{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST003017","ANALYSIS_ID":"AN004950","VERSION":"1","CREATED_ON":"12-21-2023"},

"PROJECT":{"PROJECT_TITLE":"Lipidomics and plasma hormone reveal indicators of reproductive status in Florida manatees (Trichechus manatus latirostris)","PROJECT_SUMMARY":"Florida manatees (Trichechus manatus latirostris) are protected as a threatened species, and data are lacking regarding their reproductive physiology. This study aimed to (1) quantify plasma steroid hormones in Florida manatees from two field sites, Crystal River and Indian River Lagoon, at different gestational stages and to (2) determine the relationship between plasma progesterone concentrations and lipid biochemistry in relation to pregnancy status. Ultra-high performance liquid chromatography-tandem mass spectrometric analysis was used to measure plasma steroid hormones and lipids. Pregnant female manatees were morphometrically distinct from male and non-pregnant female manatees, characterized by larger body weight and maximal girth. Progesterone concentrations in manatees were also elevated during early gestation versus late gestation. Cholesterol, an important metabolic lipid and precursor for reproductive steroids, was not different between groups. Lipidomics quantified 949 lipids and plasma concentrations of a sphingolipid, ceramide non-hydroxy fatty acid-sphingosine and several glycerophospholipids, including lysophosphatidylcholine, phosphatidylethanolamines, plasmenyl-phosphatidylserines and monomethyl phosphatidylethanolamines, were associated with pregnancy status in the Florida manatee. This research contributes to improving knowledge of manatee reproductive physiology by providing data on plasma steroid hormones relative to reproductive status and by assessing how plasma lipids in healthy Florida manatees correspond to progesterone levels. This lipid panel has potential as a diagnostic approach to identify pregnant individuals in fresh and archived samples. These biochemical and morphometric indicators of reproductive status advance the understanding of manatee physiology.","INSTITUTE":"University of Florida","DEPARTMENT":"Physiological Sciences","LABORATORY":"Dr. Martyniuk","LAST_NAME":"Brammer-Robbins","FIRST_NAME":"Elizabeth","ADDRESS":"2187 Mowry Rd., Bldg 471","EMAIL":"e.brammerrobbins@ufl.edu","PHONE":"9104652899","FUNDING_SOURCE":"National Science Foundation Graduate Research Fellowship Program under Grant No. (2019285699 to EB-R).","DOI":"http://dx.doi.org/10.21228/M8ZQ63"},

"STUDY":{"STUDY_TITLE":"Lipidomics and plasma hormone reveal indicators of reproductive status in Florida manatees (Trichechus manatus latirostris)","STUDY_SUMMARY":"Florida manatees (Trichechus manatus latirostris) are protected as a threatened species, and data are lacking regarding their reproductive physiology. This study aimed to (1) quantify plasma steroid hormones in Florida manatees from two field sites, Crystal River and Indian River Lagoon, at different gestational stages and to (2) determine the relationship between plasma progesterone concentrations and lipid biochemistry in relation to pregnancy status. Ultra-high performance liquid chromatography-tandem mass spectrometric analysis was used to measure plasma steroid hormones and lipids. Pregnant female manatees were morphometrically distinct from male and non-pregnant female manatees, characterized by larger body weight and maximal girth. Progesterone concentrations in manatees were also elevated