#METABOLOMICS WORKBENCH westcoastmetabolomics_20230727_154209 STUDY_ID:ST002817 ANALYSIS_ID:AN004586
#ANALYSIS TYPE: MS; ION MODE: Reversed phase POSITIVE ION MODE; (Institute: University of California, San Francisco)
VERSION             	1
CREATED_ON          	04-20-2024
#PROJECT
PR:PROJECT_TITLE    	Investigation of metabolism in hypertrophic cardiomyopathy
PR:PROJECT_SUMMARY  	We propose the use of targeted metabolomics to define the metabolic and
PR:PROJECT_SUMMARY  	molecular pathways altered in 2 mouse models (R92W-TnT and R403Q-MHC) of
PR:PROJECT_SUMMARY  	hypertrophic cardiomyopathy (HCM) that span the spectrum of human disease (heart
PR:PROJECT_SUMMARY  	failure and sudden death), with the goal of identifying treatment targets.
PR:PROJECT_SUMMARY  	Parallel targeted metabolomics studies will be performed in heart tissue and
PR:PROJECT_SUMMARY  	plasma at rest and following inotrope stimulation. Since energy compromise is
PR:PROJECT_SUMMARY  	expected to be most marked when the heart is subject to increased workload, as
PR:PROJECT_SUMMARY  	is the case during high-intensity exercise or inotropic stimulation, we propose
PR:PROJECT_SUMMARY  	metabolomics studies in heart tissue and plasma, at rest and following inotrope
PR:PROJECT_SUMMARY  	stimulation. We anticipate that the results of these studies will allow us to
PR:PROJECT_SUMMARY  	move forward with further investigations into specific metabolites of interest
PR:PROJECT_SUMMARY  	as biomarkers, to be tested in HCM patients in future studies.
PR:INSTITUTE        	University of California, San Francisco
PR:DEPARTMENT       	Hypertrophic Cardiomyopathy Center of Excellence
PR:LABORATORY       	UCSF Smith Cardiovascular Research Building
PR:LAST_NAME        	Abraham
PR:FIRST_NAME       	Maria Roselle
PR:ADDRESS          	555 Mission Bay Boulevard South, San Francisco, CA 94158
PR:EMAIL            	Roselle.Abraham@ucsf.edu
PR:PHONE            	415-502-3911
PR:DOI              	http://dx.doi.org/10.21228/M8RQ7M
PR:CONTRIBUTORS     	Arpana Vaniya (avaniya@ucdavis.edu), Anja Karlstaedt (Anja.Karlstaedt@cshs.org)
#STUDY
ST:STUDY_TITLE      	Investigation of metabolism in hypertrophic cardiomyopathy - Lipidomics
ST:STUDY_SUMMARY    	We propose the use of targeted metabolomics to define the metabolic and
ST:STUDY_SUMMARY    	molecular pathways altered in 2 mouse models (R92W-TnT and R403Q-MHC) of
ST:STUDY_SUMMARY    	hypertrophic cardiomyopathy (HCM) that span the spectrum of human disease (heart
ST:STUDY_SUMMARY    	failure and sudden death), with the goal of identifying treatment targets.
ST:STUDY_SUMMARY    	Parallel targeted metabolomics studies will be performed in heart tissue and
ST:STUDY_SUMMARY    	plasma at rest and following inotrope stimulation. Since energy compromise is
ST:STUDY_SUMMARY    	expected to be most marked when the heart is subject to increased workload, as
ST:STUDY_SUMMARY    	is the case during high-intensity exercise or inotropic stimulation, we propose
ST:STUDY_SUMMARY    	metabolomics studies in heart tissue and plasma, at rest and following inotrope
ST:STUDY_SUMMARY    	stimulation. We anticipate that the results of these studies will allow us to
ST:STUDY_SUMMARY    	move forward with further investigations into specific metabolites of interest
ST:STUDY_SUMMARY    	as biomarkers, to be tested in HCM patients in future studies.
