{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002391","ANALYSIS_ID":"AN003896","VERSION":"1","CREATED_ON":"12-06-2022"},

"PROJECT":{"PROJECT_TITLE":"Evaluation of Two Simultaneous Metabolomic and Proteomic Extraction Protocols Assessed by Ultra-High-Performance Liquid Chromatography Tandem Mass Spectrometry","PROJECT_SUMMARY":"Untargeted multi-omics analysis of plasma is an emerging tool for the identification of novel biomarkers for evaluating disease prognosis and for a better understanding of molecular mechanisms underlying human disease. The successful application of metabolomic and pro-teomic approaches relies on reproducibly quantifying a wide range of metabolites and proteins. Herein, we report the results of untargeted metabolomic and proteomic analyses from blood plasma samples following analyte extraction by two frequently used solvent systems: chloro-form/methanol and methanol-only. Whole blood samples were collected from participants (n=6) at University Hospital Sharjah (UHS) hospital, then plasma was separated and extracted by two methods i. methanol precipitation and, ii. 4:3 methanol:chloroform extraction. The coverage and reproducibility of the two methods were assessed by ultra-high-performance liquid chromatography-electrospray ionization quadrupole time-of-flight mass spectrometry (UHPLC-ESI-QTOF-MS). The study revealed that metabolite extraction by methanol-only showed greater reproducibility for both metabolomic and proteomic quantifications than did methanol/chloroform, while yielding similar peptide coverage. However, coverage of extracted metabolites was higher with the methanol/chloroform precipitation.","INSTITUTE":"Sharjah Institute for Medical Research","LAST_NAME":"Facility","FIRST_NAME":"Core","ADDRESS":"M32, SIMR, College of Pharmacy, Health Sciences, University of Sharjah","EMAIL":"tims-tof@sharjah.ac.ae","PHONE":"065057656","DOI":"http://dx.doi.org/10.21228/M8WH85"},

"STUDY":{"STUDY_TITLE":"Evaluation of Two Simultaneous Metabolomic and Proteomic Extraction Protocols Assessed by Ultra-High-Performance Liquid Chromatography Tandem Mass Spectrometry","STUDY_SUMMARY":"Untargeted multi-omics analysis of plasma is an emerging tool for the identification of novel biomarkers for evaluating disease prognosis and for a better understanding of molecular mechanisms underlying human disease. The successful application of metabolomic and proteomic approaches relies on reproducibly quantifying a wide range of metabolites and proteins. Herein, we report the results of untargeted metabolomic and proteomic analyses from blood plasma samples following analyte extraction by two frequently used solvent systems: chloro-form/methanol and methanol-only. Whole blood samples were collected from participants (n=6) at University Hospital Sharjah (UHS) hospital, then plasma was separated and extracted by two methods i. methanol precipitation and, ii. 4:3 methanol:chloroform extraction. The coverage and reproducibility of the two methods were assessed by ultra-high-performance liquid chromatography-electrospray ionization quadrupole time-of-flight mass spectrometry (UHPLC-ESI-QTOF-MS). The study revealed that metabolite extraction by methanol-only showed greater reproducibility for both metabolomic and proteomic quantifications than did methanol/chloroform, while yielding similar peptide coverage. However, coverage of extracted metabolites was higher with the methanol/chloroform precipitation.","INSTITUTE":"Sharjah Institute for Medical Research","LAST_NAME":"Facility","FIRST_NAME":"Core","ADDRESS":"M32, SIMR, College of Pharmacy, Health Sciences, University of Sharjah","EMAIL":"tims-tof@sharjah.ac.ae","PHONE":"065057656","SUBMIT_DATE":"2022-12-06"},