during early gestation versus late gestation. Cholesterol, an important metabolic lipid and precursor for reproductive steroids, was not different between groups. Lipidomics quantified 949 lipids and plasma concentrations of a sphingolipid, ceramide non-hydroxy fatty acid-sphingosine and several glycerophospholipids, including lysophosphatidylcholine, phosphatidylethanolamines, plasmenyl-phosphatidylserines and monomethyl phosphatidylethanolamines, were associated with pregnancy status in the Florida manatee. This research contributes to improving knowledge of manatee reproductive physiology by providing data on plasma steroid hormones relative to reproductive status and by assessing how plasma lipids in healthy Florida manatees correspond to progesterone levels. This lipid panel has potential as a diagnostic approach to identify pregnant individuals in fresh and archived samples. These biochemical and morphometric indicators of reproductive status advance the understanding of manatee physiology.","INSTITUTE":"University of Florida","LAST_NAME":"Brammer-Robbins","FIRST_NAME":"Elizabeth","ADDRESS":"2187 Mowry Rd., Bldg 471","EMAIL":"e.brammerrobbins@ufl.edu","PHONE":"9104652899","SUBMIT_DATE":"2023-12-10"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Florida manatee (Trichechus manatus latirostris)","AGE_OR_AGE_RANGE":"Adult"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"Plasma-CBC1308",
"Sample ID":"Sp28",
"Factors":{"Capture Location":"Brevard County","Reproductive Status":"NA","Sex":"M"},
"Additional sample data":{"Pool #":"7","RAW_FILE_NAME":"FullScan_Sp28_neg.raw","RAW_FILE_NAME":"FullScan_Sp28_pos.raw"}
},
{
"Subject ID":"Plasma-CBC1306",
"Sample ID":"Sp29",
"Factors":{"Capture Location":"Brevard County","Reproductive Status":"NA","Sex":"M"},
"Additional sample data":{"Pool #":"7","RAW_FILE_NAME":"FullScan_Sp29_neg.raw","RAW_FILE_NAME":"FullScan_Sp29_pos.raw"}
},
{
"Subject ID":"Plasma-CBC1305",
"Sample ID":"Sp30",
"Factors":{"Capture Location":"Brevard County","Reproductive Status":"NA","Sex":"M"},
"Additional sample data":{"Pool #":"7","RAW_FILE_NAME":"FullScan_Sp30_neg.raw","RAW_FILE_NAME":"FullScan_Sp30_pos.raw"}
},
{
"Subject ID":"Plasma-CBC1304",
"Sample ID":"Sp31",
"Factors":{"Capture Location":"Brevard County","Reproductive Status":"NA","Sex":"M"},
"Additional sample data":{"Pool #":"7","RAW_FILE_NAME":"FullScan_Sp31_neg.raw","RAW_FILE_NAME":"FullScan_Sp31_pos.raw"}
},
{
"Subject ID":"Plasma-CBC1303",
"Sample ID":"Sp32",
"Factors":{"Capture Location":"Brevard County","Reproductive Status":"NA","Sex":"M"},
"Additional sample data":{"Pool #":"7","RAW_FILE_NAME":"FullScan_Sp32_neg.raw","RAW_FILE_NAME":"FullScan_Sp32_pos.raw"}
},
{
"Subject ID":"Plasma-CBC1302",
"Sample ID":"Sp33",
"Factors":{"Capture Location":"Brevard County","Reproductive Status":"NA","Sex":"M"},
"Additional sample data":{"Pool #":"7","RAW_FILE_NAME":"FullScan_Sp33_neg.raw","RAW_FILE_NAME":"FullScan_Sp33_pos.raw"}
},
{
"Subject ID":"Plasma-CBC1301",
"Sample ID":"Sp34",
"Factors":{"Capture Location":"Brevard County","Reproductive Status":"NA","Sex":"M"},
"Additional sample data":{"Pool #":"7","RAW_FILE_NAME":"FullScan_Sp34_neg.raw","RAW_FILE_NAME":"FullScan_Sp34_pos.raw"}
},
{
"Subject ID":"Plasma-CBC1207",
"Sample ID":"Sp35",
"Factors":{"Capture Location":"Brevard County","Reproductive Status":"NA","Sex":"M"},
"Additional sample data":{"Pool #":"7","RAW_FILE_NAME":"FullScan_Sp35_neg.raw","RAW_FILE_NAME":"FullScan_Sp35_pos.raw"}
},
{
"Subject ID":"Plasma-CBC1312",
