#METABOLOMICS WORKBENCH epannkuk_20210518_084258_mwtab.txt DATATRACK_ID:2646 STUDY_ID:ST001806 ANALYSIS_ID:AN002928 PROJECT_ID:000000
VERSION             	1
CREATED_ON             	May 24, 2021, 9:34 am
#PROJECT
PR:PROJECT_SUMMARY               	An important component of ionizing radiation (IR) exposure after a radiological
PR:PROJECT_SUMMARY               	incident may include low-dose rate (LDR) exposures either externally or
PR:PROJECT_SUMMARY               	internally, such as from 137Cs deposition. LDR exposures can have different
PR:PROJECT_SUMMARY               	effects compared to acute high-dose rate exposures from a health and
PR:PROJECT_SUMMARY               	biodosimetry perspective. In this study, a novel irradiation system, VAriable
PR:PROJECT_SUMMARY               	Dose-rate External 137Cs irradiatoR (VADER), was used to expose male and female
PR:PROJECT_SUMMARY               	mice to a variable LDR over a 30-day time span to cumulative doses of 1 (only in
PR:PROJECT_SUMMARY               	males), 2, 2.8, 4.1, 8.8 (only in males), or 9.7 Gy to simulate fall-out type
PR:PROJECT_SUMMARY               	exposures. Urine and serum from mice exposed to an acute dose (~0.8 Gy/min) of
PR:PROJECT_SUMMARY               	x-rays were collected in parallel. Radiation markers were identified by global
PR:PROJECT_SUMMARY               	mass spectrometry based metabolomics and the machine learning algorithm Random
PR:PROJECT_SUMMARY               	Forests.
PR:INSTITUTE                     	Georgetown University
PR:FIRST_NAME                    	Evan
PR:ADDRESS                       	3970 Reservoir Rd, NW New Research Building E504
PR:EMAIL                         	elp44@georgetown.edu
PR:PHONE                         	2026875650
PR:PROJECT_TITLE                 	Effect of external low-dose rate radiation on mouse biofluid metabolomics
PR:LAST_NAME                     	Pannkuk
#STUDY
ST:STUDY_TITLE                   	Effect of external low-dose rate radiation on mouse biofluid metabolomic
ST:STUDY_TITLE                   	signatures (part V)
ST:STUDY_SUMMARY                 	An important component of ionizing radiation (IR) exposure after a radiological
ST:STUDY_SUMMARY                 	incident may include low-dose rate (LDR) exposures either externally or
ST:STUDY_SUMMARY                 	internally, such as from 137Cs deposition. LDR exposures can have different
ST:STUDY_SUMMARY                 	effects compared to acute high-dose rate exposures from a health and
ST:STUDY_SUMMARY                 	biodosimetry perspective. In this study, a novel irradiation system, VAriable
ST:STUDY_SUMMARY                 	Dose-rate External 137Cs irradiatoR (VADER), was used to expose male and female
ST:STUDY_SUMMARY                 	mice to a variable LDR over a 30-day time span to cumulative doses of 1 (only in
ST:STUDY_SUMMARY                 	males), 2, 2.8, 4.1, 8.8 (only in males), or 9.7 Gy to simulate fall-out type
ST:STUDY_SUMMARY                 	exposures. Urine and serum from mice exposed to an acute dose (~0.8 Gy/min) of
ST:STUDY_SUMMARY                 	x-rays were collected in parallel. Radiation markers were identified by global
ST:STUDY_SUMMARY                 	mass spectrometry based metabolomics and the machine learning algorithm Random
ST:STUDY_SUMMARY                 	Forests.