"SUBJECT":{"SUBJECT_TYPE":"Human","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"1",
"Sample ID":"A01-01-4392",
"Factors":{"Method":"Methanol;Chloroform"},
"Additional sample data":{"RAW_FILE_NAME":"A01-01-4392.d"}
},
{
"Subject ID":"1",
"Sample ID":"A01-02-4393",
"Factors":{"Method":"Methanol;Chloroform"},
"Additional sample data":{"RAW_FILE_NAME":"A01-02-4393.d"}
},
{
"Subject ID":"2",
"Sample ID":"A02-01-4394",
"Factors":{"Method":"Methanol;Chloroform"},
"Additional sample data":{"RAW_FILE_NAME":"A02-01-4394.d"}
},
{
"Subject ID":"2",
"Sample ID":"A02-02-4395",
"Factors":{"Method":"Methanol;Chloroform"},
"Additional sample data":{"RAW_FILE_NAME":"A02-02-4395.d"}
},
{
"Subject ID":"3",
"Sample ID":"A03-01-4396",
"Factors":{"Method":"Methanol;Chloroform"},
"Additional sample data":{"RAW_FILE_NAME":"A03-01-4396.d"}
},
{
"Subject ID":"3",
"Sample ID":"A03-02-4397",
"Factors":{"Method":"Methanol;Chloroform"},
"Additional sample data":{"RAW_FILE_NAME":"A03-02-4397.d"}
},
{
"Subject ID":"4",
"Sample ID":"A04-01-4398",
"Factors":{"Method":"Methanol;Chloroform"},
"Additional sample data":{"RAW_FILE_NAME":"A04-01-4398.d"}
},
{
"Subject ID":"4",
"Sample ID":"A04-02-4399",
"Factors":{"Method":"Methanol;Chloroform"},
"Additional sample data":{"RAW_FILE_NAME":"A04-02-4399.d"}
},
{
"Subject ID":"5",
"Sample ID":"A05-01-4400",
"Factors":{"Method":"Methanol;Chloroform"},
"Additional sample data":{"RAW_FILE_NAME":"A05-01-4400.d"}
},
{
"Subject ID":"5",
"Sample ID":"A05-02-4401",
"Factors":{"Method":"Methanol;Chloroform"},
"Additional sample data":{"RAW_FILE_NAME":"A05-02-4401.d"}
},
{
"Subject ID":"6",
"Sample ID":"A06-01-4402",
"Factors":{"Method":"Methanol;Chloroform"},
"Additional sample data":{"RAW_FILE_NAME":"A06-01-4402.d"}
},
{
"Subject ID":"6",
"Sample ID":"A06-02-4403",
"Factors":{"Method":"Methanol;Chloroform"},
"Additional sample data":{"RAW_FILE_NAME":"A06-02-4403.d"}
},
{
"Subject ID":"4",
"Sample ID":"RA01-01-4404",
"Factors":{"Method":"Methanol;Chloroform"},
"Additional sample data":{"RAW_FILE_NAME":"RA01-01-4404.d"}
},
{
"Subject ID":"4",
"Sample ID":"RA01-02-4405",
"Factors":{"Method":"Methanol;Chloroform"},
"Additional sample data":{"RAW_FILE_NAME":"RA01-02-4405.d"}
},
{
"Subject ID":"4",
"Sample ID":"RA02-01-4406",
"Factors":{"Method":"Methanol;Chloroform"},
"Additional sample data":{"RAW_FILE_NAME":"RA02-01-4406.d"}
},
{
"Subject ID":"4",
"Sample ID":"RA02-02-4407",
"Factors":{"Method":"Methanol;Chloroform"},
"Additional sample data":{"RAW_FILE_NAME":"RA02-02-4407.d"}
},
{
"Subject ID":"4",
"Sample ID":"RA03-01-4408",
"Factors":{"Method":"Methanol;Chloroform"},
"Additional sample data":{"RAW_FILE_NAME":"RA03-01-4408.d"}
},
{
"Subject ID":"4",
"Sample ID":"RA03-02-4409",
"Factors":{"Method":"Methanol;Chloroform"},
"Additional sample data":{"RAW_FILE_NAME":"RA03-02-4409.d"}
},
{
"Subject ID":"4",
"Sample ID":"RA04-01-4398",
"Factors":{"Method":"Methanol;Chloroform"},
"Additional sample data":{"RAW_FILE_NAME":"RA04-01-4398.d"}
},
{
"Subject ID":"4",
"Sample ID":"RA04-02-4399",
"Factors":{"Method":"Methanol;Chloroform"},
"Additional sample data":{"RAW_FILE_NAME":"RA04-02-4399.d"}
},
{
"Subject ID":"4",
"Sample ID":"RB04-01-4416",
"Factors":{"Method":"Methanol;Chloroform"},
"Additional sample data":{"RAW_FILE_NAME":"RB04-01-4416.d"}
},
{
"Subject ID":"4",
"Sample ID":"RB04-02-4417",
"Factors":{"Method":"Methanol;Chloroform"},
"Additional sample data":{"RAW_FILE_NAME":"RB04-02-4417.d"}
},
{
"Subject ID":"1",
"Sample ID":"B01-01-4410",
"Factors":{"Method":"Methanol Only"},
"Additional sample data":{"RAW_FILE_NAME":"B01-01-4410.d"}
},
{
"Subject ID":"1",
"Sample ID":"B01-02-4411",
"Factors":{"Method":"Methanol Only"},
"Additional sample data":{"RAW_FILE_NAME":"B01-02-4411.d"}
},
{
"Subject ID":"2",
"Sample ID":"B02-01-4412",
"Factors":{"Method":"Methanol Only"},
"Additional sample data":{"RAW_FILE_NAME":"B02-01-4412.d"}
},
{
"Subject ID":"2",
"Sample ID":"B02-02-4413",
"Factors":{"Method":"Methanol Only"},
"Additional sample data":{"RAW_FILE_NAME":"B02-02-4413.d"}
},
{
"Subject ID":"3",
"Sample ID":"B03-01-4414",
"Factors":{"Method":"Methanol Only"},
"Additional sample data":{"RAW_FILE_NAME":"B03-01-4414.d"}
},
{
"Subject ID":"3",
"Sample ID":"B03-02-4415",
"Factors":{"Method":"Methanol Only"},
"Additional sample data":{"RAW_FILE_NAME":"B03-02-4415.d"}
},
{
"Subject ID":"4",
"Sample ID":"B04-01-4416",
"Factors":{"Method":"Methanol Only"},
"Additional sample data":{"RAW_FILE_NAME":"B04-01-4416.d"}
},
{
"Subject ID":"4",
"Sample ID":"B04-02-4417",
"Factors":{"Method":"Methanol Only"},
"Additional sample data":{"RAW_FILE_NAME":"B04-02-4417.d"}
},
{
"Subject ID":"5",
"Sample ID":"B05-01-4418",
"Factors":{"Method":"Methanol Only"},
"Additional sample data":{"RAW_FILE_NAME":"B05-01-4418.d"}
},
{
"Subject ID":"5",
"Sample ID":"B05-02-4419",
"Factors":{"Method":"Methanol Only"},
"Additional sample data":{"RAW_FILE_NAME":"B05-02-4419.d"}
},
{
"Subject ID":"6",
"Sample ID":"B06-01-4420",
"Factors":{"Method":"Methanol Only"},
"Additional sample data":{"RAW_FILE_NAME":"B06-01-4420.d"}
},
{
"Subject ID":"6",
"Sample ID":"B06-02-4421",
"Factors":{"Method":"Methanol Only"},
"Additional sample data":{"RAW_FILE_NAME":"B06-02-4421.d"}
},
{
"Subject ID":"4",
"Sample ID":"RB01-01-4422",
"Factors":{"Method":"Methanol Only"},
"Additional sample data":{"RAW_FILE_NAME":"RB01-01-4422.d"}
},
{
"Subject ID":"4",
"Sample ID":"RB01-02-4423",
"Factors":{"Method":"Methanol Only"},
"Additional sample data":{"RAW_FILE_NAME":"RB01-02-4423.d"}
},
{
"Subject ID":"4",
"Sample ID":"RB02-01-4424",
"Factors":{"Method":"Methanol Only"},
"Additional sample data":{"RAW_FILE_NAME":"RB02-01-4424.d"}
},
{
"Subject ID":"4",
"Sample ID":"RB02-02-4425",
"Factors":{"Method":"Methanol Only"},
"Additional sample data":{"RAW_FILE_NAME":"RB02-02-4425.d"}
},
{
"Subject ID":"4",
"Sample ID":"RB03-01-4426",
"Factors":{"Method":"Methanol Only"},
"Additional sample data":{"RAW_FILE_NAME":"RB03-01-4426.d"}
},
{
"Subject ID":"4",
"Sample ID":"RB03-02-4427",
"Factors":{"Method":"Methanol Only"},
"Additional sample data":{"RAW_FILE_NAME":"RB03-02-4427.d"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Human whole blood samples (5mL) were collected from healthy males and females (n=6) via venipuncture into EDTA tube at University Hospital Sharjah. All participants gave in-formed consent for inclusion before enrollment in the study. Blood was centrifuged (14000 rpm for 15 minutes at 24°C) to separate plasma samples, which were stored at -80°C.","SAMPLE_TYPE":"Blood (plasma)"},

