#METABOLOMICS WORKBENCH TEXT OUTPUT STUDY_ID:	ANALYSIS_ID:	
VERSION             	1
CREATED_ON          	2017-06-17
#PROJECT
PR:PROJECT_TITLE    	ZS-RISP
PR:PROJECT_TYPE     	MS analysis
PR:PROJECT_SUMMARY  	To study metabolic change in macrophages after efferocytosis
PR:INSTITUTE        	Northwestern University
PR:DEPARTMENT       	Pathology
PR:LABORATORY       	Thorp Lab
PR:LAST_NAME        	Thorp
PR:FIRST_NAME       	Edward
PR:ADDRESS          	Evanston, IL
PR:EMAIL            	ebthorp@northwestern.edu
PR:PHONE            	312-503-4309
PR:FUNDING_SOURCE   	
PR:PROJECT_COMMENTS 	
PR:PUBLICATIONS     	
#STUDY
ST:STUDY_TITLE      	Metabolic change in macrophages after efferocytosis
ST:STUDY_TYPE       	MS analysis
ST:STUDY_SUMMARY    	The goal of the experiment is to study metabolic pathway alteration in macrophages after efferocytosis (when macrophages eating apoptotic cells). Peritoneal macrophages were purified and plated in the cell-culture dishes. After culturing overnight. Apoptotic cells were overlayed to macrophages for 2 hours, then un-engulfed cells were removed through washing. Macrophages were left in the plate for another 4 hours before being lifted from the plate.
ST:INSTITUTE        	University of Michigan
ST:DEPARTMENT       	Biomedical Research Core Facilities
ST:LABORATORY       	Metabolomics core
ST:LAST_NAME        	Kachman
ST:FIRST_NAME       	Maureen
ST:ADDRESS          	6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
ST:EMAIL            	mkachman@med.umich.edu
ST:PHONE            	(734) 232-8175
ST:SUBMIT_DATE      	08/04/2016 04:17:19 PM
ST:NUM_GROUPS       	4
ST:TOTAL_SUBJECTS   	1
ST:STUDY_COMMENTS   	
#SUBJECT_SAMPLE_FACTORS:          	SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data
SUBJECT_SAMPLE_FACTORS            	SU0015592	S00024013	Treatment:none	
SUBJECT_SAMPLE_FACTORS            	SU0015592	S00024014	Treatment:none	
SUBJECT_SAMPLE_FACTORS            	SU0015592	S00024015	Treatment:apoptotic cells for 2hrs	
SUBJECT_SAMPLE_FACTORS            	SU0015592	S00024016	Treatment:apoptotic cells for 2hrs	
SUBJECT_SAMPLE_FACTORS            	SU0015592	S00024017	Treatment:apoptotic cells for 2hrs	
SUBJECT_SAMPLE_FACTORS            	SU0015592	S00024018	Treatment:ko untreated	
SUBJECT_SAMPLE_FACTORS            	SU0015592	S00024019	Treatment:ko untreated	
SUBJECT_SAMPLE_FACTORS            	SU0015592	S00024020	Treatment:ko treated with apoptotic cells 2hrs	
SUBJECT_SAMPLE_FACTORS            	SU0015592	S00024021	Treatment:ko treated with apoptotic cells 2hrs	
SUBJECT_SAMPLE_FACTORS            	SU0015592	S00024022	Treatment:ko treated with apoptotic cells 2hrs	
#SUBJECT
SU:SUBJECT_TYPE                   	MOUSE
SU:SUBJECT_SPECIES                	Mus musculus
SU:TAXONOMY_ID                    	10090
#COLLECTION
CO:COLLECTION_SUMMARY             	-
#TREATMENT
TR:TREATMENT_SUMMARY              	-
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY             	-
SP:SAMPLEPREP_PROTOCOL_FILENAME   	A011 - Glycolysis-TCA-nucleotides.pdf
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_TYPE            	
