#METABOLOMICS WORKBENCH Yuanye_Chi_20240730_073919 DATATRACK_ID:5050 STUDY_ID:ST003387 ANALYSIS_ID:AN005551 PROJECT_ID:PR002098
VERSION             	1
CREATED_ON             	August 6, 2024, 10:19 pm
#PROJECT
PR:PROJECT_TITLE                 	Annotation of Metabolites in Stable Isotope Tracing Untargeted Metabolomics via
PR:PROJECT_TITLE                 	Khipu-web
PR:PROJECT_SUMMARY               	Stable isotope tracing is a crucial technique for understanding the metabolic
PR:PROJECT_SUMMARY               	wiring of biological systems, determining meta-bolic flux through pathways of
PR:PROJECT_SUMMARY               	interest, and detecting novel metabolites and pathways. Despite the potential
PR:PROJECT_SUMMARY               	insights provid-ed by this technique, its application remains limited to a small
PR:PROJECT_SUMMARY               	number of targeted molecules and pathways. Because previ-ous software tools
PR:PROJECT_SUMMARY               	usually require chemical formulas to find relevant features, and the data are
PR:PROJECT_SUMMARY               	highly complex, especially in untargeted metabolomics and when the reactions and
PR:PROJECT_SUMMARY               	metabolites downstream the labeled substrates are poorly characterized. We
PR:PROJECT_SUMMARY               	report here Khipu version 2 and its new user-friendly web application. New
PR:PROJECT_SUMMARY               	functions are added to enhance analyzing stable isotope tracing data including
PR:PROJECT_SUMMARY               	metrics that evaluate peak enrichment in labeled samples, scoring methods to
PR:PROJECT_SUMMARY               	facilitate robust detection of intensity patterns and integrated natural
PR:PROJECT_SUMMARY               	abundance correction. We demonstrate that this approach can be applied to
PR:PROJECT_SUMMARY               	untargeted metabolomics to systematically extract isotope-labeled compounds and
PR:PROJECT_SUMMARY               	annotate the unidentified me-tabolites.
PR:INSTITUTE                     	The Jackson Laboratory for Genomic Medicine
PR:LABORATORY                    	Shuzhao Li Lab
PR:LAST_NAME                     	Chi
PR:FIRST_NAME                    	Yuanye
PR:ADDRESS                       	10 Discovery Dr, Farmington, CT
PR:EMAIL                         	yuanye.chi@jax.org
PR:PHONE                         	3395456866
#STUDY
ST:STUDY_TITLE                   	Annotation of Metabolites in Stable Isotope Tracing Untargeted Metabolomics via
ST:STUDY_TITLE                   	Khipu-web
ST:STUDY_SUMMARY                 	Stable isotope tracing is a crucial technique for understanding the metabolic
ST:STUDY_SUMMARY                 	wiring of biological systems, determining meta-bolic flux through pathways of
ST:STUDY_SUMMARY                 	interest, and detecting novel metabolites and pathways. Despite the potential
ST:STUDY_SUMMARY                 	insights provid-ed by this technique, its application remains limited to a small
ST:STUDY_SUMMARY                 	number of targeted molecules and pathways. Because previ-ous software tools
ST:STUDY_SUMMARY                 	usually require chemical formulas to find relevant features, and the data are
ST:STUDY_SUMMARY                 	highly complex, especially in untargeted metabolomics and when the reactions and
ST:STUDY_SUMMARY                 	metabolites downstream the labeled substrates are poorly characterized. We
ST:STUDY_SUMMARY                 	report here Khipu version 2 and its new user-friendly web application. New
ST:STUDY_SUMMARY                 	functions are added to enhance analyzing stable isotope tracing data including
ST:STUDY_SUMMARY                 	metrics that evaluate peak enrichment in labeled samples, scoring methods to
ST:STUDY_SUMMARY                 	facilitate robust detection of intensity patterns and integrated natural
ST:STUDY_SUMMARY                 	abundance correction. We demonstrate that this approach can be applied to
ST:STUDY_SUMMARY                 	untargeted metabolomics to systematically extract isotope-labeled compounds and
ST:STUDY_SUMMARY                 	annotate the unidentified me-tabolites.