"Sample ID":"Sp57",
"Factors":{"Capture Location":"Brevard County","Reproductive Status":"NA","Sex":"M"},
"Additional sample data":{"Pool #":"7","RAW_FILE_NAME":"FullScan_Sp57_neg.raw","RAW_FILE_NAME":"FullScan_Sp57_pos.raw"}
},
{
"Subject ID":"Plasma-CBC1203",
"Sample ID":"Sp70",
"Factors":{"Capture Location":"Brevard County","Reproductive Status":"NA","Sex":"M"},
"Additional sample data":{"Pool #":"7","RAW_FILE_NAME":"FullScan_Sp70_neg.raw","RAW_FILE_NAME":"FullScan_Sp70_pos.raw"}
},
{
"Subject ID":"Plasma-CBC1202",
"Sample ID":"Sp71",
"Factors":{"Capture Location":"Brevard County","Reproductive Status":"NA","Sex":"M"},
"Additional sample data":{"Pool #":"7","RAW_FILE_NAME":"FullScan_Sp71_neg.raw","RAW_FILE_NAME":"FullScan_Sp71_pos.raw"}
},
{
"Subject ID":"Plasma-CBC1106",
"Sample ID":"Sp72",
"Factors":{"Capture Location":"Brevard County","Reproductive Status":"NA","Sex":"M"},
"Additional sample data":{"Pool #":"7","RAW_FILE_NAME":"FullScan_Sp72_neg.raw","RAW_FILE_NAME":"FullScan_Sp72_pos.raw"}
},
{
"Subject ID":"Plasma-CBC1104",
"Sample ID":"Sp73",
"Factors":{"Capture Location":"Brevard County","Reproductive Status":"NA","Sex":"M"},
"Additional sample data":{"Pool #":"7","RAW_FILE_NAME":"FullScan_Sp73_neg.raw","RAW_FILE_NAME":"FullScan_Sp73_pos.raw"}
},
{
"Subject ID":"Plasma-CBC1409",
"Sample ID":"Sp23",
"Factors":{"Capture Location":"Brevard County","Reproductive Status":"NP","Sex":"F"},
"Additional sample data":{"Pool #":"6","RAW_FILE_NAME":"FullScan_Sp23_neg.raw","RAW_FILE_NAME":"FullScan_Sp23_pos.raw"}
},
{
"Subject ID":"Plasma-CBC1311",
"Sample ID":"Sp24",
"Factors":{"Capture Location":"Brevard County","Reproductive Status":"NP","Sex":"F"},
"Additional sample data":{"Pool #":"6","RAW_FILE_NAME":"FullScan_Sp24_neg.raw","RAW_FILE_NAME":"FullScan_Sp24_pos.raw"}
},
{
"Subject ID":"Plasma-CBC1309",
"Sample ID":"Sp25",
"Factors":{"Capture Location":"Brevard County","Reproductive Status":"NP","Sex":"F"},
"Additional sample data":{"Pool #":"6","RAW_FILE_NAME":"FullScan_Sp25_neg.raw","RAW_FILE_NAME":"FullScan_Sp25_pos.raw"}
},
{
"Subject ID":"Plasma-CBC1212",
"Sample ID":"Sp26",
"Factors":{"Capture Location":"Brevard County","Reproductive Status":"NP","Sex":"F"},
"Additional sample data":{"Pool #":"6","RAW_FILE_NAME":"FullScan_Sp26_neg.raw","RAW_FILE_NAME":"FullScan_Sp26_pos.raw"}
},
{
"Subject ID":"Plasma-CBC1209",
"Sample ID":"Sp27",
"Factors":{"Capture Location":"Brevard County","Reproductive Status":"NP","Sex":"F"},
"Additional sample data":{"Pool #":"6","RAW_FILE_NAME":"FullScan_Sp27_neg.raw","RAW_FILE_NAME":"FullScan_Sp27_pos.raw"}
},
{
"Subject ID":"Plasma-CBC1008",
"Sample ID":"Sp52",
"Factors":{"Capture Location":"Brevard County","Reproductive Status":"NP","Sex":"F"},
"Additional sample data":{"Pool #":"6","RAW_FILE_NAME":"FullScan_Sp52_neg.raw","RAW_FILE_NAME":"FullScan_Sp52_pos.raw"}
},
{
"Subject ID":"Plasma-CBC1007",
"Sample ID":"Sp53",
"Factors":{"Capture Location":"Brevard County","Reproductive Status":"NP","Sex":"F"},
"Additional sample data":{"Pool #":"6","RAW_FILE_NAME":"FullScan_Sp53_neg.raw","RAW_FILE_NAME":"FullScan_Sp53_pos.raw"}
},
{
"Subject ID":"Plasma-CBC1006",
"Sample ID":"Sp54",
"Factors":{"Capture Location":"Brevard County","Reproductive Status":"NP","Sex":"F"},
"Additional sample data":{"Pool #":"6","RAW_FILE_NAME":"FullScan_Sp54_neg.raw","RAW_FILE_NAME":"FullScan_Sp54_pos.raw"}
},
{
"Subject ID":"Plasma-CBC1307",
"Sample ID":"Sp58",
"Factors":{"Capture Location":"Brevard County","Reproductive Status":"NP","Sex":"F"},