ST:INSTITUTE        	University of California, San Francisco
ST:DEPARTMENT       	Hypertrophic Cardiomyopathy Center of Excellence
ST:LABORATORY       	UCSF Smith Cardiovascular Research Building
ST:LAST_NAME        	Abraham
ST:FIRST_NAME       	Maria Roselle
ST:ADDRESS          	555 Mission Bay Boulevard South, San Francisco, CA 94158
ST:EMAIL            	Roselle.Abraham@ucsf.edu
ST:PHONE            	415-502-3911
ST:SUBMIT_DATE      	2023-07-27
ST:NUM_GROUPS       	2 groups of 2 (i.e., mutant vs control of two mouse models of HCM (R402Q-MyHC,
ST:NUM_GROUPS       	R92W-TnT)
ST:TOTAL_SUBJECTS   	32
#SUBJECT_SAMPLE_FACTORS:         	SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data
SUBJECT_SAMPLE_FACTORS           	-	M438	Treatment:Control MHC	Sample_Data:RAW_FILE_NAME=Abraham026_MX441683_posCSH_M438-011_2.d; RAW_FILE_NAME=Abraham026_MX441683_negCSH_M438-011_2.d
SUBJECT_SAMPLE_FACTORS           	-	M440	Treatment:Control MHC	Sample_Data:RAW_FILE_NAME=Abraham053_MX441683_posCSH_M440-012_2.d; RAW_FILE_NAME=Abraham053_MX441683_negCSH_M440-012_2.d
SUBJECT_SAMPLE_FACTORS           	-	M447	Treatment:Control MHC	Sample_Data:RAW_FILE_NAME=Abraham028_MX441683_posCSH_M447-009_2.d; RAW_FILE_NAME=Abraham028_MX441683_negCSH_M447-009_2.d
SUBJECT_SAMPLE_FACTORS           	-	M485	Treatment:Control MHC	Sample_Data:RAW_FILE_NAME=Abraham023_MX441683_posCSH_M485-013_2.d; RAW_FILE_NAME=Abraham023_MX441683_negCSH_M485-013_2.d
SUBJECT_SAMPLE_FACTORS           	-	M487	Treatment:Control MHC	Sample_Data:RAW_FILE_NAME=Abraham008_MX441683_posCSH_M487-014_2.d; RAW_FILE_NAME=Abraham008_MX441683_negCSH_M487-014_2.d
SUBJECT_SAMPLE_FACTORS           	-	M492	Treatment:Control MHC	Sample_Data:RAW_FILE_NAME=Abraham045_MX441683_posCSH_M492-016_2.d; RAW_FILE_NAME=Abraham045_MX441683_negCSH_M492-016_2.d
SUBJECT_SAMPLE_FACTORS           	-	M499	Treatment:Control MHC	Sample_Data:RAW_FILE_NAME=Abraham034_MX441683_posCSH_M499-010_2.d; RAW_FILE_NAME=Abraham034_MX441683_negCSH_M499-010_2.d
SUBJECT_SAMPLE_FACTORS           	-	M503	Treatment:Control MHC	Sample_Data:RAW_FILE_NAME=Abraham015_MX441683_posCSH_M503-025_2.d; RAW_FILE_NAME=Abraham015_MX441683_negCSH_M503-025_2.d
SUBJECT_SAMPLE_FACTORS           	-	T515	Treatment:Control TNT	Sample_Data:RAW_FILE_NAME=Abraham043_MX441683_posCSH_T515-041_2.d; RAW_FILE_NAME=Abraham043_MX441683_negCSH_T515-041_2.d
SUBJECT_SAMPLE_FACTORS           	-	T518	Treatment:Control TNT	Sample_Data:RAW_FILE_NAME=Abraham047_MX441683_posCSH_T518-042_2.d; RAW_FILE_NAME=Abraham047_MX441683_negCSH_T518-042_2.d
SUBJECT_SAMPLE_FACTORS           	-	T520	Treatment:Control TNT	Sample_Data:RAW_FILE_NAME=Abraham059_MX441683_posCSH_T520-043_2.d; RAW_FILE_NAME=Abraham059_MX441683_negCSH_T520-043_2.d