ST:INSTITUTE                     	The Jackson Laboratory for Genomic Medicine
ST:LAST_NAME                     	Chi
ST:FIRST_NAME                    	Yuanye
ST:ADDRESS                       	10 Discovery Dr, Farmington, CT
ST:EMAIL                         	yuanye.chi@jax.org
ST:PHONE                         	3395456866
#SUBJECT
SU:SUBJECT_TYPE                  	Cultured cells
SU:SUBJECT_SPECIES               	Homo sapiens
#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           	-	293T_Sample1_HILICneg	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample1_HILICneg.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample1_RPpos	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample1_RPpos.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample2_HILICneg	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:12hr	RAW_FILE_NAME(File Name)=293T_Sample2_HILICneg.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample2_RPpos	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:12hr	RAW_FILE_NAME(File Name)=293T_Sample2_RPpos.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample3_HILICneg	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:6hr	RAW_FILE_NAME(File Name)=293T_Sample3_HILICneg.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample3_RPpos	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:6hr	RAW_FILE_NAME(File Name)=293T_Sample3_RPpos.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample4_HILICneg	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:12hr	RAW_FILE_NAME(File Name)=293T_Sample4_HILICneg.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample4_RPpos	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:12hr	RAW_FILE_NAME(File Name)=293T_Sample4_RPpos.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample5_HILICneg	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample5_HILICneg.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample5_RPpos	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample5_RPpos.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample6_HILICneg	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:6hr	RAW_FILE_NAME(File Name)=293T_Sample6_HILICneg.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample6_RPpos	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:6hr	RAW_FILE_NAME(File Name)=293T_Sample6_RPpos.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample7_HILICneg	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:6hr	RAW_FILE_NAME(File Name)=293T_Sample7_HILICneg.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample7_RPpos	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:6hr	RAW_FILE_NAME(File Name)=293T_Sample7_RPpos.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample8_HILICneg	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:ctrl	RAW_FILE_NAME(File Name)=293T_Sample8_HILICneg.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample8_RPpos	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:ctrl	RAW_FILE_NAME(File Name)=293T_Sample8_RPpos.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample9_HILICneg	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:12hr	RAW_FILE_NAME(File Name)=293T_Sample9_HILICneg.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample9_RPpos	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:12hr	RAW_FILE_NAME(File Name)=293T_Sample9_RPpos.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample10_HILICneg	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample10_HILICneg.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample10_RPpos	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample10_RPpos.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample11_HILICneg	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample11_HILICneg.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample11_RPpos	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample11_RPpos.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample12_HILICneg	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample12_HILICneg.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample12_RPpos	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample12_RPpos.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample13_HILICneg	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample13_HILICneg.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample13_RPpos	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample13_RPpos.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample14_HILICneg	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample14_HILICneg.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample14_RPpos	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample14_RPpos.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample15_HILICneg	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample15_HILICneg.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample15_RPpos	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample15_RPpos.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample16_HILICneg	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample16_HILICneg.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample16_RPpos	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample16_RPpos.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample1_HILICpos	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample1_HILICpos.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample1_RPneg	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample1_RPneg.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample2_HILICpos	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:12hr	RAW_FILE_NAME(File Name)=293T_Sample2_HILICpos.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample2_RPneg	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:12hr	RAW_FILE_NAME(File Name)=293T_Sample2_RPneg.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample3_HILICpos	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:6hr	RAW_FILE_NAME(File Name)=293T_Sample3_HILICpos.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample3_RPneg	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:6hr	RAW_FILE_NAME(File Name)=293T_Sample3_RPneg.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample4_HILICpos	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:12hr	RAW_FILE_NAME(File Name)=293T_Sample4_HILICpos.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample4_RPneg	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:12hr	RAW_FILE_NAME(File Name)=293T_Sample4_RPneg.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample5_HILICpos	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample5_HILICpos.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample5_RPneg	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample5_RPneg.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample6_HILICpos	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:6hr	RAW_FILE_NAME(File Name)=293T_Sample6_HILICpos.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample6_RPneg	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:6hr	RAW_FILE_NAME(File Name)=293T_Sample6_RPneg.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample7_HILICpos	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:6hr	RAW_FILE_NAME(File Name)=293T_Sample7_HILICpos.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample7_RPneg	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:6hr	RAW_FILE_NAME(File Name)=293T_Sample7_RPneg.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample8_HILICpos	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:ctrl	RAW_FILE_NAME(File Name)=293T_Sample8_HILICpos.