Mass Spectrometry in Systems Biology - Systems Biology: Networks, Models, and Applications - page 24

pathological conditions [23]. In this section, we will discuss analytical
MS techniques applied to a subgroup of polar lipids, phospholipids [79].
The plasma membrane controls the flow of information from and
into the cell by transport of solutes and signaling mechanisms. Beside
proteins, various concentrations and compositions of lipids confer
versatility and plasticity to (i) membranous structures regulating the
communication between the cell and its environment and (ii) mem-
branes of different organelles. Phospholipids, major components of the
membrane bilayer, could be described by two main classes, choline
glycerophospholipids and ethanolamine glycerophospholipids, which
usually localize on the inner and outer leaflet of the membrane respec-
tively. Beside their structural role, phospholipids at the plasma
membrane constitute a reserve of precursors for second messengers in
cell signaling.
Analysis of plasma membrane structures illustrates one of the major
challenges of omics technologies: sample preparation. In order to
understand how membrane sheets integrate proteins and lipids in a
symbiotic manner, we need to simultaneously extract and conserve
these two classes of bioanalytes for further characterization by mass
spectrometry. Two preparative methods hold the promise for an
integrated proteomics-lipidomics analysis. Wu et al. developed a pro-
teomics assay to characterize membrane proteins from nonsolubilized
membrane samples [70,80]. This strategy produces two sets of bioana-
lytes: transmembrane domains embedded in lipid bilayer and the
proteolytically digested soluble domains of membrane proteins.
Potentially, lipids could also be analyzed as well as transmembrane
domains of proteins. Such an approach is one possible way to integrate
proteomics and lipidomics in one analysis. Chloroform/methanol
extraction of lipids complemented by analysis of membrane proteins
(the method proposed by Blonder et al. [81]) provides a different strat-
egy. Though similar to the above-mentioned strategy, this approach
will destroy the topology of the membrane and will hamper analysis of
posttranslational modifications [70].
The Alliance for Cellular Signaling (AfCS) outlined a framework for
global quantitative analysis of signaling pathways in B lymphocytes
and cardiac myocytes [82]. Recently, AfCS released two data sets for
one of their two model systems, the WHEI-231 B lymphoma cell line.
Shu et al. [83] identified 193 phosphorylation sites in 107 proteins using
IMAC followed by LC-MS/MS in B lymphoma cell line treated with
calyculin A (a Ser/Thr phosphatase inhibitor). As part of the AfCS
project, Forrester et al. [21], using a combination of mass spectrometry
techniques (positive ion mode, negative ion mode, MS/MS), generated
a time profile of lipids following the changes in glycerophospholipids
upon stimulation with anti-IgM. It is worth noting that these authors
relied on ESI source as the only separation tool for analysis of complex
mixtures of lipids. Difficulties in coupling MS with separating techniques