SUBJECT_SAMPLE_FACTORS           	-	T522	Treatment:Control TNT	Sample_Data:RAW_FILE_NAME=Abraham022_MX441683_posCSH_T522-044_2.d; RAW_FILE_NAME=Abraham022_MX441683_negCSH_T522-044_2.d
SUBJECT_SAMPLE_FACTORS           	-	T524	Treatment:Control TNT	Sample_Data:RAW_FILE_NAME=Abraham039_MX441683_posCSH_T524-045_2.d; RAW_FILE_NAME=Abraham039_MX441683_negCSH_T524-045_2.d
SUBJECT_SAMPLE_FACTORS           	-	T544	Treatment:Control TNT	Sample_Data:RAW_FILE_NAME=Abraham005_MX441683_posCSH_T544-046_2.d; RAW_FILE_NAME=Abraham005_MX441683_negCSH_T544-046_2.d
SUBJECT_SAMPLE_FACTORS           	-	T545	Treatment:Control TNT	Sample_Data:RAW_FILE_NAME=Abraham060_MX441683_posCSH_T545-047_2.d; RAW_FILE_NAME=Abraham060_MX441683_negCSH_T545-047_2.d
SUBJECT_SAMPLE_FACTORS           	-	T547	Treatment:Control TNT	Sample_Data:RAW_FILE_NAME=Abraham025_MX441683_posCSH_T547-048_2.d; RAW_FILE_NAME=Abraham025_MX441683_negCSH_T547-048_2.d
SUBJECT_SAMPLE_FACTORS           	-	MtdBlank001	Treatment:Method Blank	Sample_Data:RAW_FILE_NAME=MtdBlank001_MX441683_posCSH_preAbraham001_2.d; RAW_FILE_NAME=MtdBlank001_MX441683_negCSH_preAbraham001_2.d
SUBJECT_SAMPLE_FACTORS           	-	MtdBlank002	Treatment:Method Blank	Sample_Data:RAW_FILE_NAME=MtdBlank002_MX441683_posCSH_postAbraham010_2.d; RAW_FILE_NAME=MtdBlank002_MX441683_negCSH_postAbraham010_2.d
SUBJECT_SAMPLE_FACTORS           	-	MtdBlank003	Treatment:Method Blank	Sample_Data:RAW_FILE_NAME=MtdBlank003_MX441683_posCSH_postAbraham020_2.d; RAW_FILE_NAME=MtdBlank003_MX441683_negCSH_postAbraham020_2.d
SUBJECT_SAMPLE_FACTORS           	-	MtdBlank004	Treatment:Method Blank	Sample_Data:RAW_FILE_NAME=MtdBlank004_MX441683_posCSH_postAbraham030_2.d; RAW_FILE_NAME=MtdBlank004_MX441683_negCSH_postAbraham030_2.d
SUBJECT_SAMPLE_FACTORS           	-	MtdBlank005	Treatment:Method Blank	Sample_Data:RAW_FILE_NAME=MtdBlank005_MX441683_posCSH_postAbraham040_2.d; RAW_FILE_NAME=MtdBlank005_MX441683_negCSH_postAbraham040_2.d
SUBJECT_SAMPLE_FACTORS           	-	MtdBlank006	Treatment:Method Blank	Sample_Data:RAW_FILE_NAME=MtdBlank006_MX441683_posCSH_postAbraham050_2.d; RAW_FILE_NAME=MtdBlank006_MX441683_negCSH_postAbraham050_2.d
SUBJECT_SAMPLE_FACTORS           	-	MtdBlank007	Treatment:Method Blank	Sample_Data:RAW_FILE_NAME=MtdBlank007_MX441683_posCSH_postAbraham060_2.d; RAW_FILE_NAME=MtdBlank007_MX441683_negCSH_postAbraham060_2.d
SUBJECT_SAMPLE_FACTORS           	-	MtdBlank008	Treatment:Method Blank	Sample_Data:RAW_FILE_NAME=MtdBlank008_MX441683_posCSH_postAbraham064_2.d; RAW_FILE_NAME=MtdBlank008_MX441683_negCSH_postAbraham064_2.d