ST:INSTITUTE                     	Georgetown University
ST:LAST_NAME                     	Pannkuk
ST:FIRST_NAME                    	Evan
ST:ADDRESS                       	3970 Reservoir Rd, NW New Research Building E504
ST:EMAIL                         	elp44@georgetown.edu
ST:PHONE                         	2026875650
#SUBJECT
SU:SUBJECT_TYPE                  	Mammal
SU:SUBJECT_SPECIES               	Mus musculus
SU:TAXONOMY_ID                   	10090
SU:GENDER                        	Male
#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           	1	114V	Factor:LDR | Factor:D5	RAW_FILE_NAME=NEG_012
SUBJECT_SAMPLE_FACTORS           	3	93A	Factor:Control | Factor:D3	RAW_FILE_NAME=NEG_013
SUBJECT_SAMPLE_FACTORS           	4	63A	Factor:HDR | Factor:D1	RAW_FILE_NAME=NEG_014
SUBJECT_SAMPLE_FACTORS           	5	113V	Factor:LDR | Factor:D5	RAW_FILE_NAME=NEG_015
SUBJECT_SAMPLE_FACTORS           	6	123V	Factor:LDR | Factor:D20	RAW_FILE_NAME=NEG_016
SUBJECT_SAMPLE_FACTORS           	9	159V	Factor:Control | Factor:D30	RAW_FILE_NAME=NEG_019
SUBJECT_SAMPLE_FACTORS           	11	99A	Factor:Control | Factor:D5	RAW_FILE_NAME=NEG_020
SUBJECT_SAMPLE_FACTORS           	13	153V	Factor:Control | Factor:D20	RAW_FILE_NAME=NEG_021
SUBJECT_SAMPLE_FACTORS           	14	151V	Factor:Control | Factor:D20	RAW_FILE_NAME=NEG_022
SUBJECT_SAMPLE_FACTORS           	16	89A	Factor:Control | Factor:D2	RAW_FILE_NAME=NEG_023
SUBJECT_SAMPLE_FACTORS           	17	87A	Factor:Control | Factor:D2	RAW_FILE_NAME=NEG_029
SUBJECT_SAMPLE_FACTORS           	18	90A	Factor:Control | Factor:D2	RAW_FILE_NAME=NEG_030
SUBJECT_SAMPLE_FACTORS           	20	115V	Factor:LDR | Factor:D5	RAW_FILE_NAME=NEG_031
SUBJECT_SAMPLE_FACTORS           	21	72A	Factor:HDR | Factor:D3	RAW_FILE_NAME=NEG_032
SUBJECT_SAMPLE_FACTORS           	22	186V	Factor:Control | Factor:D3	RAW_FILE_NAME=NEG_033
SUBJECT_SAMPLE_FACTORS           	23	77A	Factor:HDR | Factor:D5	RAW_FILE_NAME=NEG_036
SUBJECT_SAMPLE_FACTORS           	25	100A	Factor:Control | Factor:D5	RAW_FILE_NAME=NEG_037
SUBJECT_SAMPLE_FACTORS           	27	172V	Factor:LDR | Factor:D2	RAW_FILE_NAME=NEG_038
SUBJECT_SAMPLE_FACTORS           	30	130V	Factor:LDR | Factor:D30	RAW_FILE_NAME=NEG_039
SUBJECT_SAMPLE_FACTORS           	31	126V	Factor:LDR | Factor:D30	RAW_FILE_NAME=NEG_040
SUBJECT_SAMPLE_FACTORS           	33	75A	Factor:HDR | Factor:D3	RAW_FILE_NAME=NEG_046
SUBJECT_SAMPLE_FACTORS           	34	171V	Factor:LDR | Factor:D2	RAW_FILE_NAME=NEG_047
SUBJECT_SAMPLE_FACTORS           	37	158V	Factor:Control | Factor:D30	RAW_FILE_NAME=NEG_048
SUBJECT_SAMPLE_FACTORS           	38	176V	Factor:Control | Factor:D2	RAW_FILE_NAME=NEG_049
SUBJECT_SAMPLE_FACTORS           	39	156V	Factor:Control | Factor:D30	RAW_FILE_NAME=NEG_050
SUBJECT_SAMPLE_FACTORS           	40	152V	Factor:Control | Factor:D20	RAW_FILE_NAME=NEG_053