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample8_RPneg	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:ctrl	RAW_FILE_NAME(File Name)=293T_Sample8_RPneg.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample9_HILICpos	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:12hr	RAW_FILE_NAME(File Name)=293T_Sample9_HILICpos.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample9_RPneg	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:12hr	RAW_FILE_NAME(File Name)=293T_Sample9_RPneg.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample10_HILICpos	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample10_HILICpos.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample10_RPneg	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample10_RPneg.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample11_HILICpos	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample11_HILICpos.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample11_RPneg	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample11_RPneg.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample12_HILICpos	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample12_HILICpos.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample12_RPneg	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample12_RPneg.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample13_HILICpos	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample13_HILICpos.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample13_RPneg	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample13_RPneg.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample14_HILICpos	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample14_HILICpos.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample14_RPneg	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample14_RPneg.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample15_HILICpos	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample15_HILICpos.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample15_RPneg	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample15_RPneg.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample16_HILICpos	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample16_HILICpos.mzML
SUBJECT_SAMPLE_FACTORS           	-	293T_Sample16_RPneg	Sample source:human embryonic kidney (HEK)  293T cells | Label Time Point:1hr	RAW_FILE_NAME(File Name)=293T_Sample16_RPneg.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_009	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:ctrl	RAW_FILE_NAME(File Name)=MT_20240318_009.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_010	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:ctrl	RAW_FILE_NAME(File Name)=MT_20240318_010.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_011	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:ctrl	RAW_FILE_NAME(File Name)=MT_20240318_011.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_012	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:ctrl	RAW_FILE_NAME(File Name)=MT_20240318_012.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_013	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:2hr	RAW_FILE_NAME(File Name)=MT_20240318_013.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_014	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:2hr	RAW_FILE_NAME(File Name)=MT_20240318_014.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_015	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:ctrl	RAW_FILE_NAME(File Name)=MT_20240318_015.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_016	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:ctrl	RAW_FILE_NAME(File Name)=MT_20240318_016.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_017	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:12hr	RAW_FILE_NAME(File Name)=MT_20240318_017.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_018	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:12hr	RAW_FILE_NAME(File Name)=MT_20240318_018.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_019	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:2hr	RAW_FILE_NAME(File Name)=MT_20240318_019.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_020	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:2hr	RAW_FILE_NAME(File Name)=MT_20240318_020.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_021	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:6hr	RAW_FILE_NAME(File Name)=MT_20240318_021.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_022	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:6hr	RAW_FILE_NAME(File Name)=MT_20240318_022.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_023	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:6hr	RAW_FILE_NAME(File Name)=MT_20240318_023.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_024	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:6hr	RAW_FILE_NAME(File Name)=MT_20240318_024.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_025	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:12hr	RAW_FILE_NAME(File Name)=MT_20240318_025.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_026	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:12hr	RAW_FILE_NAME(File Name)=MT_20240318_026.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_027	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:ctrl	RAW_FILE_NAME(File Name)=MT_20240318_027.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_028	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:ctrl	RAW_FILE_NAME(File Name)=MT_20240318_028.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_031	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:6hr	RAW_FILE_NAME(File Name)=MT_20240318_031.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_032	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:6hr	RAW_FILE_NAME(File Name)=MT_20240318_032.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_033	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:12hr	RAW_FILE_NAME(File Name)=MT_20240318_033.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_034	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:12hr	RAW_FILE_NAME(File Name)=MT_20240318_034.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_035	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:6hr	RAW_FILE_NAME(File Name)=MT_20240318_035.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_036	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:6hr	RAW_FILE_NAME(File Name)=MT_20240318_036.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_037	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:6hr	RAW_FILE_NAME(File Name)=MT_20240318_037.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_038	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:6hr	RAW_FILE_NAME(File Name)=MT_20240318_038.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_039	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:12hr	RAW_FILE_NAME(File Name)=MT_20240318_039.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_040	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:12hr	RAW_FILE_NAME(File Name)=MT_20240318_040.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_041	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:6hr	RAW_FILE_NAME(File Name)=MT_20240318_041.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_042	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:6hr	RAW_FILE_NAME(File Name)=MT_20240318_042.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_043	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:2hr	RAW_FILE_NAME(File Name)=MT_20240318_043.