"Additional sample data":{"Pool #":"6","RAW_FILE_NAME":"FullScan_Sp58_neg.raw","RAW_FILE_NAME":"FullScan_Sp58_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1510",
"Sample ID":"Sp15",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"NA","Sex":"M"},
"Additional sample data":{"Pool #":"5","RAW_FILE_NAME":"FullScan_Sp15_neg.raw","RAW_FILE_NAME":"FullScan_Sp15_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1507",
"Sample ID":"Sp16",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"NA","Sex":"M"},
"Additional sample data":{"Pool #":"5","RAW_FILE_NAME":"FullScan_Sp16_neg.raw","RAW_FILE_NAME":"FullScan_Sp16_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1419",
"Sample ID":"Sp17",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"NA","Sex":"M"},
"Additional sample data":{"Pool #":"5","RAW_FILE_NAME":"FullScan_Sp17_neg.raw","RAW_FILE_NAME":"FullScan_Sp17_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1408",
"Sample ID":"Sp18",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"NA","Sex":"M"},
"Additional sample data":{"Pool #":"5","RAW_FILE_NAME":"FullScan_Sp18_neg.raw","RAW_FILE_NAME":"FullScan_Sp18_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1310",
"Sample ID":"Sp19",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"NA","Sex":"M"},
"Additional sample data":{"Pool #":"5","RAW_FILE_NAME":"FullScan_Sp19_neg.raw","RAW_FILE_NAME":"FullScan_Sp19_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1305",
"Sample ID":"Sp20",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"NA","Sex":"M"},
"Additional sample data":{"Pool #":"5","RAW_FILE_NAME":"FullScan_Sp20_neg.raw","RAW_FILE_NAME":"FullScan_Sp20_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1213",
"Sample ID":"Sp21",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"NA","Sex":"M"},
"Additional sample data":{"Pool #":"5","RAW_FILE_NAME":"FullScan_Sp21_neg.raw","RAW_FILE_NAME":"FullScan_Sp21_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1205",
"Sample ID":"Sp22",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"NA","Sex":"M"},
"Additional sample data":{"Pool #":"5","RAW_FILE_NAME":"FullScan_Sp22_neg.raw","RAW_FILE_NAME":"FullScan_Sp22_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1907",
"Sample ID":"Sp60",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"NA","Sex":"M"},
"Additional sample data":{"Pool #":"5","RAW_FILE_NAME":"FullScan_Sp60_neg.raw","RAW_FILE_NAME":"FullScan_Sp60_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1904",
"Sample ID":"Sp61",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"NA","Sex":"M"},
"Additional sample data":{"Pool #":"5","RAW_FILE_NAME":"FullScan_Sp61_neg.raw","RAW_FILE_NAME":"FullScan_Sp61_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1833",
"Sample ID":"Sp62",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"NA","Sex":"M"},
"Additional sample data":{"Pool #":"5","RAW_FILE_NAME":"FullScan_Sp62_neg.raw","RAW_FILE_NAME":"FullScan_Sp62_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1825",
"Sample ID":"Sp63",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"NA","Sex":"M"},
"Additional sample data":{"Pool #":"5","RAW_FILE_NAME":"FullScan_Sp63_neg.raw","RAW_FILE_NAME":"FullScan_Sp63_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1805",
"Sample ID":"Sp64",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"NA","Sex":"M"},
"Additional sample data":{"Pool #":"5","RAW_FILE_NAME":"FullScan_Sp64_neg.raw","RAW_FILE_NAME":"FullScan_Sp64_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1709",
