Our group plans on using the same tissue sample for MS-based proteomics and lipidomics. Our current method for protein extraction is using RIPA buffer to homogenize followed by the FASP protocol. For lipid extraction, we use the Folch Method or the MTBE Method. We would like to see if we can use the same homogenate to run proteomics and lipidomics experiments.
You could try using a very weak hydrophobic chromatography resin Butyl-S-Sepharose:https://www.gelifesciences.co.jp/catalog/pdf/11002634.pdf
At normal conditions (e.g. PBS) the majority of the proteins would pass through, while lipids be retained on the column.
RIPA buffer is not MS compatible since it has many non-volatile components. You may have to use SPE to clean up your proteomics sample before injection.
An example of SPE for LC/MS/MS.
http://agilent.com/cs/library/applications/5991-8007EN.pdf?utm_content=sf109750041&utm_campaign=Agilent%20Technologies&utm_medium=spredfast&utm_source=linkedin&sf109750041=1
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