{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002552","ANALYSIS_ID":"AN004202","VERSION":"1","CREATED_ON":"April 6, 2023, 3:03 pm"},

"PROJECT":{"PROJECT_TITLE":"Biomarker discovery in galactosemia: Metabolomics with UPLC/HRMS in dried blood spots","PROJECT_TYPE":"newborn screening","PROJECT_SUMMARY":"Galactosemia (GAL) is an autosomal recessive genetic disorder characterized by galactose metabolism disturbances. GAL develops non-preventable life-threatening complications even with a reduced content of galactose and lactose patient’s diet. Thus, the underlying pathophysiology of long-term complications in GAL remains poorly understood. The current study used a metabolomics approach using ultra-performance liquid chromatography coupled with high-resolution mass spectrometry to investigate the metabolomic changes in the dried blood spots of 15 patients with GAL and 39 healthy individuals. Compared to the control group, 2,819 metabolites underwent significant changes in patients with GAL. In all, 480 human endogenous metabolites were identified, of which 209 and 271 were upregulated and downregulated, respectively. PA (8:0/LTE4) and ganglioside GT1c (d18:0/20:0) metabolites showed the most significant difference between GAL and the healthy group, with an area under the curve of 1 and 0.995, respectively. Additionally, our findings showed novel potential biomarkers for GAL, such as 17-alpha-estradiol-3-glucuronide and 16-alpha-hydroxy DHEA 3-sulfatediphosphate. In conclusion, this metabolomics study deepened the understanding of the pathophysiology of GAL and presented metabolites that might serve as potential prognostic biomarkers to monitor the progression or support the clinical diagnosis of GAL.","INSTITUTE":"King Saud University","DEPARTMENT":"Metabolomics","LABORATORY":"Metabolomics","LAST_NAME":"AlMalki","FIRST_NAME":"Reem","ADDRESS":"King Fahad road, Riyadh, KSA, 00000, Saudi Arabia","EMAIL":"439203044@student.ksu.edu.sa","PHONE":"+966534045397"},

"STUDY":{"STUDY_TITLE":"Biomarker discovery in galactosemia: Metabolomics with UPLC/HRMS in dried blood spots","STUDY_TYPE":"Newborn screening","STUDY_SUMMARY":"Galactosemia (GAL) is an autosomal recessive genetic disorder characterized by galactose metabolism disturbances. GAL develops non-preventable life-threatening complications even with a reduced content of galactose and lactose patient’s diet. Thus, the underlying pathophysiology of long-term complications in GAL remains poorly understood. The current study used a metabolomics approach using ultra-performance liquid chromatography coupled with high-resolution mass spectrometry to investigate the metabolomic changes in the dried blood spots of 15 patients with GAL and 39 healthy individuals. Compared to the control group, 2,819 metabolites underwent significant changes in patients with GAL. In all, 480 human endogenous metabolites were identified, of which 209 and 271 were upregulated and downregulated, respectively. PA (8:0/LTE4) and ganglioside GT1c (d18:0/20:0) metabolites showed the most significant difference between GAL and the healthy group, with an area under the curve of 1 and 0.995, respectively. Additionally, our findings showed novel potential biomarkers for GAL, such as 17-alpha-estradiol-3-glucuronide and 16-alpha-hydroxy DHEA 3-sulfatediphosphate. In conclusion, this metabolomics study deepened the understanding of the pathophysiology of GAL and presented metabolites that might serve as potential prognostic biomarkers to monitor the progression or support the clinical diagnosis of GAL.","INSTITUTE":"King Saud University","LAST_NAME":"AlMalki","FIRST_NAME":"Reem","ADDRESS":"King Fahad road, Riyadh, KSA, 00000, Saudi Arabia","EMAIL":"439203044@student.ksu.edu.sa","PHONE":"+966534045397","NUM_GROUPS":"2","PUBLICATIONS":"Yes"},