SUBJECT_SAMPLE_FACTORS           	42	70A	Factor:HDR | Factor:D2	RAW_FILE_NAME=NEG_054
SUBJECT_SAMPLE_FACTORS           	44	95A	Factor:Control | Factor:D3	RAW_FILE_NAME=NEG_055
SUBJECT_SAMPLE_FACTORS           	45	157V	Factor:Control | Factor:D30	RAW_FILE_NAME=NEG_056
SUBJECT_SAMPLE_FACTORS           	47	5V	Factor:LDR | Factor:D1	RAW_FILE_NAME=NEG_057
SUBJECT_SAMPLE_FACTORS           	48	178V	Factor:Control | Factor:D2	RAW_FILE_NAME=NEG_063
SUBJECT_SAMPLE_FACTORS           	49	67A	Factor:HDR | Factor:D2	RAW_FILE_NAME=NEG_064
SUBJECT_SAMPLE_FACTORS           	50	112V	Factor:LDR | Factor:D5	RAW_FILE_NAME=NEG_065
SUBJECT_SAMPLE_FACTORS           	51	2V	Factor:LDR | Factor:D1	RAW_FILE_NAME=NEG_066
SUBJECT_SAMPLE_FACTORS           	52	96A	Factor:Control | Factor:D5	RAW_FILE_NAME=NEG_067
SUBJECT_SAMPLE_FACTORS           	53	160V	Factor:Control | Factor:D30	RAW_FILE_NAME=NEG_070
SUBJECT_SAMPLE_FACTORS           	55	97A	Factor:Control | Factor:D5	RAW_FILE_NAME=NEG_071
SUBJECT_SAMPLE_FACTORS           	58	84A	Factor:Control | Factor:D1	RAW_FILE_NAME=NEG_072
SUBJECT_SAMPLE_FACTORS           	59	122V	Factor:LDR | Factor:D20	RAW_FILE_NAME=NEG_073
SUBJECT_SAMPLE_FACTORS           	61	174V	Factor:LDR | Factor:D2	RAW_FILE_NAME=NEG_074
SUBJECT_SAMPLE_FACTORS           	63	88A	Factor:Control | Factor:D2	RAW_FILE_NAME=NEG_080
SUBJECT_SAMPLE_FACTORS           	65	173V	Factor:LDR | Factor:D2	RAW_FILE_NAME=NEG_081
SUBJECT_SAMPLE_FACTORS           	66	69A	Factor:HDR | Factor:D2	RAW_FILE_NAME=NEG_082
SUBJECT_SAMPLE_FACTORS           	69	154V	Factor:Control | Factor:D20	RAW_FILE_NAME=NEG_083
SUBJECT_SAMPLE_FACTORS           	70	82A	Factor:Control | Factor:D1	RAW_FILE_NAME=NEG_084
SUBJECT_SAMPLE_FACTORS           	71	68A	Factor:HDR | Factor:D2	RAW_FILE_NAME=NEG_087
SUBJECT_SAMPLE_FACTORS           	72	71A	Factor:HDR | Factor:D3	RAW_FILE_NAME=NEG_088
SUBJECT_SAMPLE_FACTORS           	73	183V	Factor:LDR | Factor:D3	RAW_FILE_NAME=NEG_089
SUBJECT_SAMPLE_FACTORS           	74	3V	Factor:LDR | Factor:D1	RAW_FILE_NAME=NEG_090
SUBJECT_SAMPLE_FACTORS           	75	155V	Factor:Control | Factor:D20	RAW_FILE_NAME=NEG_091
SUBJECT_SAMPLE_FACTORS           	76	175V	Factor:LDR | Factor:D2	RAW_FILE_NAME=NEG_097
SUBJECT_SAMPLE_FACTORS           	78	62A	Factor:HDR | Factor:D1	RAW_FILE_NAME=NEG_098
SUBJECT_SAMPLE_FACTORS           	79	190V	Factor:Control | Factor:D3	RAW_FILE_NAME=NEG_099
SUBJECT_SAMPLE_FACTORS           	80	141V	Factor:Control | Factor:D5	RAW_FILE_NAME=NEG_100
SUBJECT_SAMPLE_FACTORS           	81	85A	Factor:Control | Factor:D1	RAW_FILE_NAME=NEG_101
SUBJECT_SAMPLE_FACTORS           	82	177V	Factor:Control | Factor:D2	RAW_FILE_NAME=NEG_104
SUBJECT_SAMPLE_FACTORS           	83	78A	Factor:HDR | Factor:D5	RAW_FILE_NAME=NEG_105
SUBJECT_SAMPLE_FACTORS           	84	64A	Factor:HDR | Factor:D1	RAW_FILE_NAME=NEG_106
SUBJECT_SAMPLE_FACTORS           	85	184V	Factor:LDR | Factor:D3	RAW_FILE_NAME=NEG_107
