{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000790","ANALYSIS_ID":"AN001258","VERSION":"1","CREATED_ON":"July 12, 2017, 2:37 pm"},

"PROJECT":{"PROJECT_TITLE":"Mayo Pilot and Feasibility: Identifying metabolic adaptations characteristic of multiple myeloma cells via mass spectrometry-based metabolite profiling","PROJECT_SUMMARY":"Mayo Pilot and Feasibility: Identifying metabolic adaptations characteristic of multiple myeloma cells via mass spectrometry-based metabolite profiling","INSTITUTE":"Mayo Clinic","LAST_NAME":"Gonsalves","FIRST_NAME":"Wilson","ADDRESS":"200 First St. SW, Rochester, Minnesota, 55905, USA","EMAIL":"gonsalves.wilson@mayo.edu","PHONE":"507-266-0792"},

"STUDY":{"STUDY_TITLE":"Identifying metabolic adaptations characteristic of multiple myeloma cells via targeted sphingolipids concentrations from bone marrow and peripheral plasma","STUDY_SUMMARY":"Will be assessing the targeted sphingolipids concentrations of high risk versus low risk smoldering myeloma patients based on peripheral blood plasma and bone marrow plasma.","INSTITUTE":"Mayo Clinic","LAST_NAME":"Gonsalves","FIRST_NAME":"Wilson","ADDRESS":"200 First St. SW, Rochester, Minnesota, 55905, USA","EMAIL":"gonsalves.wilson@mayo.edu","PHONE":"507-266-0792"},