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_044	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:2hr	RAW_FILE_NAME(File Name)=MT_20240318_044.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_045	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:2hr	RAW_FILE_NAME(File Name)=MT_20240318_045.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_046	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:2hr	RAW_FILE_NAME(File Name)=MT_20240318_046.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_047	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:ctrl	RAW_FILE_NAME(File Name)=MT_20240318_047.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_048	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:ctrl	RAW_FILE_NAME(File Name)=MT_20240318_048.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_049	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:12hr	RAW_FILE_NAME(File Name)=MT_20240318_049.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_050	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:12hr	RAW_FILE_NAME(File Name)=MT_20240318_050.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_053	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:12hr	RAW_FILE_NAME(File Name)=MT_20240318_053.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_054	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:12hr	RAW_FILE_NAME(File Name)=MT_20240318_054.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_055	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:2hr	RAW_FILE_NAME(File Name)=MT_20240318_055.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_056	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:2hr	RAW_FILE_NAME(File Name)=MT_20240318_056.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_057	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:ctrl	RAW_FILE_NAME(File Name)=MT_20240318_057.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_058	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:ctrl	RAW_FILE_NAME(File Name)=MT_20240318_058.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_059	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:2hr	RAW_FILE_NAME(File Name)=MT_20240318_059.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240318_060	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:2hr	RAW_FILE_NAME(File Name)=MT_20240318_060.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_009	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:ctrl	RAW_FILE_NAME(File Name)=MT_20240319_009.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_010	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:ctrl	RAW_FILE_NAME(File Name)=MT_20240319_010.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_011	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:ctrl	RAW_FILE_NAME(File Name)=MT_20240319_011.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_012	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:ctrl	RAW_FILE_NAME(File Name)=MT_20240319_012.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_013	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:2hr	RAW_FILE_NAME(File Name)=MT_20240319_013.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_014	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:2hr	RAW_FILE_NAME(File Name)=MT_20240319_014.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_015	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:ctrl	RAW_FILE_NAME(File Name)=MT_20240319_015.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_016	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:ctrl	RAW_FILE_NAME(File Name)=MT_20240319_016.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_017	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:12hr	RAW_FILE_NAME(File Name)=MT_20240319_017.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_018	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:12hr	RAW_FILE_NAME(File Name)=MT_20240319_018.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_019	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:2hr	RAW_FILE_NAME(File Name)=MT_20240319_019.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_020	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:2hr	RAW_FILE_NAME(File Name)=MT_20240319_020.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_021	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:6hr	RAW_FILE_NAME(File Name)=MT_20240319_021.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_022	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:6hr	RAW_FILE_NAME(File Name)=MT_20240319_022.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_023	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:6hr	RAW_FILE_NAME(File Name)=MT_20240319_023.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_024	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:6hr	RAW_FILE_NAME(File Name)=MT_20240319_024.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_025	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:12hr	RAW_FILE_NAME(File Name)=MT_20240319_025.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_026	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:12hr	RAW_FILE_NAME(File Name)=MT_20240319_026.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_027	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:ctrl	RAW_FILE_NAME(File Name)=MT_20240319_027.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_028	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:ctrl	RAW_FILE_NAME(File Name)=MT_20240319_028.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_031	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:6hr	RAW_FILE_NAME(File Name)=MT_20240319_031.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_032	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:6hr	RAW_FILE_NAME(File Name)=MT_20240319_032.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_033	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:12hr	RAW_FILE_NAME(File Name)=MT_20240319_033.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_034	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:12hr	RAW_FILE_NAME(File Name)=MT_20240319_034.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_035	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:6hr	RAW_FILE_NAME(File Name)=MT_20240319_035.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_036	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:6hr	RAW_FILE_NAME(File Name)=MT_20240319_036.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_037	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:6hr	RAW_FILE_NAME(File Name)=MT_20240319_037.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_038	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:6hr	RAW_FILE_NAME(File Name)=MT_20240319_038.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_039	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:12hr	RAW_FILE_NAME(File Name)=MT_20240319_039.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_040	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:12hr	RAW_FILE_NAME(File Name)=MT_20240319_040.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_041	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:6hr	RAW_FILE_NAME(File Name)=MT_20240319_041.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_042	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:6hr	RAW_FILE_NAME(File Name)=MT_20240319_042.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_043	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:2hr	RAW_FILE_NAME(File Name)=MT_20240319_043.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_044	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:2hr	RAW_FILE_NAME(File Name)=MT_20240319_044.