SUBJECT_SAMPLE_FACTORS           	89	143V	Factor:Control | Factor:D5	RAW_FILE_NAME=NEG_108
SUBJECT_SAMPLE_FACTORS           	90	94A	Factor:Control | Factor:D3	RAW_FILE_NAME=NEG_114
SUBJECT_SAMPLE_FACTORS           	91	4V	Factor:LDR | Factor:D1	RAW_FILE_NAME=NEG_115
SUBJECT_SAMPLE_FACTORS           	92	180V	Factor:Control | Factor:D2	RAW_FILE_NAME=NEG_116
SUBJECT_SAMPLE_FACTORS           	93	80A	Factor:HDR | Factor:D5	RAW_FILE_NAME=NEG_117
SUBJECT_SAMPLE_FACTORS           	95	121V	Factor:LDR | Factor:D20	RAW_FILE_NAME=NEG_118
SUBJECT_SAMPLE_FACTORS           	96	66A	Factor:HDR | Factor:D2	RAW_FILE_NAME=NEG_121
SUBJECT_SAMPLE_FACTORS           	97	187V	Factor:Control | Factor:D3	RAW_FILE_NAME=NEG_122
SUBJECT_SAMPLE_FACTORS           	101	86A	Factor:Control | Factor:D2	RAW_FILE_NAME=NEG_123
SUBJECT_SAMPLE_FACTORS           	104	92A	Factor:Control | Factor:D3	RAW_FILE_NAME=NEG_124
SUBJECT_SAMPLE_FACTORS           	105	185V	Factor:LDR | Factor:D3	RAW_FILE_NAME=NEG_125
SUBJECT_SAMPLE_FACTORS           	106	179V	Factor:Control | Factor:D2	RAW_FILE_NAME=NEG_131
SUBJECT_SAMPLE_FACTORS           	110	144V	Factor:Control | Factor:D5	RAW_FILE_NAME=NEG_132
SUBJECT_SAMPLE_FACTORS           	111	189V	Factor:Control | Factor:D3	RAW_FILE_NAME=NEG_133
SUBJECT_SAMPLE_FACTORS           	112	124V	Factor:LDR | Factor:D20	RAW_FILE_NAME=NEG_134
SUBJECT_SAMPLE_FACTORS           	113	33V	Factor:Control | Factor:D1	RAW_FILE_NAME=NEG_135
SUBJECT_SAMPLE_FACTORS           	114	73A	Factor:HDR | Factor:D3	RAW_FILE_NAME=NEG_138
SUBJECT_SAMPLE_FACTORS           	117	81A	Factor:Control | Factor:D1	RAW_FILE_NAME=NEG_139
SUBJECT_SAMPLE_FACTORS           	118	128V	Factor:LDR | Factor:D30	RAW_FILE_NAME=NEG_140
SUBJECT_SAMPLE_FACTORS           	119	127V	Factor:LDR | Factor:D30	RAW_FILE_NAME=NEG_141
SUBJECT_SAMPLE_FACTORS           	120	111V	Factor:LDR | Factor:D5	RAW_FILE_NAME=NEG_142
SUBJECT_SAMPLE_FACTORS           	121	65A	Factor:HDR | Factor:D1	RAW_FILE_NAME=NEG_148
SUBJECT_SAMPLE_FACTORS           	123	1V	Factor:LDR | Factor:D1	RAW_FILE_NAME=NEG_149
SUBJECT_SAMPLE_FACTORS           	126	181V	Factor:LDR | Factor:D3	RAW_FILE_NAME=NEG_150
SUBJECT_SAMPLE_FACTORS           	127	142V	Factor:Control | Factor:D5	RAW_FILE_NAME=NEG_151
SUBJECT_SAMPLE_FACTORS           	130	182V	Factor:LDR | Factor:D3	RAW_FILE_NAME=NEG_152
SUBJECT_SAMPLE_FACTORS           	131	188V	Factor:Control | Factor:D3	RAW_FILE_NAME=NEG_155
SUBJECT_SAMPLE_FACTORS           	133	145V	Factor:Control | Factor:D5	RAW_FILE_NAME=NEG_156
SUBJECT_SAMPLE_FACTORS           	134	83A	Factor:Control | Factor:D1	RAW_FILE_NAME=NEG_157
SUBJECT_SAMPLE_FACTORS           	135	76A	Factor:HDR | Factor:D5	RAW_FILE_NAME=NEG_158
SUBJECT_SAMPLE_FACTORS           	136	129V	Factor:LDR | Factor:D30	RAW_FILE_NAME=NEG_159
SUBJECT_SAMPLE_FACTORS           	137	34V	Factor:Control | Factor:D1	RAW_FILE_NAME=NEG_165