CH:INSTRUMENT_NAME                	GC_7890N MS_5975 (Agilent)
CH:COLUMN_NAME                    	 ()
CH:METHODS_FILENAME               	HEIDI_FAMES.M
#ANALYSIS
AN:ANALYSIS_TYPE                  	MS
AN:INSTRUMENT_NAME                	GC_7890N MS_5975 (Agilent)
AN:ANALYSIS_PROTOCOL_FILE         	A011 - Glycolysis-TCA-nucleotides.pdf
AN:ACQUISITION_PARAMETERS_FILE    	HEIDI_FAMES.M
AN:PROCESSING_PARAMETERS_FILE     	-
#MS
MS:INSTRUMENT_TYPE                	Q
MS:MS_TYPE                        	EI
MS:ION_MODE                       	POSITIVE
#MS_METABOLITE_DATA
MS_METABOLITE_DATA:UNITS	pmol/ug protein
MS_METABOLITE_DATA_START
Sample	S00024013	S00024014	S00024015	S00024016	S00024017	S00024018	S00024019	S00024020	S00024021	S00024022
Factors	Treatment:none	Treatment:none	Treatment:apoptotic cells for 2hrs	Treatment:apoptotic cells for 2hrs	Treatment:apoptotic cells for 2hrs	Treatment:ko untreated	Treatment:ko untreated	Treatment:ko treated with apoptotic cells 2hrs	Treatment:ko treated with apoptotic cells 2hrs	Treatment:ko treated with apoptotic cells 2hrs
D-ERYTHROSE 4-PHOSPHATE	.00106586	0	.001958876	.001292215	0	.007599994	.008146643	.003979795	.005497746	.003390573
D-FRUCTOSE, 1,6-BIS(DIHYDROGEN PHOSPHATE)	.003890481	.001945037	.005114715	.002222935	.004980454	.008437272	.006940036	.007476818	.006812015	.008952233
CITRIC ACID	.020915117	.017025853	.021440712	.028471986	.017258225	.065730765	.069203622	.071994548	.054862786	.037426972
FAD	0	0	0	0	0	0	0	.0000348907	.000044205	0
MALIC ACID	.012652249	.011595965	.024237432	.034194884	.021873915	.032693286	.044060541	.039575982	.037726584	.031340399
ADENOSINE TRIPHOSPHATE	.002151351	.00204589	.002234721	.002060296	.002174957	.003671275	.003597657	.002302726	.001890725	.002201398
ROBISON ESTER	.005113045	.003987889	.00426487	.003153601	.002516779	.006615638	.020124577	.008297248	.008095753	.00623114
SUCROSE	0	0	0	0	0	.001716088	.002007621	.012244551	.014661049	.008125526
ADENOSINE 5'-DIPHOSPHATE	.002222532	.00201846	.002886605	.002735473	.003192554	.005605718	.00544571	.005237412	.003537134	.004722127
ADENOSINE 5'-MONOPHOSPHATE	.006053719	.003565046	.003834798	.003334564	.006877784	.013749327	.014710731	.013603214	.004438048	.012762911
GLYCERATE 3-PHOSPHATE	0	0	0	0	0	.000232519	0	0	0	0
RIBOSE PHOSPHATE	.006054687	.007080436	.01366128	.015745723	.007121562	.012813887	.014748332	.013491506	.021274454	.010218364
6-PHOSPHOGLUCONIC ACID	.001497523	.001529843	.001540677	.001544017	.001526052	.002816493	.002646342	.001274555	.001234628	.001294086
MS_METABOLITE_DATA_END
#METABOLITES
METABOLITES_START
metabolite_name	moverz_quant	ri	ri_type	pubchem_id	inchi_key	kegg_id	other_id	other_id_type
D-ERYTHROSE 4-PHOSPHATE				122357				
D-FRUCTOSE, 1,6-BIS(DIHYDROGEN PHOSPHATE)				21125049				
CITRIC ACID				311				
FAD				46906035				
MALIC ACID				525				
ADENOSINE TRIPHOSPHATE				5957				
ROBISON ESTER				5958				
SUCROSE				5988				
ADENOSINE 5'-DIPHOSPHATE				6022				
ADENOSINE 5'-MONOPHOSPHATE				6083				
GLYCERATE 3-PHOSPHATE				724				
RIBOSE PHOSPHATE				77982				
6-PHOSPHOGLUCONIC ACID				91493				
METABOLITES_END
