Summary of study ST000221

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000181. The data can be accessed directly via it's Project DOI: 10.21228/M8R30R This work is supported by NIH grant, U2C- DK119886.

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Study IDST000221
Study TitleNormal plasma cells,Low proliferation multiple myeloma and High proliferation multiple myeloma cells
Study Typedifferential metabolomics
Study SummaryCD138 sorted bone marrow plasma cell were obtained from a normal patient, a multiple myelow with slow proliferation and a multiple myelow with rapid proliferation.
Institute
Mayo Clinic
DepartmentHematology
Last NameGonsalves
First NameWilliam
EmailDasari.Surendra@mayo.edu
Submit Date2015-06-20
Num Groups1
Total Subjects1
Raw Data AvailableYes
Raw Data File Type(s).xml,.xsd,.stg, .bin, .cd,.cG
Uploaded File Size73 G
Analysis Type DetailLC-MS
Release Date2016-06-18
Release Version1
William Gonsalves William Gonsalves
https://dx.doi.org/10.21228/M8R30R
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000181
Project DOI:doi: 10.21228/M8R30R
Project Title:Identification of altered metabolites in normal plasma cells, slow progression multiple myeloma and fast progression multiple meyloma
Project Type:Untargeted LC-MS Metabolomics
Project Summary:This experiment is comparing the metabolite profiles between normal plasma cells and clonal plasma cells from multiple myeloma patients.
Institute:Mayo Clinic
Department:Neurology
Last Name:Gonsalves
First Name:Wilson
Address:200 First Street SW, Rochester, MN 55905
Email:Dasari.Surendra@mayo.edu
Phone:507-284-0513

Subject:

Subject ID:SU000240
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Human

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Cognitive Status
SA010737BM049394SC004fast MM
SA010738BM049429SC001normal
SA010739BM049411SC003slow MM
Showing results 1 to 3 of 3

Collection:

Collection ID:CO000228
Collection Summary:Bone marrow cells were collected after fasting. Collected cells were CD138 sorted and frozen in -80C until analysis.
Sample Type:Bone marrow cells
Collection Location:Illiac crest

Treatment:

Treatment ID:TR000248

Sample Preparation:

Sampleprep ID:SP000242
Sampleprep Summary:1) Incubated cell pellets on ice for 15 min
2) Added PBS to cells and vortex well
3) Sonicate for 1 min in ice bath
4) Added MeOH+ACN mixture to cells and vortex well
5) Sonicated for 1 min in ice bath
6) Incubated on ice for 30 min + spin for 20 min at 18K RPM
7) Combined 110 ul from each sample into a pool sample (330 ul total)
8) Split pool into two fractions of 150 ul each (hilic & C18)
9) Split remaning sample into 150 ul x 2 (hilic & C18)

Combined analysis:

Analysis ID AN000327 AN000328 AN000329 AN000330
Analysis type MS MS MS MS
Chromatography type Reversed phase Reversed phase HILIC HILIC
Chromatography system Waters Acquity Waters Acquity Waters Acquity Waters Acquity
Column high-strength silica 2.1 150 mm, 1.8 m; Waters high-strength silica 2.1 150 mm, 1.8 m; Waters ethylene-bridged hybrid 2.1 150 mm, 1.7 m; Waters ethylene-bridged hybrid 2.1 150 mm, 1.7 m; Waters
MS Type ESI ESI ESI ESI
MS instrument type TOF TOF TOF TOF
MS instrument name Agilent 6220 TOF Agilent 6220 TOF Agilent 6220 TOF Agilent 6220 TOF
Ion Mode POSITIVE NEGATIVE POSITIVE NEGATIVE
Units Peak area Peak area Peak area Peak area

Chromatography:

Chromatography ID:CH000246
Chromatography Summary:C18
Chromatography Comments:Metabolite separation was achieved using an Acquity UPLC system (Waters, Milford, MA) with both hydrophilic interaction chromatography (HILIC) (ethylene-bridged hybrid 2.1150 mm, 1.7 mm; Waters) and reversed-phase liquid chromatography C18 (RPLC) (high-strength silica 2.1150 mm, 1.8 m; Waters). For each column, the run time was 20 min at a flow rate of 400 L/min. Reverse-phase chromatography was performed using 99% solvent A (5 mmol/L NH4 acetate, 0.1% formic acid, and 1% acetonitrile) to 100% solvent B (95% acetonitrile with 0.1% formic acid). The gradient was 0 min, 0% B; 1 min, 0% B; 3 min, 5% B; 13.0 min, 100% B; 16 min, 100% B; 16.5 min, 0% B; and 20 min, 0% B. The hydrophilic interaction chromatography gradient was as follows: 0 min, 100% B; 1 min, 100% B; 5 min, 90% B; 13.0 min, 0% B; 16 min, 0% B; 16.5 min, 100% B; and 20 min, 100% B. The injection volume of each sample was 5 L and column was maintained at 50C.
Instrument Name:Waters Acquity
Column Name:high-strength silica 2.1 150 mm, 1.8 m; Waters
Chromatography Type:Reversed phase
  
