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.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000221 |
| Study Title | Normal plasma cells,Low proliferation multiple myeloma and High proliferation multiple myeloma cells |
| Study Type | differential metabolomics |
| Study Summary | CD138 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 |
| Department | Hematology |
| Last Name | Gonsalves |
| First Name | William |
| Dasari.Surendra@mayo.edu | |
| Submit Date | 2015-06-20 |
| Num Groups | 1 |
| Total Subjects | 1 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Uploaded File Size | 73 G |
| Analysis Type Detail | LC-MS |
| Release Date | 2016-06-18 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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: | Mammals |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Cognitive Status |
|---|---|---|
| SA010737 | BM049394SC004 | fast MM |
| SA010738 | BM049429SC001 | normal |
| SA010739 | BM049411SC003 | slow 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 |
|---|---|---|---|---|
| Chromatography ID | CH000246 | CH000246 | CH000247 | CH000247 |
| MS ID | MS000276 | MS000277 | MS000278 | MS000279 |
| 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 | Waters high-strength silica (150 x 2.1mm,1.8um) | Waters high-strength silica (150 x 2.1mm,1.8um) | Waters ethylene-bridged hybrid (150 x 2.1mm,1.7um) | Waters ethylene-bridged hybrid (150 x 2.1mm,1.7um) |
| 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: | Waters high-strength silica (150 x 2.1mm,1.8um) |
| 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: | Waters ethylene-bridged hybrid (150 x 2.1mm,1.7um) |
| 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 |