SUBJECT_SAMPLE_FACTORS           	139	61A	Factor:HDR | Factor:D1	RAW_FILE_NAME=NEG_166
SUBJECT_SAMPLE_FACTORS           	141	125V	Factor:LDR | Factor:D20	RAW_FILE_NAME=NEG_167
SUBJECT_SAMPLE_FACTORS           	143	91A	Factor:Control | Factor:D3	RAW_FILE_NAME=NEG_168
SUBJECT_SAMPLE_FACTORS           	144	32V	Factor:Control | Factor:D1	RAW_FILE_NAME=NEG_169
SUBJECT_SAMPLE_FACTORS           	145	79A	Factor:HDR | Factor:D5	RAW_FILE_NAME=NEG_172
SUBJECT_SAMPLE_FACTORS           	146	35V	Factor:Control | Factor:D1	RAW_FILE_NAME=NEG_173
SUBJECT_SAMPLE_FACTORS           	147	98A	Factor:Control | Factor:D5	RAW_FILE_NAME=NEG_174
SUBJECT_SAMPLE_FACTORS           	149	74A	Factor:HDR | Factor:D3	RAW_FILE_NAME=NEG_175
#COLLECTION
CO:COLLECTION_SUMMARY            	Serum was collected after irradiation
CO:SAMPLE_TYPE                   	Blood (serum)
#TREATMENT
TR:TREATMENT_SUMMARY             	The VADER was designed to deliver controlled dose rates in the range 0.1 – 1
TR:TREATMENT_SUMMARY             	Gy/day to a cohort of up to 15 mice. The VADER uses ~0.5 Ci of retired 137Cs
TR:TREATMENT_SUMMARY             	brachytherapy seeds that are arranged in two platters placed above and below a
TR:TREATMENT_SUMMARY             	“mouse hotel”. The platters can be placed ~0.5 – 60 cm above and below the
TR:TREATMENT_SUMMARY             	mouse hotel allowing implementation of time-variable dose rates. Offline
TR:TREATMENT_SUMMARY             	dosimetry of the VADER was performed annually using a NIST traceable 10x6-6
TR:TREATMENT_SUMMARY             	ionization chamber (Radcal Corp., Monrovia, CA). Dose uniformity across the
TR:TREATMENT_SUMMARY             	surface was measured using EBT3 film (Ashland, Covington, KY, USA) and the
TR:TREATMENT_SUMMARY             	variation was 15% across the hotel. A lead and high-density concrete brick
TR:TREATMENT_SUMMARY             	shield ensured minimal radiation doses to occupationally exposed personnel
TR:TREATMENT_SUMMARY             	(operators) inside (< 0.1 mGy/wk) and outside the room (< 0.02 mGy/wk). The
TR:TREATMENT_SUMMARY             	mouse hotel consists of an acrylic box (35 x 35 x 12 cm) allowing housing of ≤
TR:TREATMENT_SUMMARY             	15 mice with bedding material and food/water ad libitum. Temperature (20 –
TR:TREATMENT_SUMMARY             	25°C), humidity (40 – 60%), airflow and lighting were fully controlled to
TR:TREATMENT_SUMMARY             	required animal care standards (temperature/humidity sensor, HWg HTemp, TruePath
TR:TREATMENT_SUMMARY             	Technologies Victor, NY). Environmental controls and monitoring were integrated
TR:TREATMENT_SUMMARY             	into the mouse hotel for easy replacement in case of radiation damage. Mice were
TR:TREATMENT_SUMMARY             	monitored in real time using a 180° fisheye ELP USB camera (Amazon).