Chromatography ID:CH000247
Chromatography Summary:HILIC
Chromatography Comments:Metabolite separation was achieved using an Acquity UPLC system (Waters, Milford, MA) with both hydrophilic interaction chromatography (HILIC) (ethylene-bridged hybrid 2.1150 mm, 1.7 mm; Waters) and reversed-phase liquid chromatography C18 (RPLC) (high-strength silica 2.1150 mm, 1.8 m; Waters). For each column, the run time was 20 min at a flow rate of 400 L/min. Reverse-phase chromatography was performed using 99% solvent A (5 mmol/L NH4 acetate, 0.1% formic acid, and 1% acetonitrile) to 100% solvent B (95% acetonitrile with 0.1% formic acid). The gradient was 0 min, 0% B; 1 min, 0% B; 3 min, 5% B; 13.0 min, 100% B; 16 min, 100% B; 16.5 min, 0% B; and 20 min, 0% B. The hydrophilic interaction chromatography gradient was as follows: 0 min, 100% B; 1 min, 100% B; 5 min, 90% B; 13.0 min, 0% B; 16 min, 0% B; 16.5 min, 100% B; and 20 min, 100% B. The injection volume of each sample was 5 L and column was maintained at 50C.
Instrument Name:Waters Acquity
Column Name:ethylene-bridged hybrid 2.1 150 mm, 1.7 m; Waters
Chromatography Type:HILIC

MS:

MS ID:MS000276
Analysis ID:AN000327
Instrument Name:Agilent 6220 TOF
Instrument Type:TOF
MS Type:ESI
MS Comments:C18-PESI (+ve ESI) A 6220 ToF-MS (Agilent Technologies) was operated in both positive and negative electrospray ionization (ESI) modes using a scan range of 50?1,200 m/z. The mass accuracy and mass resolution were 5 parts per million (ppm) and 20,000 ppm, respectively. The instrument settings were as follows: nebulizer gas temperature 325°C, capillary voltage 3.5 kV, capillary temperature 300°C, fragmentor voltage 150 V, skimmer voltage 58 V, octapole voltage 250 V, cycle time 0.5 s, and run time 15.0 min.
Ion Mode:POSITIVE
  
MS ID:MS000277
Analysis ID:AN000328
Instrument Name:Agilent 6220 TOF
Instrument Type:TOF
MS Type:ESI
MS Comments:C18-NESI (-ve ESI) A 6220 ToF-MS (Agilent Technologies) was operated in both positive and negative electrospray ionization (ESI) modes using a scan range of 50?1,200 m/z. The mass accuracy and mass resolution were 5 parts per million (ppm) and 20,000 ppm, respectively. The instrument settings were as follows: nebulizer gas temperature 325°C, capillary voltage 3.5 kV, capillary temperature 300°C, fragmentor voltage 150 V, skimmer voltage 58 V, octapole voltage 250 V, cycle time 0.5 s, and run time 15.0 min.
Ion Mode:NEGATIVE
  
MS ID:MS000278
Analysis ID:AN000329
Instrument Name:Agilent 6220 TOF
Instrument Type:TOF
MS Type:ESI
MS Comments:HILIC-PESI (+ve ESI) A 6220 ToF-MS (Agilent Technologies) was operated in both positive and negative electrospray ionization (ESI) modes using a scan range of 50?1,200 m/z. The mass accuracy and mass resolution were 5 parts per million (ppm) and 20,000 ppm, respectively. The instrument settings were as follows: nebulizer gas temperature 325°C, capillary voltage 3.5 kV, capillary temperature 300°C, fragmentor voltage 150 V, skimmer voltage 58 V, octapole voltage 250 V, cycle time 0.5 s, and run time 15.0 min.
Ion Mode:POSITIVE
  
MS ID:MS000279
Analysis ID:AN000330
Instrument Name:Agilent 6220 TOF
Instrument Type:TOF
MS Type:ESI
MS Comments:HILIC-PESI (-ve ESI) A 6220 ToF-MS (Agilent Technologies) was operated in both positive and negative electrospray ionization (ESI) modes using a scan range of 50?1,200 m/z. The mass accuracy and mass resolution were 5 parts per million (ppm) and 20,000 ppm, respectively. The instrument settings were as follows: nebulizer gas temperature 325°C, capillary voltage 3.5 kV, capillary temperature 300°C, fragmentor voltage 150 V, skimmer voltage 58 V, octapole voltage 250 V, cycle time 0.5 s, and run time 15.0 min.
Ion Mode:NEGATIVE
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