"TREATMENT":{"TREATMENT_SUMMARY":"No treatment was applied, we were comparing extraction methods."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Sample preparation 2.3.1Methanol precipitation for metabolomic extraction. 100 µL from each plasma sample was transferred to Eppendorf, then a volume of 300 µL of methanol was added to the aliquot. Samples were vortexed, then chilled at -20 °C for 2 hours followed by centrifugation (14000 rpm, 15 minutes, 24°C) to precipitate protein. The metabolite-containing supernatants were collected and transferred to glass vials for dry-ing using the EZ-2 Plus (GeneVac, Ipswich, UK) at 40 ±1°C and the protein pellets that remained were air dried for proteomics (see section 2.4). Dried metabolite samples were resuspended with 200 µl (0.1% formic acid in water), and vortexed for 2 min. The samples were filtered using a hydrophilic nylon syringe filter (0.45 μm pore size) and placed with-in glass inserts prior to being analyzed by Q-TOF MS. 4.3.2 Methanol: chloroform for metabolomic extraction. 100 µL from each sample was transferred to Eppendorf, then a volume of 400 µL of methanol and 300 µL of chloroform was added to the aliquot. Samples were vortexed then centrifuged (14000 rpm, 15 minutes, 24°C). Two metabolite-containing layers, an upper aqueous- and lower organic phase, were obtained separated by a thin white proteinaceous disc. The upper layer for each sample was transferred to glass vials and a volume of 400 µL of methanol was added, followed by vortexing and centrifugation to pellet the protein disc, after which the remaining supernatant was transferred to the same glass vials as be-fore for drying step and the protein pellets that remained were air dried for proteomics. Dried metabolomics samples were resuspended with 200 µL (0.1% formic acid in water) to be injected into HPLC and analyzed by Q-TOF MS."},