"SUBJECT":{"SUBJECT_TYPE":"Human","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"ms6273-1",
"Factors":{"grouping":"Slow Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"peripheral"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-2",
"Factors":{"grouping":"Quick Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"peripheral"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-3",
"Factors":{"grouping":"Quick Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"peripheral"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-4",
"Factors":{"grouping":"Slow Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"peripheral"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-5",
"Factors":{"grouping":"Quick Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"peripheral"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-6",
"Factors":{"grouping":"Slow Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"peripheral"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-7",
"Factors":{"grouping":"Quick Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"peripheral"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-8",
"Factors":{"grouping":"Slow Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"peripheral"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-9",
"Factors":{"grouping":"Quick Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"peripheral"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-10",
"Factors":{"grouping":"Slow Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"peripheral"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-11",
"Factors":{"grouping":"Quick Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"peripheral"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-12",
"Factors":{"grouping":"Quick Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"peripheral"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-13",
"Factors":{"grouping":"Quick Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"peripheral"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-14",
"Factors":{"grouping":"Slow Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"peripheral"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-15",
"Factors":{"grouping":"Quick Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"peripheral"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-16",
"Factors":{"grouping":"Quick Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"peripheral"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-17",
"Factors":{"grouping":"Quick Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"peripheral"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-18",
"Factors":{"grouping":"Slow Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"peripheral"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-19",
"Factors":{"grouping":"Quick Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"peripheral"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-20",
"Factors":{"grouping":"Quick Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"peripheral"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-21",
"Factors":{"grouping":"Slow Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"peripheral"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-22",
"Factors":{"grouping":"Quick Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"peripheral"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-23",
"Factors":{"grouping":"Slow Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"peripheral"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-24",
"Factors":{"grouping":"Quick Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"peripheral"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-25",
"Factors":{"grouping":"Slow Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"peripheral"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-26",
"Factors":{"grouping":"Quick Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"bone marrow"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-27",
"Factors":{"grouping":"Slow Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"bone marrow"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-28",
"Factors":{"grouping":"Slow Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"bone marrow"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-29",
"Factors":{"grouping":"Quick Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"bone marrow"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-30",
"Factors":{"grouping":"Quick Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"bone marrow"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-31",
"Factors":{"grouping":"Slow Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"bone marrow"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-32",
"Factors":{"grouping":"Quick Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"bone marrow"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-33",
"Factors":{"grouping":"Quick Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"bone marrow"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-34",
"Factors":{"grouping":"Slow Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"bone marrow"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-35",
"Factors":{"grouping":"Quick Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"bone marrow"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-36",
"Factors":{"grouping":"Slow Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"bone marrow"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-37",
"Factors":{"grouping":"Slow Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"bone marrow"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-38",
"Factors":{"grouping":"Quick Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"bone marrow"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-39",
"Factors":{"grouping":"Slow Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"bone marrow"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-40",
"Factors":{"grouping":"Slow Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"bone marrow"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-41",
"Factors":{"grouping":"Quick Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"bone marrow"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-42",
"Factors":{"grouping":"Quick Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"bone marrow"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-43",
"Factors":{"grouping":"Quick Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"bone marrow"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-44",
"Factors":{"grouping":"Slow Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"bone marrow"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-45",
"Factors":{"grouping":"Quick Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"bone marrow"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-46",
"Factors":{"grouping":"Slow Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"bone marrow"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-47",
"Factors":{"grouping":"Quick Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"bone marrow"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-48",
"Factors":{"grouping":"Quick Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"bone marrow"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-49",
"Factors":{"grouping":"Quick Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"bone marrow"}
},
{
"Subject ID":"-",
"Sample ID":"ms6273-50",
"Factors":{"grouping":"Quick Progressors"},
"Additional sample data":{"Sample type":"plasma","type":"bone marrow"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"In order to analyze the metabolites of clonal PCs (intracellular) and BM plasma (extracellular) separately, they have to be separated out from the BM samples. Thus, upon acquiring the BM samples from patients they will be placed in centrifuged at 2500 rpm for 10 minutes to separate out the plasma from the cellular fraction. The separated BM plasma is then stored in separate vials and snap frozen under liquid nitrogen for 20 seconds before storing at -80οC for further analysis. The leftover cellular component present as a pellet will be washed and reconstituted with an equal volume of RPMI 1640 medium. Erythrocytes are lysed using ammonium chloride lysing solution. After incubation on ice for 5 min, the cell suspension is diluted with RPMI medium. The cells are again pelleted by centrifugation and then suspended in RoboSep buffer (250ml PBS, 2% BSA, 1mM EDTA). The clonal CD138 positive PCs are purified using positive selection by mixing the cells with a CD138 positive selection cocktail and anti-CD138 magnetic-activated cell separation microbeads (ROBOSEP™ cell separation system, StemCell Technologies Inc) in the automated RoboSep cell separation system. The purified samples containing only CD138 positive cells are re‐suspended and then centrifuged to form a cell pellet. The goal will be to obtain at least 1-2 x 107 clonal PCs per sample. The cell pellet will be snap frozen under liquid nitrogen for 20 seconds before storing at -80οC for further analysis. Both the BM plasma samples as well as the clonal PCs pellet will be provided to the metabolomics core for sample preparation for LC-MS analysis. For Aim 2, we will be using stored BM samples from SMM patients that have already had their BM plasma and clonal PCs separated from each other and stored at -80οC. It is important to note that all these samples were collected and frozen in a timely manner. Furthermore consistency in sample collection, storage and processing is imperative for the optimal conduct of metabolomics-based experiments. This ensures that all samples being analyzed and compared with each other would have been manipulated similarly, limiting any handling biases. All patient samples in the Predolin Foundation Biobank were collected and stored by following a standardized operating procedure. BM samples were processed for BM plasma separation and clonal PCs enrichment but were then immediately snap frozen for storage at -80οC within approximately 3 hours of collection from the patient. All samples were collected in patients who have been fasting for at least 6 to 8 hours prior. To further ensure consistency in our analysis of this study, we will only use samples that have never been thawed since initial storage to preserve the stability of the metabolites originally present in the samples."},

"TREATMENT":{"TREATMENT_SUMMARY":"We will use matched BM plasma and purified clonal marrow PCs from the BM samples of SMM patients collected at the time of their diagnosis and stored within the Mayo Clinic Predolin Foundation Biobank. We will select BM samples from patients with SMM who progressed to MM within 2 years of their samples being collected and stored; this will constitute the high risk SMM group. We will also select BM samples from SMM patients who have not progressed to MM within at least 2 years of follow up of their samples being collected and stored; this will constitute the standard risk SMM group. The strength of this approach is that we will utilize stored SMM samples from one of the most comprehensively characterized monoclonal gammopathy biobanks available. Secondly, all samples will be obtained from collection dates at least 2 years prior in order to ensure adequate follow-up time to assess their current clinical status. This would avoid the need to prospectively collect samples from SMM patients and clinically follow them for a number of years before we are able to gauge who were clinically high or standard risk for progression. There are over 700 SMM patients who have had their BM samples collected and stored in the biobank from 1996 to 2013; more than half these patients have progressed to MM."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"sphingolipids concetrations"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Waters Acquity","COLUMN_NAME":"Waters Acquity BEH C8 (150 x 2mm, 1.7um)"},

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

"MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Thermo Quantum Ultra","INSTRUMENT_TYPE":"Triple quadrupole","MS_TYPE":"ESI","ION_MODE":"POSITIVE"},

"MS_METABOLITE_DATA":{
"Units":"uM",

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}