"Sample ID":"Sp65",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"NA","Sex":"M"},
"Additional sample data":{"Pool #":"5","RAW_FILE_NAME":"FullScan_Sp65_neg.raw","RAW_FILE_NAME":"FullScan_Sp65_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1706",
"Sample ID":"Sp66",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"NA","Sex":"M"},
"Additional sample data":{"Pool #":"5","RAW_FILE_NAME":"FullScan_Sp66_neg.raw","RAW_FILE_NAME":"FullScan_Sp66_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1625",
"Sample ID":"Sp67",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"NA","Sex":"M"},
"Additional sample data":{"Pool #":"5","RAW_FILE_NAME":"FullScan_Sp67_neg.raw","RAW_FILE_NAME":"FullScan_Sp67_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1623",
"Sample ID":"Sp68",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"NA","Sex":"M"},
"Additional sample data":{"Pool #":"5","RAW_FILE_NAME":"FullScan_Sp68_neg.raw","RAW_FILE_NAME":"FullScan_Sp68_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1523",
"Sample ID":"Sp69",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"NA","Sex":"M"},
"Additional sample data":{"Pool #":"5","RAW_FILE_NAME":"FullScan_Sp69_neg.raw","RAW_FILE_NAME":"FullScan_Sp69_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1906",
"Sample ID":"Sp01",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"NP","Sex":"F"},
"Additional sample data":{"Pool #":"2","RAW_FILE_NAME":"FullScan_Sp01_neg.raw","RAW_FILE_NAME":"FullScan_Sp01_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1832",
"Sample ID":"Sp02",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"NP","Sex":"F"},
"Additional sample data":{"Pool #":"2","RAW_FILE_NAME":"FullScan_Sp02_neg.raw","RAW_FILE_NAME":"FullScan_Sp02_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1819",
"Sample ID":"Sp03",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"NP","Sex":"F"},
"Additional sample data":{"Pool #":"2","RAW_FILE_NAME":"FullScan_Sp03_neg.raw","RAW_FILE_NAME":"FullScan_Sp03_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1810",
"Sample ID":"Sp04",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"NP","Sex":"F"},
"Additional sample data":{"Pool #":"2","RAW_FILE_NAME":"FullScan_Sp04_neg.raw","RAW_FILE_NAME":"FullScan_Sp04_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1714",
"Sample ID":"Sp05",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"NP","Sex":"F"},
"Additional sample data":{"Pool #":"2","RAW_FILE_NAME":"FullScan_Sp05_neg.raw","RAW_FILE_NAME":"FullScan_Sp05_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1632",
"Sample ID":"Sp06",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"NP","Sex":"F"},
"Additional sample data":{"Pool #":"2","RAW_FILE_NAME":"FullScan_Sp06_neg.raw","RAW_FILE_NAME":"FullScan_Sp06_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1611",
"Sample ID":"Sp07",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"NP","Sex":"F"},
"Additional sample data":{"Pool #":"2","RAW_FILE_NAME":"FullScan_Sp07_neg.raw","RAW_FILE_NAME":"FullScan_Sp07_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1501",
"Sample ID":"Sp08",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"NP","Sex":"F"},
"Additional sample data":{"Pool #":"2","RAW_FILE_NAME":"FullScan_Sp08_neg.raw","RAW_FILE_NAME":"FullScan_Sp08_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1823",
"Sample ID":"Sp36",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"NP","Sex":"F"},