SUBJECT_SAMPLE_FACTORS           	-	M439	Treatment:MHC	Sample_Data:RAW_FILE_NAME=Abraham044_MX441683_posCSH_M439-026_2.d; RAW_FILE_NAME=Abraham044_MX441683_negCSH_M439-026_2.d
SUBJECT_SAMPLE_FACTORS           	-	M441	Treatment:MHC	Sample_Data:RAW_FILE_NAME=Abraham017_MX441683_posCSH_M441-027_2.d; RAW_FILE_NAME=Abraham017_MX441683_negCSH_M441-027_2.d
SUBJECT_SAMPLE_FACTORS           	-	M483	Treatment:MHC	Sample_Data:RAW_FILE_NAME=Abraham014_MX441683_posCSH_M483-029_2.d; RAW_FILE_NAME=Abraham014_MX441683_negCSH_M483-029_2.d
SUBJECT_SAMPLE_FACTORS           	-	M486	Treatment:MHC	Sample_Data:RAW_FILE_NAME=Abraham032_MX441683_posCSH_M486-030_2.d; RAW_FILE_NAME=Abraham032_MX441683_negCSH_M486-030_2.d
SUBJECT_SAMPLE_FACTORS           	-	M498	Treatment:MHC	Sample_Data:RAW_FILE_NAME=Abraham052_MX441683_posCSH_M498-032_2.d; RAW_FILE_NAME=Abraham052_MX441683_negCSH_M498-032_2.d
SUBJECT_SAMPLE_FACTORS           	-	M500	Treatment:MHC	Sample_Data:RAW_FILE_NAME=Abraham048_MX441683_posCSH_M500-015_2.d; RAW_FILE_NAME=Abraham048_MX441683_negCSH_M500-015_2.d
SUBJECT_SAMPLE_FACTORS           	-	M504	Treatment:MHC	Sample_Data:RAW_FILE_NAME=Abraham035_MX441683_posCSH_M504-028_2.d; RAW_FILE_NAME=Abraham035_MX441683_negCSH_M504-028_2.d
SUBJECT_SAMPLE_FACTORS           	-	M540	Treatment:MHC	Sample_Data:RAW_FILE_NAME=Abraham030_MX441683_posCSH_M540-031_2.d; RAW_FILE_NAME=Abraham030_MX441683_negCSH_M540-031_2.d
SUBJECT_SAMPLE_FACTORS           	-	Pool001	Treatment:Pool QC	Sample_Data:RAW_FILE_NAME=Pool001_MX441683_posCSH_preAbraham001_2.d; RAW_FILE_NAME=Pool001_MX441683_negCSH_preAbraham001_2.d
SUBJECT_SAMPLE_FACTORS           	-	Pool002	Treatment:Pool QC	Sample_Data:RAW_FILE_NAME=Pool002_MX441683_posCSH_postAbraham010_2.d; RAW_FILE_NAME=Pool002_MX441683_negCSH_postAbraham010_2.d
SUBJECT_SAMPLE_FACTORS           	-	Pool003	Treatment:Pool QC	Sample_Data:RAW_FILE_NAME=Pool003_MX441683_posCSH_postAbraham020_2.d; RAW_FILE_NAME=Pool003_MX441683_negCSH_postAbraham020_2.d
SUBJECT_SAMPLE_FACTORS           	-	Pool004	Treatment:Pool QC	Sample_Data:RAW_FILE_NAME=Pool004_MX441683_posCSH_postAbraham030_2.d; RAW_FILE_NAME=Pool004_MX441683_negCSH_postAbraham030_2.d
SUBJECT_SAMPLE_FACTORS           	-	Pool005	Treatment:Pool QC	Sample_Data:RAW_FILE_NAME=Pool005_MX441683_posCSH_postAbraham040_2.d; RAW_FILE_NAME=Pool005_MX441683_negCSH_postAbraham040_2.d
SUBJECT_SAMPLE_FACTORS           	-	Pool006	Treatment:Pool QC	Sample_Data:RAW_FILE_NAME=Pool006_MX441683_posCSH_postAbraham050_2.d; RAW_FILE_NAME=Pool006_MX441683_negCSH_postAbraham050_2.d
SUBJECT_SAMPLE_FACTORS           	-	Pool007	Treatment:Pool QC	Sample_Data:RAW_FILE_NAME=Pool007_MX441683_posCSH_postAbraham060_2.d; RAW_FILE_NAME=Pool007_MX441683_negCSH_postAbraham060_2.d