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_045	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:2hr	RAW_FILE_NAME(File Name)=MT_20240319_045.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_046	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:2hr	RAW_FILE_NAME(File Name)=MT_20240319_046.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_047	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:ctrl	RAW_FILE_NAME(File Name)=MT_20240319_047.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_048	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:ctrl	RAW_FILE_NAME(File Name)=MT_20240319_048.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_049	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:12hr	RAW_FILE_NAME(File Name)=MT_20240319_049.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_050	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:12hr	RAW_FILE_NAME(File Name)=MT_20240319_050.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_053	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:12hr	RAW_FILE_NAME(File Name)=MT_20240319_053.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_054	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:12hr	RAW_FILE_NAME(File Name)=MT_20240319_054.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_055	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:2hr	RAW_FILE_NAME(File Name)=MT_20240319_055.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_056	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:2hr	RAW_FILE_NAME(File Name)=MT_20240319_056.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_057	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:ctrl	RAW_FILE_NAME(File Name)=MT_20240319_057.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_058	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:ctrl	RAW_FILE_NAME(File Name)=MT_20240319_058.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_059	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:2hr	RAW_FILE_NAME(File Name)=MT_20240319_059.mzML
SUBJECT_SAMPLE_FACTORS           	-	MT_20240319_060	Sample source:acute myeloid leukemia (AML) cell | Label Time Point:2hr	RAW_FILE_NAME(File Name)=MT_20240319_060.mzML
#COLLECTION
CO:COLLECTION_SUMMARY            	Culturing of HEK 293T Cells HEK 293T cells were purchased from ATCC (CRL-3216,
CO:COLLECTION_SUMMARY            	Manassas, Virginia, USA) and cultured using a modification of methods published
CO:COLLECTION_SUMMARY            	by Lu et al. 2023 2. Cell culture media was prepared by mixing 50mL of fetal
CO:COLLECTION_SUMMARY            	bovine serum (FBS, A3840101, Thermo Fisher Scientific) with 5mL of a 5000U/mL
CO:COLLECTION_SUMMARY            	penicillin/streptomycin solution (15070063, Thermo Fisher Scientific) to 450 mL
CO:COLLECTION_SUMMARY            	of high glucose DMEM (11965092, Thermo Fisher Scientific). Frozen culture media
CO:COLLECTION_SUMMARY            	consisted of 60% culture media, 30% FBS and 10% DMSO prepared in 15-mL tubes and
CO:COLLECTION_SUMMARY            	stored at -20°C. Cells were kept in liquid nitrogen prior to recovery (day 1)
CO:COLLECTION_SUMMARY            	and were thawed within 1 minute in an incubator pre-warmed to 37°C. 1mL of
CO:COLLECTION_SUMMARY            	culture media was absorbed in a 5-mL pipette then used to transfer all cell
CO:COLLECTION_SUMMARY            	suspensions to a new 15mL tube which was then centrifuged at 300g for 4 minutes
CO:COLLECTION_SUMMARY            	at room temperature. The supernatant was discarded and 1mL of media was used to
CO:COLLECTION_SUMMARY            	then re-suspend the cells. The cell suspension was then transferred to a T25
CO:COLLECTION_SUMMARY            	plate containing 4mL of media which was then incubated at 37C and 5% CO2. After
CO:COLLECTION_SUMMARY            	overnight incubation, on day 2, cells were checked for confluency via
CO:COLLECTION_SUMMARY            	micrograph. At approximately 80 to 90% confluency, cells were washed with 2mL
CO:COLLECTION_SUMMARY            	PBS (J61196-AP, Thermo Fisher Scientific) and the wash discarded without
CO:COLLECTION_SUMMARY            	disturbing adhered cells. 0.5mL of trypsin buffer (1 ×, sterile;
CO:COLLECTION_SUMMARY            	sterile-filtered, BioReagent, suitable for cell culture, 0.5 g porcine trypsin
CO:COLLECTION_SUMMARY            	and 0.2 g EDTA in 100 mL, 4Na per liter of Hanks′ Balanced Salt Solution with
CO:COLLECTION_SUMMARY            	phenol red) was added and then incubated at room temperature or at 37C depending
CO:COLLECTION_SUMMARY            	on the amount of adherence for 5 minutes. 1.5mL of culture media was then added
CO:COLLECTION_SUMMARY            	to resuspend the cells and then transferred to a 15mL tube. After centrifuging
CO:COLLECTION_SUMMARY            	at 300g for 4 minutes at room temperature, the supernatant was discarded and the
CO:COLLECTION_SUMMARY            	cells resuspended in 1mL of culture media prior to transfer to a 10-cm plate
CO:COLLECTION_SUMMARY            	containing 9mL of culture media. Samples were incubated overnight at 37C and
CO:COLLECTION_SUMMARY            	5% CO2. This process was repeated on day 3 and 4 with the 10-cm plate and
CO:COLLECTION_SUMMARY            	increased resuspension volumes, 3mL on day 3 and 7 mL of frozen media on day 4.
CO:COLLECTION_SUMMARY            	At the end of day 4, one plate was retained for the isotope labeling experiments
CO:COLLECTION_SUMMARY            	while the remaining was was transferred to frozen vials 1mL at a time for a
CO:COLLECTION_SUMMARY            	target density of 10^6 cells/mL that were then stored at -80C for the
CO:COLLECTION_SUMMARY            	entirety of day 5 prior to liquid nitrogen storage on day 6. Culturing of THP1
CO:COLLECTION_SUMMARY            	and MOLM 13 cells Two acute myeloid leukemia (AML) cell lines, THP1 (ACC 16) and
CO:COLLECTION_SUMMARY            	MOLM13 (ACC 554), were obtained from DSMZ and cultured using a modification of
CO:COLLECTION_SUMMARY            	methods from Wang et al. 2023 1. Fresh culture media was prepared by mixing 50mL
CO:COLLECTION_SUMMARY            	of fetal bovine serum (FBS) (Corning, 35-011-CV), 5mL of a 5000U/mL
CO:COLLECTION_SUMMARY            	penicillin/streptomycin solution (Corning, 30-009-CI), 5mL of glutamax (Gibco,
CO:COLLECTION_SUMMARY            	35-050-061) to 500 mL of RPMI-1640 media (Corning, 10-040-CV). MOLM-13 cells
CO:COLLECTION_SUMMARY            	were obtained in a frozen cryovial and stored in liquid nitrogen prior to
CO:COLLECTION_SUMMARY            	recovery (day 1) and were thawed within 1 minute in an incubator pre-warmed to
CO:COLLECTION_SUMMARY            	37C. 1mL of culture media was absorbed in a 5-mL pipette then transfer all
CO:COLLECTION_SUMMARY            	cell suspensions to a new 15mL tube containing 9mL of 1xPBS, which was then
CO:COLLECTION_SUMMARY            	centrifuged at 400g for 5 minutes at room temperature. The supernatant was
CO:COLLECTION_SUMMARY            	discarded and 1mL of media was used to then re-suspend the cells. The cell
CO:COLLECTION_SUMMARY            	suspension was then transferred to a T25 plate containing 4mL of media which was
CO:COLLECTION_SUMMARY            	then incubated at 37C and 5% CO2. After overnight incubation, on day 2, cells
CO:COLLECTION_SUMMARY            	were checked for confluency via micrograph. At approximately 80 to 90%
CO:COLLECTION_SUMMARY            	confluency, the cells were centrifuged at 400g for 5 minutes. The cells were
CO:COLLECTION_SUMMARY            	resuspended with 2mL of media and then split into two 10-cm disc containing 9mL
CO:COLLECTION_SUMMARY            	of culture media. Culture discs were incubated overnight at 37C and 5% CO2.