"Additional sample data":{"Pool #":"2","RAW_FILE_NAME":"FullScan_Sp36_neg.raw","RAW_FILE_NAME":"FullScan_Sp36_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1402",
"Sample ID":"Sp39",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"NP","Sex":"F"},
"Additional sample data":{"Pool #":"2","RAW_FILE_NAME":"FullScan_Sp39_neg.raw","RAW_FILE_NAME":"FullScan_Sp39_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1317",
"Sample ID":"Sp40",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"NP","Sex":"F"},
"Additional sample data":{"Pool #":"2","RAW_FILE_NAME":"FullScan_Sp40_neg.raw","RAW_FILE_NAME":"FullScan_Sp40_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1208",
"Sample ID":"Sp41",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"NP","Sex":"F"},
"Additional sample data":{"Pool #":"2","RAW_FILE_NAME":"FullScan_Sp41_neg.raw","RAW_FILE_NAME":"FullScan_Sp41_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1905",
"Sample ID":"Sp09",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"P","Sex":"F"},
"Additional sample data":{"Pool #":"1","RAW_FILE_NAME":"FullScan_Sp09_neg.raw","RAW_FILE_NAME":"FullScan_Sp09_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1902",
"Sample ID":"Sp10",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"P","Sex":"F"},
"Additional sample data":{"Pool #":"1","RAW_FILE_NAME":"FullScan_Sp10_neg.raw","RAW_FILE_NAME":"FullScan_Sp10_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1901",
"Sample ID":"Sp11",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"P","Sex":"F"},
"Additional sample data":{"Pool #":"1","RAW_FILE_NAME":"FullScan_Sp11_neg.raw","RAW_FILE_NAME":"FullScan_Sp11_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1705",
"Sample ID":"Sp12",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"P","Sex":"F"},
"Additional sample data":{"Pool #":"1","RAW_FILE_NAME":"FullScan_Sp12_neg.raw","RAW_FILE_NAME":"FullScan_Sp12_pos.raw"}
},
{
"Subject ID":"Plasma-CCR1528",
"Sample ID":"Sp13",
"Factors":{"Capture Location":"Crystal River","Reproductive Status":"P","Sex":"F"},
"Additional sample data":{"Pool #":"1","RAW_FILE_NAME":"FullScan_Sp13_neg.raw","RAW_FILE_NAME":"FullScan_Sp13_pos.raw"}
},
{
"Subject ID":"Quality Control 1",
"Sample ID":"QC01",
"Factors":{"Capture Location":"-","Reproductive Status":"-","Sex":"-"},
"Additional sample data":{"Pool #":"-","RAW_FILE_NAME":"FullScan_QC01_neg.raw","RAW_FILE_NAME":"FullScan_QC01_pos.raw"}
},
{
"Subject ID":"Quality Control 2",
"Sample ID":"QC02",
"Factors":{"Capture Location":"-","Reproductive Status":"-","Sex":"-"},
"Additional sample data":{"Pool #":"-","RAW_FILE_NAME":"FullScan_QC02_neg.raw","RAW_FILE_NAME":"FullScan_QC02_pos.raw"}
},
{
"Subject ID":"Quality Control 3",
"Sample ID":"QC03",
"Factors":{"Capture Location":"-","Reproductive Status":"-","Sex":"-"},
"Additional sample data":{"Pool #":"-","RAW_FILE_NAME":"FullScan_QC03_neg.raw","RAW_FILE_NAME":"FullScan_QC03_pos.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Target01",
"Factors":{"Capture Location":"-","Reproductive Status":"-","Sex":"-"},
"Additional sample data":{"Pool #":"1","RAW_FILE_NAME":"FullScan_Target01_neg.raw","RAW_FILE_NAME":"FullScan_Target01_pos.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Target02",
"Factors":{"Capture Location":"-","Reproductive Status":"-","Sex":"-"},
"Additional sample data":{"Pool #":"2","RAW_FILE_NAME":"FullScan_Target02_neg.raw","RAW_FILE_NAME":"FullScan_Target02_pos.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Target03",
"Factors":{"Capture Location":"-","Reproductive Status":"-","Sex":"-"},
