887013 3757859 345003 654393 451246 532452 376302 170994 392019 1798739 1304294 486177 2687408 2339898 255806 531199 1972093 4260610 2422827 487889 795406 1520471 225939 622165 430947 877343 505508 403667 230002 625705 375869 508851 976964 525008 5174336 457394 615424 802615 1227145 1308708 1015880 942436 820260 728871 768433 183788 N/F N/F 20212 N/F N/F N/F N/F MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name GSH-13C2_15N GSH_13C2-15N-Ellmans GSH GSH_Ellmans GSSG METABOLITES_END #END