CO:COLLECTION_SUMMARY            	THP1 was obtained in T25 plate cultured in 10mL culture media. The cell
CO:COLLECTION_SUMMARY            	suspension was then transferred to a T75 plate adding 10mL of media which was
CO:COLLECTION_SUMMARY            	then incubated at 37C and 5% CO2. At approximately 80 to 90% confluency, the
CO:COLLECTION_SUMMARY            	cells were centrifuged at 400g for 5 minutes and resuspended with 5mL of culture
CO:COLLECTION_SUMMARY            	media. For subsequent culture, 1mL of cell suspension was added in each 10-cm
CO:COLLECTION_SUMMARY            	disc and 4mL of media was added. This process was repeated for both cells to
CO:COLLECTION_SUMMARY            	have enough culture disc for subsequent experiment and storage. For storage,
CO:COLLECTION_SUMMARY            	frozen culture media consisted of 60% culture media, 30% FBS and 10% DMSO
CO:COLLECTION_SUMMARY            	prepared in 15-mL tubes and stored at -20C. Ten 10-cm disc of THP1 and five
CO:COLLECTION_SUMMARY            	10-cm disc for MOLM13 were retained for isotope tracing experiment and the
CO:COLLECTION_SUMMARY            	remaining was transferred to frozen vials 1mL at a time for a target density of
CO:COLLECTION_SUMMARY            	3*106 cells/mL that were then stored at -80C for 24 hour prior to liquid
CO:COLLECTION_SUMMARY            	nitrogen storage.
CO:SAMPLE_TYPE                   	iPSC cells
#TREATMENT
TR:TREATMENT_SUMMARY             	Isotope Labeling of HEK 293T Cells First, a 10-cm plate of 293T cells was
TR:TREATMENT_SUMMARY             	suspended with 7.2mL of culture media and four 6-well plates were prepared in
TR:TREATMENT_SUMMARY             	which 3 plates contain 2.5mL of culture media in 4 wells while the remaining
TR:TREATMENT_SUMMARY             	plate contains 2.5mL of culture media in all six wells. 200µL of cell
TR:TREATMENT_SUMMARY             	suspension was added to each media-containing well and then incubated at 37C
TR:TREATMENT_SUMMARY             	and 5% CO2 overnight. In isotope labeling experiment, culture media was prepared
TR:TREATMENT_SUMMARY             	by mixing 50mL of dialyzed fetal bovine serum (A3382001) with 5mL of a 5000U/mL
TR:TREATMENT_SUMMARY             	penicillin/streptomycin solution to 450 mL of glucose- and glutamine-free DMEM
TR:TREATMENT_SUMMARY             	(A1443001). An isotope labeled culture media was created by mixing
TR:TREATMENT_SUMMARY             	[U-13C6]-D-Glucose (CLM-1396, Cambridge Isotope Laboratories) and
TR:TREATMENT_SUMMARY             	13C5-L-Glutamine (CLM-1822-H-PK, Cambridge Isotope Laboratories) along with an
TR:TREATMENT_SUMMARY             	appropriate amount of unlabeled glucose and glutamine (G7021 and G8540,
TR:TREATMENT_SUMMARY             	Millipore Sigma, Sigma Aldrich) to 25mL of culture media to yield a 12.5mM
TR:TREATMENT_SUMMARY             	[U-13C6]-D-Glucose, 2mM 13C5L-Glutamine, 12.5mM D-Glucose, and 2mM L-glutamine
TR:TREATMENT_SUMMARY             	concentration. 13mLs of a control unlabeled media was created with a
TR:TREATMENT_SUMMARY             	concentration of 25mM for unlabeled glucose and 4 mM for unlabeled glutamine.
TR:TREATMENT_SUMMARY             	For two of the fully populated 6-well plates, the culture media was replaced
TR:TREATMENT_SUMMARY             	with 2mL of the labeled media while the culture media of the remaining 6 wells
TR:TREATMENT_SUMMARY             	were replaced with control media and then incubated at 37C and 5% CO2. At 2h,
TR:TREATMENT_SUMMARY             	6h, and 12h, cells were harvested from each labeled well while the control was
TR:TREATMENT_SUMMARY             	harvested at 6h. Harvesting consisted of aspirating 1 mL of culture medium to a
TR:TREATMENT_SUMMARY             	new 1.5 mL tube and centrifuging at 300g for 5 minutes at room temperature.