SUBJECT_SAMPLE_FACTORS           	-	Pool008	Treatment:Pool QC	Sample_Data:RAW_FILE_NAME=Pool008_MX441683_posCSH_postAbraham064_2.d; RAW_FILE_NAME=Pool008_MX441683_negCSH_postAbraham064_2.d
SUBJECT_SAMPLE_FACTORS           	-	Biorec001	Treatment:QC	Sample_Data:RAW_FILE_NAME=Biorec001_MX441683_posCSH_preAbraham001_2.d; RAW_FILE_NAME=Biorec001_MX441683_negCSH_preAbraham001_2.d
SUBJECT_SAMPLE_FACTORS           	-	Biorec002	Treatment:QC	Sample_Data:RAW_FILE_NAME=Biorec002_MX441683_posCSH_postAbraham010_2.d; RAW_FILE_NAME=Biorec002_MX441683_negCSH_postAbraham010_2.d
SUBJECT_SAMPLE_FACTORS           	-	Biorec003	Treatment:QC	Sample_Data:RAW_FILE_NAME=Biorec003_MX441683_posCSH_postAbraham020_2.d; RAW_FILE_NAME=Biorec003_MX441683_negCSH_postAbraham020_2.d
SUBJECT_SAMPLE_FACTORS           	-	Biorec004	Treatment:QC	Sample_Data:RAW_FILE_NAME=Biorec004_MX441683_posCSH_postAbraham030_2.d; RAW_FILE_NAME=Biorec004_MX441683_negCSH_postAbraham030_2.d
SUBJECT_SAMPLE_FACTORS           	-	Biorec005	Treatment:QC	Sample_Data:RAW_FILE_NAME=Biorec005_MX441683_posCSH_postAbraham040_2.d; RAW_FILE_NAME=Biorec005_MX441683_negCSH_postAbraham040_2.d
SUBJECT_SAMPLE_FACTORS           	-	Biorec006	Treatment:QC	Sample_Data:RAW_FILE_NAME=Biorec006_MX441683_posCSH_postAbraham050_2.d; RAW_FILE_NAME=Biorec006_MX441683_negCSH_postAbraham050_2.d
SUBJECT_SAMPLE_FACTORS           	-	Biorec007	Treatment:QC	Sample_Data:RAW_FILE_NAME=Biorec007_MX441683_posCSH_postAbraham060_2.d; RAW_FILE_NAME=Biorec007_MX441683_negCSH_postAbraham060_2.d
SUBJECT_SAMPLE_FACTORS           	-	Biorec008	Treatment:QC	Sample_Data:RAW_FILE_NAME=Biorec008_MX441683_posCSH_postAbraham064_2.d; RAW_FILE_NAME=Biorec008_MX441683_negCSH_postAbraham064_2.d
SUBJECT_SAMPLE_FACTORS           	-	T519	Treatment:TNT	Sample_Data:RAW_FILE_NAME=Abraham018_MX441683_posCSH_T519-057_2.d; RAW_FILE_NAME=Abraham018_MX441683_negCSH_T519-057_2.d
SUBJECT_SAMPLE_FACTORS           	-	T521	Treatment:TNT	Sample_Data:RAW_FILE_NAME=Abraham002_MX441683_posCSH_T521-058_2.d; RAW_FILE_NAME=Abraham002_MX441683_negCSH_T521-058_2.d
SUBJECT_SAMPLE_FACTORS           	-	T523	Treatment:TNT	Sample_Data:RAW_FILE_NAME=Abraham031_MX441683_posCSH_T523-059_2.d; RAW_FILE_NAME=Abraham031_MX441683_negCSH_T523-059_2.d
SUBJECT_SAMPLE_FACTORS           	-	T525	Treatment:TNT	Sample_Data:RAW_FILE_NAME=Abraham029_MX441683_posCSH_T525-060_2.d; RAW_FILE_NAME=Abraham029_MX441683_negCSH_T525-060_2.d
SUBJECT_SAMPLE_FACTORS           	-	T527	Treatment:TNT	Sample_Data:RAW_FILE_NAME=Abraham062_MX441683_posCSH_T527-061_2.d; RAW_FILE_NAME=Abraham062_MX441683_negCSH_T527-061_2.d