"CHROMATOGRAPHY":{"INSTRUMENT_NAME":"Bruker Elute","COLUMN_NAME":"Hamilton Intensity Solo 2 C18(100 x 2.1 mm, 1.8 um)","CHROMATOGRAPHY_TYPE":"Reversed phase"},

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

"MS":{"INSTRUMENT_NAME":"Bruker timsTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","MS_COMMENTS":"Metabolomics Data Processing. For metabolomic analysis, MetaboScape® 4.0 program (Bruker Daltonics, Billerica, MA, USA) was employed for data processing, feature extrac-tion and metabolite identification. The T-ReX 2D/3D workflow was used to identify the molecular features with the following settings: The minimum peak length was set to 7 spectra and the minimum intensity threshold was 1000 counts for peaks detection. The peak area was employed for quantification and the injected external calibrant in the in-terval of 0–0.3 min was used to recalibrate the mass spectra. The selected mass to charge ratio (m/z) and retention time for scanning were in the ranges of 20–1300 m/z and 0.3–30 min, respectively. MS/MS spectra for features were averaged on import and features found at least in 12 of the 40 injections were taken into further consideration. Metabolites were identified by matching to the human metabolome database (HMDB) by combined MS/MS, precursor m/z values, and isotopic pattern scores. Where multiple features matched a given database entry, the annotation quality score (AQ score) was used to select only the best matching feature.","ION_MODE":"POSITIVE"},

"MS_METABOLITE_DATA":{
"Units":"AU",

"Data":[{"Metabolite":"1_3-Dimethyluric 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acid","A01-01-4392":"1454.0000","A01-02-4393":"1362.0000","A02-01-4394":"1856.0000","A02-02-4395":"1552.0000","A03-01-4396":"1938.0000","A03-02-4397":"1376.0000","A04-01-4398":"380.0000","A04-02-4399":"276.0000","A05-01-4400":"1306.0000","A05-02-4401":"1322.0000","A06-01-4402":"1144.0000","A06-02-4403":"912.0000","RA01-01-4404":"1256.0000","RA01-02-4405":"1826.0000","RA02-01-4406":"1272.0000","RA02-02-4407":"1482.0000","RA03-01-4408":"","RA03-02-4409":"314.0000","RA04-01-4398":"380.0000","RA04-02-4399":"276.0000","RB04-01-4416":"","RB04-02-4417":"","B01-01-4410":"","B01-02-4411":"","B02-01-4412":"","B02-02-4413":"","B03-01-4414":"","B03-02-4415":"","B04-01-4416":"","B04-02-4417":"","B05-01-4418":"","B05-02-4419":"","B06-01-4420":"","B06-02-4421":"","RB01-01-4422":"","RB01-02-4423":"","RB02-01-4424":"","RB02-02-4425":"","RB03-01-4426":"","RB03-02-4427":""},{"Metabolite":"2-Aminobenzoic acid","A01-01-4392":"1016.0000","A01-02-4393":"","A02-01-4394":"520.0000","A02-02-4395":"616.0000","A03-01-4396":"","A03-02-4397":"198.0000","A04-01-4398":"1058.0000","A04-02-4399":"1270.0000","A05-01-4400":"","A05-02-4401":"","A06-01-4402":"","A06-02-4403":"228.0000","RA01-01-4404":"1258.0000","RA01-02-4405":"1092.0000","RA02-01-4406":"","RA02-02-4407":"1204.0000","RA03-01-4408":"1030.0000","RA03-02-4409":"1260.0000","RA04-01-4398":"1058.0000","RA04-02-4399":"1270.0000","RB04-01-4416":"1726.0000","RB04-02-4417":"1782.0000","B01-01-4410":"1768.0000","B01-02-4411":"1454.0000","B02-01-4412":"","B02-02-4413":"","B03-01-4414":"","B03-02-4415":"268.0000","B04-01-4416":"1726.0000","B04-02-4417":"1782.0000","B05-01-4418":"212.0000","B05-02-4419":"208.0000","B06-01-4420":"","B06-02-4421":"","RB01-01-4422":"1514.0000","RB01-02-4423":"1518.0000","RB02-01-4424":"1396.0000","RB02-02-4425":"1482.0000","RB03-01-4426":"1676.0000","RB03-02-4427":"1408.0000"},{"Metabolite":"2-Hydroxy-3-methylbutyric 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}

}