We have had increasing evidence that non-peptide molecules are coming through our sample prep techniques and affecting the LC-MS systems. We are pretty sure about the effect of triton and other detergents such as CHAPS but similar effects from samples that do not contain detergents suggests that other molecules such as lipids may be involved.

Lipids and detergents both share a similar structure with a hydrophobic region being attached to a hydrophilic region. The hydrophilic head can either strongly or weakly anionic or cationic or polar. Lipids such as phopholipids are actually zwitterionic with an amine group (weak cation) and a phosphate group (strong anion). This link provides an overview of bothe detergents and the different types of lipid structures in nature: http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/lipids.htm. This link provides a more detailed summary of lipid classes:http://lipidlibrary.aocs.org/Lipids/whatlip/index.htm. This link explores how detergents work with proteins: http://onlinelibrary.wiley.com/doi/10.1002/9780470015902.a0006201.pub2/full.

The negative effect of phospholipids on LC-MS procedures is of increasing notice and the recent trend is to have rapid ways of removing lipids and proteins from blood fluids as rapidly as possible: http://www.sigmaaldrich.com/analytical-chromatography/sample-preparation/spe/hybridspe-ppt.html.

The best time to remove lipids and detergents is before digestion please see the article on comparing sample preparation techniques [XXXX}

If your methods do not allow protein clean up then there are methods for removing lipids and detergents from peptides although this is a more challenging process, see this article on lipid and detergent removal from peptide samples {XXXX}

Other links:

Detergent removal: https://abrf.org/ABRFNews/1997/December1997/dec97detergent.html

Tags:#basics, contamination

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