Approaches and Applications of Quantitative LC-MS for Proteomics and Activitomics - LC-MS/MS in Proteomics: Methods and Applications - page 9

combinations of mutations on tumour suppressors and onco-
genes may affect metabolism in cancer cells. Because of its ability
for in-depth analysis of metabolites (which reflect the activities
of metabolic enzymes), LC-MS-based activitomic/metabolomic
studies should contribute to the advancement of this field.

LC-MS is increasingly used to multiplex the quantitative analy-
sis of lipids, whose levels, in turn, reflect the activity of enzymes
involved in their production, modification and degradation.
Lipidomics can therefore be regarded as an activitomic approach
to quantify the activity of enzymes with roles in lipid metabolism,
including lipid kinases and phosphatases. As with protein kinases
and protein phosphatases, lipid kinases and phosphatases have
important roles in controlling signalling pathways with roles in
fundamental biological processes and in diseases such as cancer.
Therefore, quantifying the activity of lipid kinases/phosphatase
pairs also has numerous applications

2.1.3. Lipidomics

in basic and applied

research.
Phosphoinositide (PI) research is an example of a lipidomic/
activitomic application in which LC-MS could have a major role
( 29 ) . PI signalling has roles in insulin and antigen signalling
and in cancer. Once activated, receptors for growth factors, anti-
gens and certain hormones recruit PI-kinases to plasma mem-
branes and cellular endomembranes, where they phosphorylate
PIs to produce PI-phosphates (PIPs). PI 3-kinases (PI3K) are
well-studied contributors of the pool of PIP species, many of
which are second messengers that activate several intracellular
pathways through their ability to interact with proteins contain-
ing phospholipid recognition domains (including FYVE and PH
domains) ( 30 ) .
The PIK3CA gene, encoding for a catalytic isoform of PI3K
termed p110 , is an oncogene found to be frequently activated

(via mutations and overexpression) in many different forms of
cancer, while the lipid phosphatase opposing the p110

α

α

reac-
tion (termed PTEN) is frequently inactivated in several differ-
ent tumour types. Taken together, the PI signalling pathway is
one of the most frequently deregulated pathways in cancer ( 31 ) .
In addition to PI3K and PTEN, several other lipid kinases and
phosphatases contribute to the production of PIPs with different
phosphate content and with different isometry. Thus class I PI3Ks
preferentially phosphorylate PI-4,5-bisphosphate (PI-4,5-P2) to
produce PI-3,4,5-trisphosphate (PIP3), while classes II and III
PI3K use PI as a substrate to produce PI-3P. PI4K and PI5K
lipid kinases also exist that phosphorylated PI at 4 and 5 positions
to produce PI4P and PI5P, respectively ( 32 , 33 ) . This complex-
ity is increased by the existence of the lipid phosphatases, SHIP1
and SHIP2, that dephosphorylate PIP3 at different positions than
PTEN to form PI-3,5-P2 and PI-3,4-P2 ( 34 ) .