LC-MS-based untargeted
metabolomics have been proven to be an extremely
promising technique to discover biomarkers and explore the mechanisms
underlying diseases, which, however, relies heavily on sample pretreatment
for metabolite extraction. In the present study, a systematic and
pragmatic evaluation of eight protocols employing conventional metabolites
extraction strategies, protein precipitation (PPT), and liquid–liquid
extraction (LLE), with and without proteinase K (PK) incubation, was
performed simultaneously, using human plasma and a mixture of 39 endogenous
metabolite standards. These protocols were as follows: (1) PPT with
methanol, (2) PPT with acetonitrile, (3) PPT with 2-propanol, (4)
two-step LLE of CH2Cl2–MeOH, followed
by MeOH–H2O, (5) PK incubation combining two-step
LLE of CH2Cl2–MeOH followed by MeOH–H2O, (6) two-step LLE of CHCl3–MeOH, followed
by MeOH–H2O, (7) PK incubation combining two-step
LLE of CHCl3–MeOH, followed by MeOH–H2O, (8) PK incubation combining MeOH–EtOH PPT. The results
suggested that two-step LLE produced broader metabolome coverage than
protein precipitation, and the addition of proteinase K enhanced the
extraction performance further. Taken together, PK incubation combining
two-step LLE of CHCl3–MeOH, followed by MeOH–H2O, was determined to be the most suitable extraction method,
because of its broad metabolome coverage, high reproducibility, and
satisfactory recovery. Next, the developed optimal sample preparation
method was applied successfully to profile the plasma metabolome of
colorectal adenoma and uncover its potential mechanism for significant
differential changes in linoleic acid and phospholipid metabolism.