SUBJECT_SAMPLE_FACTORS           	-	T540	Treatment:TNT	Sample_Data:RAW_FILE_NAME=Abraham061_MX441683_posCSH_T540-062_2.d; RAW_FILE_NAME=Abraham061_MX441683_negCSH_T540-062_2.d
SUBJECT_SAMPLE_FACTORS           	-	T542	Treatment:TNT	Sample_Data:RAW_FILE_NAME=Abraham058_MX441683_posCSH_T542-063_2.d; RAW_FILE_NAME=Abraham058_MX441683_negCSH_T542-063_2.d
SUBJECT_SAMPLE_FACTORS           	-	T546	Treatment:TNT	Sample_Data:RAW_FILE_NAME=Abraham001_MX441683_posCSH_T546-064_2.d; RAW_FILE_NAME=Abraham001_MX441683_negCSH_T546-064_2.d
#SUBJECT
SU:SUBJECT_TYPE                  	Mammal
SU:SUBJECT_SPECIES               	Mus musculus
SU:TAXONOMY_ID                   	10090
#COLLECTION
CO:COLLECTION_SUMMARY            	Excision while the heart still beating and flash freeze within 15 seconds of
CO:COLLECTION_SUMMARY            	excision
CO:SAMPLE_TYPE                   	Heart
#TREATMENT
TR:TREATMENT_SUMMARY             	Saline IP and heparine SC injection in control & mutant group. After 10 minutes
TR:TREATMENT_SUMMARY             	of saline injection we performed cervical dislocation, whole heart excision and
TR:TREATMENT_SUMMARY             	flash freeze within 15 seconds of excision.
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	2 mg of lyophilized tissue extracted with 225 uL MeOH + 188 uL H2O + 750 uL
SP:SAMPLEPREP_SUMMARY            	MTBE. 350 uL of the organic layer was dried and resuspended 90:10 MeOH + Toluene
SP:SAMPLEPREP_SUMMARY            	with internal standards.
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_SUMMARY        	Low pH polar (LC/MS Pos early)
CH:INSTRUMENT_NAME               	Waters Acquity
CH:COLUMN_NAME                   	Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um)
CH:COLUMN_TEMPERATURE            	-
CH:FLOW_GRADIENT                 	-
CH:FLOW_RATE                     	-
CH:SOLVENT_A                     	-
CH:SOLVENT_B                     	-
CH:CHROMATOGRAPHY_TYPE           	Reversed phase
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
AN:ANALYSIS_DISPLAY              	Reversed phase POSITIVE ION MODE
AN:NUM_FACTORS                   	1
AN:NUM_METABOLITES               	217
AN:UNITS                         	raw area counts rescaled to set the median equal to 1
#MS
MS:INSTRUMENT_NAME               	Thermo Q Exactive Orbitrap
MS:INSTRUMENT_TYPE               	Orbitrap
MS:MS_TYPE                       	ESI
MS:MS_COMMENTS                   	Metabolon (LC/MS Pos early)
MS:ION_MODE                      	POSITIVE
#MS_METABOLITE_DATA
MS_METABOLITE_DATA:UNITS	
MS_METABOLITE_DATA_START
Samples
Factors
MS_METABOLITE_DATA_END
#METABOLITES
METABOLITES_START
metabolite_name	pubchem_id	inchi_key	kegg_id	other_id	other_id_type	ri	ri_type	moverz_quant	
METABOLITES_END