Protocols

Protocol IDs are assigned by LIPID MAPS® Laboratory Information Management (LIMS) software1. The format of the IDs is as follows:

  • Procedure protocols begin with the letters "PP." Solution protocols begin with the letters "PS."
  • The last 2 numbers of a protocol ID indicate the version number. "00" indicates the initial version. Subsequent revisions of the protocol possess IDs that end with "01", "02", and so on.
  • The version with the largest set of ending numbers is the currently accepted protocol. Previous versions are considered obsolete.

Any core can write a protocol. Except for core D, the title of the new protocol should include the core.
Core D has responsibility for composing consortium-wide protocols involving preparation, handling, and treatment of cells and tissues. Other cores can write protocols that provide additional detail in these areas for their own guidance, provided:

  • The protocols do not contradict or conflict with Core D protocols.
  • The protocols reference pertinent Core D protocols.
  • The protocol title includes the core.

See Also

Please see also our Lipidomics Methods tutorials.

References

1. A Laboratory information management system for high throughput experimental lipidomics: Minimal information required for the analysis of lipidomics experiments (MIALE). Byrnes R, Fahy E and Subramaniam S. Journal of the Association for Laboratory Automation 12, 230-238 (2007) [doi:10.1016/j.jala.2007.04.002]

Equipment and supplies

Recommended EquipmentEquipment 
Tissue Culture SuppliesSupplies 
RAW 264.7 Tissue Culture SuppliesPP0000001600Added 08/27/07
RAW 264.7 Cells Recommended EquipmentPP0000001700Added 08/27/07

Procedure Protocols

General

Thawing and Passage ProcedurePP0000000101 
Thawing and passage procedure for RAW 264.7 cellsPP0000000100Added 08/27/07
Use of AnimalsPP0000001100Added 08/27/07
Ordering MicePP0000001200Added 08/27/07
Ordering Mice for Foam CellsPP0000002900Added 08/22/06
LIPID MAPS DNA AssayPP0000002700 
Fatty Acid Mass Spectrometry ProtocolPP0000003800Added 10/09/12
Fatty Acid Mass Spectrometry ProtocolPP0000005300Added 10/09/12
Fatty Acid Mass Spectrometry ProtocolPP0000005301Added 10/09/12
Harvesting and Plating Thioglycollate Elicited Macrophages for LM DistributionPP0000004101Added 05/21/08
Core D - Procedure Protocol ATP, Kdo2-Lipid A TreatmentPP0000004601Added 01/04/10
Core D - Procedure Protocol ATP, Kdo2-Lipid A TreatmentPP0000004602Added 01/12/10
Procedure Protocol for Harvesting and Plating Bone Marrow Derived Macrophages for LIPID MAPS DistributionPP0000004701Added 01/04/10
Procedure Protocol for Harvesting and Plating Bone Marrow Derived Macrophages for LIPID MAPS DistributionPP0000004702Added 01/12/10
Protocol ATP/POVPC-peptide Costimulation Time coursePP0000005101Added 10/09/12
Protocol ATP/PAPC/oxidized PAPC Costimulation Time coursePP0000005200Added 10/09/12

Kdo2-Lipid A Treatment

LPS Induction (Serum-deprived)PP0000000600 
10% Serum Kdo2-Lipid A TreatmentPP0000001000Added 08/27/07
10% Serum Kdo2-Lipid A TreatmentPP0000001001 
10% Serum Kdo2-Lipid A TreatmentPP0000001002 
10% Serum Kdo2-Lipid A TreatmentPP0000001003 
10% Serum Kdo2-Lipid A TreatmentPP0000001004 
0.5% Serum Kdo2-Lipid A TreatmentPP0000000500Added 08/27/07
0.5% Serum Kdo2-Lipid A TreatmentPP0000000501Added 08/27/07

Primary Macrophages

Eliciting Bio-Gel Derived MacrophagesPP0000001300Added 08/27/07
Eliciting Foam CellsPP0000003000Added 08/22/06
Eliciting Thioglycollate Derived MacrophagesPP0000001400Added 08/27/07
Eliciting Thioglycollate derived MacrophagesPP0000001401Added 06/20/07
Harvesting and Plating Bone Marrow-derived MacrophagesPP0000003500Added 06/20/07
Harvesting and Plating Primary MacrophagesPP0000001501 
Harvesting and Plating Thioglycollate Elicited MacrophagesPP0000001502Added 06/20/07
Harvesting Foam CellsPP0000003100Added 08/22/06
Harvesting MacrophagesPP0000001500Added 08/27/07
Kdo2-Lipid A Treatment of Thioglycollate and Bone Marrow Derived MacrophagesPP0000001801Added 06/20/07
Primary Macrophage TreatmentPP0000001800 

