Summary of study ST000242

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 PR000195. The data can be accessed directly via it's Project DOI: 10.21228/M8630S This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

Show all samples  |  Download all metabolite data  |  Perform analysis on untargeted data  |  Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data (Contains raw data)
Study IDST000242
Study TitleWhole unconditioned medium (Defined culture media, M199),Whole M1 medium,Whole M2 medium
Study Typedifferential metabolomics
Study Summary Media was flash frozen with N2 and stored at -80 C. Samples can be stored at -80 C until use. ~1 ml aliquots. The following media has been provided to the metabolomics core in biological triplicates. Complete (Whole) Media: 1) Whole unconditioned medium (Defined culture media, M199) 2) Whole M1 medium 3) Whole M2 medium
Institute
Mayo Clinic
DepartmentPhysiology and Biomedical Engineering
Last NameFarrugia
First NameGianrico
EmailDasari.Surendra@mayo.edu
Submit Date2015-06-26
Num Groups1
Raw Data AvailableYes
Raw Data File Type(s).xml,.cd,.cg,.xsd,.bin,.m
Analysis Type DetailLC-MS
Release Date2016-07-08
Release Version2
Gianrico Farrugia Gianrico Farrugia
https://dx.doi.org/10.21228/M8630S
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000195
Project DOI:doi: 10.21228/M8630S
Project Title:Metabolimic Analysis of Conditioned Macrophage Media
Project Type:Untargeted LC-MS Metabolomics
Project Summary:We are studying the secreted components from pro-inflammatory macrophages, coined M1. We use a macrophage at the opposite end of the macrophage phenotype spectrum as a control, the anti-inflammatory macrophage, coined M2. M1 macrophage conditioned media has a <3 kD factor that reduces survival of a cell of interest in primary culture. This factor is not present in M2 macrophage conditioned media <3 kD, as there is no effect on primary cell numbers. The goal of this project is to analyze the components present in the M1 conditioned <3 kD media and compare to the M2 conditioned < 3kD media.
Institute:Mayo Clinic
Department:Physiology and Biomedical Engineering
Last Name:Farrugia
First Name:Gianrico
Address:200 First Street SW, Rochester, MN 55905
Email:Dasari.Surendra@mayo.edu
Phone:507-284-0513

Subject:

Subject ID:SU000262
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 Sample Status
SA011163ms5047-2-3Whole M1 medium
SA011164ms5047-2-2Whole M1 medium
SA011165ms5047-2-1Whole M1 medium
SA011166ms5047-3-3Whole M2 medium
SA011167ms5047-3-1Whole M2 medium
SA011168ms5047-3-2Whole M2 medium
SA011160ms5047-1-3 Whole unconditioned medium (Defined culture media, M199)
SA011161ms5047-1-2 Whole unconditioned medium (Defined culture media, M199)
SA011162ms5047-1-1 Whole unconditioned medium (Defined culture media, M199)
Showing results 1 to 9 of 9

Collection:

Collection ID:CO000253
Collection Summary:Whole media
Sample Type:Media

Treatment:

Treatment ID:TR000273
Treatment Summary:Media was flash frozen with N2 and stored at -80 C. Samples can be stored at -80 C until use. ~1 ml aliquots.
The following media has been provided to the metabolomics core in biological triplicates.
Complete (Whole) Media:1) Whole unconditioned macrophage medium (Defined culture media, M199)2) Whole M1 macrophage medium
3) Whole M2 macrophage medium

Sample Preparation:

Sampleprep ID:SP000267
Sampleprep Summary:Quality-control samples used in the study were prepared from pooled samples spiked with a selection of standards. All samples (200 μL) were thawed on ice at 4°C followed by deproteinization with methanol (1:4 ratio of plasma to methanol) and vortexed for 10 s, followed by incubation at −20°C for 2 h. The samples were then centrifuged at 15,871g for 30 min at 4°C. The supernatants were lyophilized (Savant, Holbrook, NY) and stored at −20°C prior to analysis. The samples were reconstituted in 50% H2O/acetonitrile and passed through a Microcon YM3 filter (Millipore Corporation). The supernatants were transferred to analytical vials, stored in the autosampler at 4°C, and analyzed within 48 h of reconstitution in buffer.

Combined analysis:

Analysis ID AN000375 AN000376 AN000377 AN000378
Analysis type MS MS MS MS
Chromatography type Reversed phase Reversed phase Reversed phase Reversed phase
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 high-strength silica 2.1 150 mm, 1.8 m; Waters high-strength silica 2.1 150 mm, 1.8 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:CH000271
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

MS:

MS ID:MS000321
Analysis ID:AN000375
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:MS000322
Analysis ID:AN000376
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:MS000323
Analysis ID:AN000377
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:MS000324
Analysis ID:AN000378
Instrument Name:Agilent 6220 TOF
Instrument Type:TOF
MS Type:ESI
MS Comments:HILIC-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
  logo