TR:TREATMENT_SUMMARY             	After centrifugation, 500µL of supernatant was transferred to a new 1.5mL tube
TR:TREATMENT_SUMMARY             	and stored at -80C for future analysis. The remaining supernatant was
TR:TREATMENT_SUMMARY             	discarded. Cell pellets were harvested by first pipetting any remaining media
TR:TREATMENT_SUMMARY             	out of the well without disturbing the cells. The well was then washed with 2mL
TR:TREATMENT_SUMMARY             	of 1x PBS, and the wash volume aspirated before adding an additional 2mL of 1x
TR:TREATMENT_SUMMARY             	PBS. Cells were then scraped gently with a cell lifter and then transferred to a
TR:TREATMENT_SUMMARY             	15mL tube containing 2mL of 1x PBS. These tubes were then centrifuged at 300g
TR:TREATMENT_SUMMARY             	for 5 minutes at room temperature and the supernatant discarded. The cell pellet
TR:TREATMENT_SUMMARY             	was resuspended with 1mL of 1x PBS and then counted with a hemocytometer as
TR:TREATMENT_SUMMARY             	previously described. Cell pellets were then transferred with 1mL of 1x PBS to a
TR:TREATMENT_SUMMARY             	1.5mL tube that were then centrifuged at 300g for 5 minutes at room temperature.
TR:TREATMENT_SUMMARY             	The supernatant was then discarded, and the cell pellets stored at -80C for
TR:TREATMENT_SUMMARY             	future use. Culturing of THP1 and MOLM 13 cells Two acute myeloid leukemia (AML)
TR:TREATMENT_SUMMARY             	cell lines, THP1 (ACC 16) and MOLM13 (ACC 554), were obtained from DSMZ and
TR:TREATMENT_SUMMARY             	cultured using a modification of methods from Wang et al. 2023 1. Fresh culture
TR:TREATMENT_SUMMARY             	media was prepared by mixing 50mL of fetal bovine serum (FBS) (Corning,
TR:TREATMENT_SUMMARY             	35-011-CV), 5mL of a 5000U/mL penicillin/streptomycin solution (Corning,
TR:TREATMENT_SUMMARY             	30-009-CI), 5mL of glutamax (Gibco, 35-050-061) to 500 mL of RPMI-1640 media
TR:TREATMENT_SUMMARY             	(Corning, 10-040-CV). MOLM-13 cells were obtained in a frozen cryovial and
TR:TREATMENT_SUMMARY             	stored in liquid nitrogen prior to recovery (day 1) and were thawed within 1
TR:TREATMENT_SUMMARY             	minute in an incubator pre-warmed to 37C. 1mL of culture media was absorbed
TR:TREATMENT_SUMMARY             	in a 5-mL pipette then transfer all cell suspensions to a new 15mL tube
TR:TREATMENT_SUMMARY             	containing 9mL of 1xPBS, which was then centrifuged at 400g for 5 minutes at
TR:TREATMENT_SUMMARY             	room temperature. The supernatant was discarded and 1mL of media was used to
TR:TREATMENT_SUMMARY             	then re-suspend the cells. The cell suspension was then transferred to a T25
TR:TREATMENT_SUMMARY             	plate containing 4mL of media which was then incubated at 37C and 5% CO2.
TR:TREATMENT_SUMMARY             	After overnight incubation, on day 2, cells were checked for confluency via
TR:TREATMENT_SUMMARY             	micrograph. At approximately 80 to 90% confluency, the cells were centrifuged at
TR:TREATMENT_SUMMARY             	400g for 5 minutes. The cells were resuspended with 2mL of media and then split
TR:TREATMENT_SUMMARY             	into two 10-cm disc containing 9mL of culture media. Culture discs were
TR:TREATMENT_SUMMARY             	incubated overnight at 37C and 5% CO2. THP1 was obtained in T25 plate
TR:TREATMENT_SUMMARY             	cultured in 10mL culture media. The cell suspension was then transferred to a
TR:TREATMENT_SUMMARY             	T75 plate adding 10mL of media which was then incubated at 37C and 5% CO2. At
TR:TREATMENT_SUMMARY             	approximately 80 to 90% confluency, the cells were centrifuged at 400g for 5
TR:TREATMENT_SUMMARY             	minutes and resuspended with 5mL of culture media. For subsequent culture, 1mL
TR:TREATMENT_SUMMARY             	of cell suspension was added in each 10-cm disc and 4mL of media was added. This
TR:TREATMENT_SUMMARY             	process was repeated for both cells to have enough culture disc for subsequent
TR:TREATMENT_SUMMARY             	experiment and storage. For storage, frozen culture media consisted of 60%
TR:TREATMENT_SUMMARY             	culture media, 30% FBS and 10% DMSO prepared in 15-mL tubes and stored at
TR:TREATMENT_SUMMARY             	-20C. Ten 10-cm disc of THP1 and five 10-cm disc for MOLM13 were retained for
TR:TREATMENT_SUMMARY             	isotope tracing experiment and the remaining was transferred to frozen vials 1mL
TR:TREATMENT_SUMMARY             	at a time for a target density of 3*106 cells/mL that were then stored at
TR:TREATMENT_SUMMARY             	-80C for 24 hour prior to liquid nitrogen storage.