Core D - Macrophage Biology and Functional Genomics

Core D - Procedure Protocol Compactin, Kdo2 Lipid A Treatment 2008PP0000004000Added 10/09/12
Core D - 25OHC TreatmentPP0000004900Added 11/24/10

Core E - Glycerolipids/Cholesteryl Esters

Core E - LM Thawing and Passage for RAW 264.7PP0000001900Added 08/27/07
Core E - 0.5% Serum Kdo2-Lipid A TreatmentPP0000002000Added 08/27/07
Core E - 10% Serum Kdo2-Lipid A TreatmentPP0000002100Added 08/27/07
Core E - Analysis of Neutral LipidsPP0000002200Added 08/27/07
Core E - Analysis of Neutral Lipids from Human Plasma June 4, 2010PP0000005000Added 10/09/12
Core E - Analysis of Neutral Lipids from Cells June 4, 2010PP0000005500Added 10/09/12

Core G - Eicosanoids

Core G - Eicosanoid MSPP0000000200Added 08/27/07
Core G - Eicosanoid MSPP0000000201Added 08/27/07
Core G - Eicosanoid MSPP0000000204Added 08/27/07
Core G - Eicosanoid MSPP0000000205Added 08/27/07
Core G - Eicosanoid MSPP0000000206Added 08/27/07
Core G - RAW subcellular fractionationPP0000004300Added 05/19/08
Core G - RAW subcellular fractionationPP0000004301Added 06/10/08

Core H - Glycerophospholipids

Core H - Direct Injection MSPP0000000900Added 08/27/07
Core H - HPLC phospholipid protocolPP0000000800Added 08/27/07
Phospholipid LC-MS ParametersPP0000002600Added 08/27/07
Core H - Glycerophospholipid ExtractionPP0000004200Added 04/23/08

Core J - Sterols

Core J - 10% NCLPPS, Compactin, Kdo2-Lipid A TreatmentPP0000002300Added 08/27/07
Core J - Compactin Kdo2-Lipid A Treatment in Dye-Free GMedPP0000002400Added 08/27/07
Core J - Sterol Extraction and LCMSPP0000002500Added 08/27/07
Core J - Compactin Kdo2-Lipid A TreatmentPP0000002800Added 08/27/07
Core J - Compactin Kdo2-Lipid A ModifiedPP0000003300Added 08/27/07
Core J - Compactin Kdo2lipidA RNAPP0000003400Added 08/27/07
Core J - Sterol Extraction and QuantitationPP0000003200Added 08/27/07
Core J - Sterol Extraction and QuantitationPP0000003201Added 08/27/07
Core J - Foam Cell Sterol Extraction and QuantitationPP0000003600Added 05/21/07
Core J - Sterol Extraction, Cleanup, and QuantitationPP0000003700Added 05/21/07
Core J - Procedure Protocol - Compactin, Kdo2 Lipid A Treatment 2008PP0000003900Added 11/22/10
Core J - Procedure Protocol Compactin, Kdo2 Lipid A Treatment in Dye-Free Growth Medium 2008PP0000004400Added 10/09/12
Core J - Human Plasma Samples First Set of Practice and NIST PlasmasPP0000004500Added 10/09/12

Core K - Prenols and Other Lipids

Core K - Human plasma SRM neutral folch extraction and lipid analysisPP0000004800Added 10/09/12

Solution Protocols

Kdo2-Lipid A solutions

Sonicated Kdo2-Lipid A Working SolutionPS0000001400 
Sonicated Kdo2-Lipid A Working SolutionPS0000001401 
Sonicated Stock Kdo2-Lipid APS0000000700Added 08/27/07
Sonicated Stock Kdo2-Lipid APS0000000701 
Compactin StockPP0000003900Added 11/22/10