"Additional sample data":{"Pool #":"3","RAW_FILE_NAME":"FullScan_Target03_neg.raw","RAW_FILE_NAME":"FullScan_Target03_pos.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Target04",
"Factors":{"Capture Location":"-","Reproductive Status":"-","Sex":"-"},
"Additional sample data":{"Pool #":"4","RAW_FILE_NAME":"FullScan_Target04_neg.raw","RAW_FILE_NAME":"FullScan_Target04_pos.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Target05",
"Factors":{"Capture Location":"-","Reproductive Status":"-","Sex":"-"},
"Additional sample data":{"Pool #":"5","RAW_FILE_NAME":"FullScan_Target05_neg.raw","RAW_FILE_NAME":"FullScan_Target05_pos.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Target06",
"Factors":{"Capture Location":"-","Reproductive Status":"-","Sex":"-"},
"Additional sample data":{"Pool #":"6","RAW_FILE_NAME":"FullScan_Target06_neg.raw","RAW_FILE_NAME":"FullScan_Target06_pos.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Target07",
"Factors":{"Capture Location":"-","Reproductive Status":"-","Sex":"-"},
"Additional sample data":{"Pool #":"7","RAW_FILE_NAME":"FullScan_Target07_neg.raw","RAW_FILE_NAME":"FullScan_Target07_pos.raw"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Blood samples were collected from wild FL manatees at manatee health assessments. Blood was collected in 7-mL lithium heparinized vacutainers and centrifuged at 3200 rpm for 10 min onsite at atmospheric temperature. The plasma supernatant was transferred to cryovials in 1 mL aliquots. Plasma samples were kept on dry ice during transport and stored at -80 °C at USGS and University of Florida (UF) until analysis.","COLLECTION_PROTOCOL_FILENAME":"Collection Summary.txt","SAMPLE_TYPE":"Blood (plasma)","STORAGE_CONDITIONS":"-80℃","COLLECTION_VIALS":"lithium heparinized vacutainers","STORAGE_VIALS":"Cryovials"},

"TREATMENT":{"TREATMENT_SUMMARY":"Plasma was not treated. Lipids were measured and compared between pregnant and non-pregnant manatees."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Lithium heparinized manatee plasma samples, quality control samples, extraction and solvent blanks, and pooled group samples were extracted via the Folch extraction method (2:1 chloroform: methanol) (Folch et al., 1957). The plasma samples were thawed on ice and briefly homogenized. Next, 50 µL of each sample was added to a glass test tube. Three quality control samples were prepared the same manner using 50 µL of SRM 1950. All samples, except the solvent blanks, were spiked with 50 µL of deuterium-labeled internal standards from 10 different lipid classes at known concentrations (diluted 1:10) (Splash Lipidomix, Avanti Polar Lipids, Alabaster, AL). Biphasic extraction was conducted by adding 3 mL of 2:1 chloroform:methanol solution to each test tube including the quality control samples and extraction blanks. The samples were then vortexed for 10 s, 500 µL of Optima-grade water was added, and the tubes were inverted 5 times. All samples were centrifuged at 2500 g for 5 min at 4 °C. The resulting bottom lipid containing layer was then removed and transferred to a new glass test tube using glass Pasteur pipettes. Samples were divided into sub-groups determined by study site, sex, and reproductive status. Extract pools were created by equal contributions from each sample within a group. Finally, the samples, controls, and pools were evaporated under a steady stream of nitrogen at 25 °C for about 25 min. The samples were then reconstituted with 100 µL of