"SUBJECT":{"SUBJECT_TYPE":"Human","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606","GENDER":"Male and female"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"Patient",
"Sample ID":"GALT_AB1_20587853",
"Factors":{"Factor":"Patient"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_AB1_20587853.raw"}
},
{
"Subject ID":"Patient",
"Sample ID":"GALT_AB2_21780341",
"Factors":{"Factor":"Patient"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_AB2_21780341.raw"}
},
{
"Subject ID":"Patient",
"Sample ID":"GALT_AB3_21745506",
"Factors":{"Factor":"Patient"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_AB3_21745506.raw"}
},
{
"Subject ID":"Patient",
"Sample ID":"GALT_AB4_21100457",
"Factors":{"Factor":"Patient"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_AB4_21100457.raw"}
},
{
"Subject ID":"Patient",
"Sample ID":"GALT_AB6_21770900",
"Factors":{"Factor":"Patient"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_AB6_21770900.raw"}
},
{
"Subject ID":"Patient",
"Sample ID":"GALT_AB8_21112212",
"Factors":{"Factor":"Patient"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_AB8_21112212.raw"}
},
{
"Subject ID":"Patient",
"Sample ID":"GALT_AB9_21775172",
"Factors":{"Factor":"Patient"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_AB9_21775172.raw"}
},
{
"Subject ID":"Patient",
"Sample ID":"GALT_AB12_21780943",
"Factors":{"Factor":"Patient"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_AB12_21780943.raw"}
},
{
"Subject ID":"Patient",
"Sample ID":"GALT_AB13_21769782",
"Factors":{"Factor":"Patient"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_AB13_21769782.raw"}
},
{
"Subject ID":"Patient",
"Sample ID":"GALT_AB14_21799507",
"Factors":{"Factor":"Patient"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_AB14_21799507.raw"}
},
{
"Subject ID":"Patient",
"Sample ID":"GALT_AB15_21745524",
"Factors":{"Factor":"Patient"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_AB15_21745524.raw"}
},
{
"Subject ID":"Patient",
"Sample ID":"GALT_AB16_20428037",
"Factors":{"Factor":"Patient"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_AB16_20428037.raw"}
},
{
"Subject ID":"Patient",
"Sample ID":"GALT_AB17_20758512",
"Factors":{"Factor":"Patient"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_AB17_20758512.raw"}
},
{
"Subject ID":"Patient",
"Sample ID":"GALT_AB18_21012310",
"Factors":{"Factor":"Patient"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_AB18_21012310.raw"}
},
{
"Subject ID":"Patient",
"Sample ID":"GALT_AB19_21744172",
"Factors":{"Factor":"Patient"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_AB19_21744172.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR1_21799701",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR1_21799701.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR2_21799835",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR2_21799835.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR3_21799729",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR3_21799729.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR4_21752056",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR4_21752056.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR5_21756742",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR5_21756742.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR6_21799686",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR6_21799686.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR7_21798410",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR7_21798410.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR8_21756982",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR8_21756982.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR9_21756292",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR9_21756292.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR10_21756779",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR10_21756779.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR11_21798863",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR11_21798863.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR12_21798942",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR12_21798942.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR13_21756636",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR13_21756636.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR14_21756609",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR14_21756609.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR15_21798906",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR15_21798906.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR16_21794987",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR16_21794987.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR17_21798924",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR17_21798924.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR18_21756973",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR18_21756973.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR19_21756645",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR19_21756645.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR20_21798933",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR20_21798933.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR21_21756964",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR21_21756964.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR22_21799695",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR22_21799695.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR23_21752092",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR23_21752092.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR24_21799792",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR24_21799792.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR25_21757006",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR25_21757006.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR26_21799932",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR26_21799932.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR28_21799871",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR28_21799871.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR29_21798155",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR29_21798155.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR30_21799710",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR30_21799710.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR31_21756654",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR31_21756654.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR32_21799969",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR32_21799969.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR33_21798474",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR33_21798474.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR34_21799978",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR34_21799978.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR35_21799853",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR35_21799853.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR36_21799941",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR36_21799941.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR37_21798960",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR37_21798960.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR38_21783126",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR38_21783126.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR39_21799677",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR39_21799677.raw"}
},
{
"Subject ID":"Ctrl",
"Sample ID":"GALT_NR40_21798479",
"Factors":{"Factor":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"GALT_NR40_21798479.raw"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Fifty-four DBS samples were collected from genetically and biochemically confirmed GAL (n = 15) patients at King Faisal Specialist Hospital and Research center (KFSHRC) and healthy controls (n = 39).","COLLECTION_PROTOCOL_FILENAME":"Characteristics of the study population and metabolites extraction","SAMPLE_TYPE":"Blood (plasma)"},

"TREATMENT":{"TREATMENT_SUMMARY":"no treatment use"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Metabolites extraction The polar metabolites were extracted from DBS samples using our developed standard protocol (Jacob et al., 2018). Five 3 mm size DBS disks were used for metabolite extraction using methanol, acetonitrile, and water (40:40:20%) for protein precipitation. The mixture was mixed at 25°C and 600 rpm for 2 hours in a thermomixer (Eppendorf, Germany). Pooled QC samples were prepared using aliquots from the study samples. Afterward, the supernatants were transferred to another set of tubes, evaporated in SpeedVacc (Christ, City, Germany), and stored at −80°C until LCMS analysis.","SAMPLEPREP_PROTOCOL_FILENAME":"Metabolites extraction","PROCESSING_STORAGE_CONDITIONS":"-20℃","EXTRACT_STORAGE":"Room temperature"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Waters Acquity","COLUMN_NAME":"Waters Acquity UPLC XSelect HSS C18 (100 × 2.1mm, 2.5um)","SOLVENT_A":"100% water; 0.1% formic acid","SOLVENT_B":"50% methanol/50% acetonitrile; 0.1% formic acid","FLOW_GRADIENT":"0–16 min 95%–5% A, 16–19 min 5% A, 19–20 min 5%–95% A, and 20–22 min, 95%– 95% A","FLOW_RATE":"300 μl/min.","COLUMN_TEMPERATURE":"55","METHODS_FILENAME":"UPLCHRMS"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Waters Xevo-G2-S","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"The DIA data were collected with a Masslynx™ V4.1 workstation in continuum mode (Waters Inc., Milford, MA, USA). The raw MS data were processed following a standard pipeline using the Progenesis QI v.3.0 software.","MS_RESULTS_FILE":"ST002552_AN004202_Results.txt UNITS:peak area  Has m/z:Yes Has RT:No RT units:Minutes"}

}