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	Samples were prepared and analyzed as previously described.18, 19 Briefly, serum
SP:SAMPLEPREP_SUMMARY            	(5 μl) was deproteinized (195 μl 66% cold acetonitrile [ACN]) with internal
SP:SAMPLEPREP_SUMMARY            	standards (2 μM debrisoquine [M+H]+ = 176.1188; 30 μM 4-nitrobenzoic acid
SP:SAMPLEPREP_SUMMARY            	[M-H]- = 166.0141), vortexed, incubated on ice (10 min), and centrifuged for 10
SP:SAMPLEPREP_SUMMARY            	min (max speed, 4 °C).
SP:PROCESSING_STORAGE_CONDITIONS 	-80℃
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_SUMMARY        	Mobile phases consisted of the following: solvent A (water/0.1% formic acid
CH:CHROMATOGRAPHY_SUMMARY        	[FA]), solvent B (ACN/0.1% FA), solvent C (isopropanol [IPA]/ACN (90:10)/0.1%
CH:CHROMATOGRAPHY_SUMMARY        	FA). The gradient for urine was (solvent A and B) 4.0 min 5% B, 4.0 min 20% B,
CH:CHROMATOGRAPHY_SUMMARY        	5.1 min 95% B, and 1.9 min 5% B at a flow rate of 0.5 ml/min. The gradient for
CH:CHROMATOGRAPHY_SUMMARY        	serum was (solvent A, B, and C) 4.0 min 98:2 A:B, 4.0 min 40:60 A:B, 1.5 min
CH:CHROMATOGRAPHY_SUMMARY        	2:98 A:B, 2.0 min 2:98 A:C, 0.5 min 50:50 A:C, and 1.0 min 98:2 A:B at a flow
CH:CHROMATOGRAPHY_SUMMARY        	rate of 0.5 ml/min.
CH:CHROMATOGRAPHY_TYPE           	Reversed phase
CH:INSTRUMENT_NAME               	Waters Acquity
CH:COLUMN_NAME                   	Waters Acquity BEH C18 (50 x 2.1mm, 1.7 um)
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:INSTRUMENT_NAME               	Waters Synapt G2 S QTOF
MS:INSTRUMENT_TYPE               	QTOF
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	NEGATIVE
MS:MS_COMMENTS                   	Negative and positive electrospray ionization (ESI) data-independent modes were
MS:MS_COMMENTS                   	used for data acquisition with leucine enkephalin ([M+H]+ = 556.2771, [M-H]- =
MS:MS_COMMENTS                   	554.2615) as Lock-Spray®. Operating conditions for ESI were: capillary voltage
MS:MS_COMMENTS                   	2.75 kV, cone voltage 30 V, desolvation temperature 500°C, desolvation gas flow
MS:MS_COMMENTS                   	1000 L/Hr.
MS:MS_RESULTS_FILE               	ST001806_AN002928_Results.txt	UNITS:peak area	Has m/z:Yes	Has RT:Yes	RT units:Minutes
#END