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	Single Phase Cell Pellet Extraction Pellets were transferred to a 1.5 mL
SP:SAMPLEPREP_SUMMARY            	Eppendorf tube for extraction. An empty tube was also extracted to serve as a
SP:SAMPLEPREP_SUMMARY            	process blank. To each cell pellet, 100µL of ice cold (4ºC) 80% MeOH in water
SP:SAMPLEPREP_SUMMARY            	was added and 4µL of an IS spike-in solution was added for the AML cell
SP:SAMPLEPREP_SUMMARY            	samples. This IS solution is a stock solution prepared by mixing 0.12 mL of 1 M
SP:SAMPLEPREP_SUMMARY            	D-Glucose-13C6, 0.2 mL of 5 mM Caffeine-3-methyl-13C1, 0.6 mL of 10 mM
SP:SAMPLEPREP_SUMMARY            	L-Methionine-13C5, 0.6 mL of 20 mM L-Glutamic acid-13C5, 0.8 mL of 10 mM
SP:SAMPLEPREP_SUMMARY            	Uracil-15N2, 4 mL of 2 mM L-Tyrosine-15N1 and 3.68 mL water in 15-mL tube.
SP:SAMPLEPREP_SUMMARY            	Samples were then vortexed vigorously for 30 seconds and then subjected to 3
SP:SAMPLEPREP_SUMMARY            	freeze-thaw cycles. Each freeze-thaw cycle consisted of placing the sample in
SP:SAMPLEPREP_SUMMARY            	liquid nitrogen for 30 seconds, then thawing in an ice bath and sonicating for 3
SP:SAMPLEPREP_SUMMARY            	minutes. The sample was then vortexed for 10 additional seconds prior to
SP:SAMPLEPREP_SUMMARY            	centrifuging the sample at 20,817g for 20 minutes at 4ºC. 100µL of the
SP:SAMPLEPREP_SUMMARY            	resulting supernatant was then transferred to a new 1.5mL eppendorf tube. For
SP:SAMPLEPREP_SUMMARY            	the AML samples, 10µL of each study sample, labeled and unlabelled, was
SP:SAMPLEPREP_SUMMARY            	aliquoted to a new 1.5mL eppendorf tube for the creation of a pooled QC sample.
SP:SAMPLEPREP_SUMMARY            	For subsequent DDA experiments, a new unlabeled pooled sample was created in a
SP:SAMPLEPREP_SUMMARY            	similar fashion using 20µL from each of the unlabelled samples only. Samples
SP:SAMPLEPREP_SUMMARY            	from both cell lines, THP1 and MOLM13, were used for both pooled samples. For
SP:SAMPLEPREP_SUMMARY            	293T cells, the same procedure was used to create the pooled samples for both QC
SP:SAMPLEPREP_SUMMARY            	and unlabeled DDA; however, a volume of 10µL was aliquoted each time. For 293T
SP:SAMPLEPREP_SUMMARY            	cells 30µL of the supernatant was transferred to an autosampler vial while for
SP:SAMPLEPREP_SUMMARY            	AML cells 60µL was transferred. For all samples, 3µL was injected for each
SP:SAMPLEPREP_SUMMARY            	LC-MS method, both full scan and DDA.
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_TYPE           	Reversed phase
CH:INSTRUMENT_NAME               	Thermo Vanquish
CH:COLUMN_NAME                   	Thermo Hypersil GOLD (50 x 2.1mm, 3um)
CH:SOLVENT_A                     	100% water; 0.1% formic acid
CH:SOLVENT_B                     	100% acetonitrile; 0.1% formic
CH:FLOW_GRADIENT                 	0-0.1 min: 15% B, 0.10-2.01 min: 30% B, 2.01-11.0 min: 82% B, 11.0-11.5 min: 99%
CH:FLOW_GRADIENT                 	B, 11.5-12.0 min: 99% B and 8 min cleaning and column equilibration.
CH:FLOW_RATE                     	0.4 ml/min
CH:COLUMN_TEMPERATURE            	45
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:INSTRUMENT_NAME               	Thermo Q Exactive HF-X Orbitrap
MS:INSTRUMENT_TYPE               	Orbitrap
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	POSITIVE
MS:MS_COMMENTS                   	mass range, 66.7-1000 m/z; spray voltage, 3500 V (ESI+), 2500 V (ESI-); sheath
MS:MS_COMMENTS                   	gas flow rate, 55 Arb; auxiliary gas flow rate, 15 Arb; sweep gas, 3 Arb;
MS:MS_COMMENTS                   	capillary temperature, 300 °C; auxiliary gas heater temperature, 425°C; full
MS:MS_COMMENTS                   	scan mass resolution, 60,000 (MS1); AGC, 1e6; maximum injection time, 30 ms.
MS:MS_COMMENTS                   	Data dependent acquisition of MS2 spectra were collected on both instruments for
MS:MS_COMMENTS                   	all chromatography and ionization combinations using pooled unlabeled samples.
MS:MS_COMMENTS                   	isolation window (m/z), 1.2; stepped HCD collision energy (%), 20,40,80;
MS:MS_COMMENTS                   	dd-MS/MS resolution, 30,000; normalized AGC target, 1e5; maximum injection time,
MS:MS_COMMENTS                   	50 ms.
MS:MS_RESULTS_FILE               	ST003387_AN005551_Results.txt	UNITS:peak intensity	Has m/z:Yes	Has RT:Yes	RT units:Seconds
#END