Primary Macrophages

Bio-Gel (2%)PS0000001500Added 08/27/07
Thioglycollate Medium (3%)PS0000001600Added 08/27/07
Primary Macrophage Growth Medium 1PS0000001700Added 08/27/07
Primary Macrophage Growth Medium 1PS0000001701Added 08/22/06
Primary Macrophage Serum Deprivation Medium 1PS0000001900Added 08/27/07
Bone Marrow-derived Macrophage Growth MediumPS0000002900Added 06/20/07
Stock Recombinant Human Macrophage Colony Stimulating Factor (M-CSF)PP0000003100Added 06/14/11
Bone Marrow-derived Macrophage Growth MediumPS0000003201Added 06/14/11
Bone Marrow Derived Macrophage Growth Medium 3PS0000004500Added 10/09/12

Cultured Macrophage Cell Lines

RAW 264.7 Growth MediumPS0000000800 
RAW 264.7 Growth Medium 1PS0000000900Added 08/27/07
RAW 264.7 Growth Medium 1PS0000000901Added 08/27/07
RAW 264.7 Growth Medium 1PS0000001100Added 08/27/07
RAW 264.7 Growth Medium 1PS0000001101Added 08/27/07
RAW 264.7 Growth Medium 1PS0000001102Added 08/27/07
RAW 264.7 Growth Medium 1PS0000001200Added 08/27/07
RAW 264.7 Serum Deprivation Medium 1PS0000001000Added 08/27/07
ATP-Magnesium StockPS0000004000Added 10/09/12
25-HydroxycholesterolPS0000004600Added 10/09/12
Dye-free complete DMEM solutionPS0000005000Added 10/09/12

Core E - Glycerolipids/Cholesteryl Esters

Core E - Neutral Lipid Internal StandardPS0000002000Added 08/27/07
Core E - Cholesterol Ester Internal Standard.PS0000003000Added 08/27/07

Core F - Lipid Synthesis

Core F - Avanti Sphingomyelin MixturePS0000004200Added 10/09/12
Core F - Avanti Ceramide MixturePS0000004300Added 10/09/12
Core F - Avanti Glucosyl ceramide MixturePS0000004400Added 10/09/12

Core G - Eicosanoids

Core G - Dye-Free Growth MediumPS0000002300Added 08/27/07
Core G - Dye-Free Growth MediumPS0000002400Added 08/27/07
Core G - Eicosanoid Primary StandardPS0000000200Added 08/27/07
Core G - Eicosanoid Primary StandardPS0000000601Added 08/27/07
Core G - Eicosanoid Primary StandardPS0000000602Added 08/27/07
Core G - Eicosanoid Primary StandardPS0000000603Added 08/27/07
Core G - Eicosanoid Primary StandardPS0000000604Added 08/27/07
Core G - Eicosanoid Internal StandardPS0000000500Added 08/27/07
Core G - Eicosanoid Internal StandardPS0000000501Added 08/27/07
Core G - Eicosanoid Internal Standards DeuteratedPS0000000101Added 08/27/07
Core G - ATP stock solutionPS0000004800Added 10/09/12
Core G - PAPC stock solutionPS0000005100Added 10/09/12
Core G - oxidized PAPC (oxPAPC) stock solutionPS0000005200Added 10/09/12

Core J - Sterols

Core J - old 4B OHC D7 standardPS0000002500Added 08/27/07
Core J - old 7-Oxo D7standardPS0000002600Added 08/27/07
Core J - old C D7 StandardPS0000002700Added 08/27/07
Core J - Mevalonate 20mMPS0000002200Added 08/27/07
Core J - Mevalonate 50mMPS0000002800Added 08/27/07
Core J - 10% NCLPPS0000002100Added 08/27/07

Key LIPID MAPS® Resources
Publications
- publications related to projects funded through the LIPID MAPS® consortium
Lipid Classification System
- the first internationally accepted lipid classification system
Lipid Standards
- MS/MS spectra, annotations for principal product ions, and acquisition parameters
Experimental Data
- centralized studies on macrophages, lipidomics data on human plasma, and more
Structure Database (LMSD)
- over 40,000 unique structures of biologically relevant lipids
Proteome Database (LMPD)
- over 12,500 lipid-associated proteins from major research species
Pathways
- manually curated lipid metabolism and signaling pathways
LIPID MAPS® REST Service
- web-based/programmatic access to lipid structure and lipid-related gene/protein data
MS analysis tools
- tools for searching various lipid classes by precursor or product ion
Structure Drawing Tools
- draw and save lipid structures using online menus
Protocols
- LIPID MAPS® techniques for lipidomics and macrophage cell culture

LIPID MAPS® is funded by a grant from the Wellcome Trust.

logo LIPID MAPS® is funded by a grant from the Wellcome Trust.