isopropanol and vortexed for 10 s. The reconstituted solutions were then transferred to autosampler vial inserts inside glass autosampler vials for UHPLC-MS/MS analysis.","SAMPLEPREP_PROTOCOL_FILENAME":"Sample Prep.txt"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"The extracted lipid samples, pooled groups, quality controls, and blanks were analyzed by UHPLC-MS/MS on a Thermo Vanquish UHPLC system coupled to a Thermo Q-Exactive Orbitrap mass spectrometer. The column used was a Waters Acquity BEH, 100 mm x 2.1 mm x 1.7 µm. Mobile phase A and B contained 60:40 acetonitrile/water (v/v) and 90:10 isopropanol/acetonitrile (v/v) respectively, with both phases containing 5mM ammonium formate and 0.1% formic acid. The mobile phase gradient was as follows: a linear increase of solvent B from 40% to 55% over 7 min, then increased to 65% by min 8, held at 65% for 4 min, linear increase to 95% over 8 min, increased to 100% over 2 min, solvent B was held at 100% for 5 min before decreasing to 40% in a tenth of a min. Finally, solvent B was held at 100% for another 3 min. The sample injection volume was 10 µL at a flow rate of 0.25 mL/min, the column compartment was 45 °C, and the autosampler temperature was 10 °C.","INSTRUMENT_NAME":"Thermo Vanquish","COLUMN_NAME":"Waters ACQUITY UPLC BEH C18(100 x 2.1mm,1.7um)","COLUMN_TEMPERATURE":"45","FLOW_GRADIENT":"a linear increase of solvent B from 40% to 55% over 7 min, then increased to 65% by min 8, held at 65% for 4 min, linear increase to 95% over 8 min, increased to 100% over 2 min, solvent B was held at 100% for 5 min before decreasing to 40% in a tenth of a min. Finally, solvent B was held at 100% for another 3 min.","FLOW_RATE":"0.25 mL/min","SOLVENT_A":"60:40 acetonitrile/water (v/v), 5mM ammonium formate and 0.1% formic acid","SOLVENT_B":"90:10 isopropanol/acetonitrile (v/v), 5mM ammonium formate and 0.1% formic acid","CHROMATOGRAPHY_TYPE":"Reversed phase"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","ANALYSIS_PROTOCOL_FILE":"MS Metadata.txt"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","MS_COMMENTS":"All samples were analyzed in full scan positive and negative ion modes with spray voltages +3.0kV and -3.0kV, respectively, at 70,000 resolution at m/z 200, the scan range was m/z 100-1500 and source temperature at 300 °C. Tandem mass spectra were collected via criterion based on data-dependent acquisition for the top-10 ions with stepped normalized collision energy 20, 25, and 30, an isolation window of 1Da, dynamic exclusion of 6 s, and using IE-Omics for the generation of exclusion lists in iterative-exclusion experiments (Koelmel, Kroeger, Gill, et al., 2017). Extracted Lipid Data Analysis LipidMatch software was implemented to identify and integrate the detected lipids (Koelmel, Kroeger, Ulmer, et al., 2017). The peak areas were normalized relative to the internal standards of the same subclass as the lipid of interest. For lipids that did not have an internal standard of the same subclass, the internal standard with the closest chemical structure was used (i.e., internal standard with the same head group). Otherwise, the internal standard with the closest chromatographic retention time (same ionization polarity) was used for analytes without a corresponding internal standard of the same lipid subclass. The plasma lipid concentrations were reported as µg/mL.","ION_MODE":"POSITIVE","MS_RESULTS_FILE":"ST003017_AN004950_Results.txt UNITS:Peak area Has m/z:Yes Has RT:Yes RT units:Seconds"}

}