Mapping the Genotype–Phenotype Relationship in Cellular Signaling Networks: Building Bridges Over the Unknown - Systems Biology: Networks, Models, and Applications - page 150

Mass spectrometry has enjoyed tremendous success in the character-
ization of intermediate phenotypes by delineating the composition of
protein complexes and posttranslational modifications on proteins [60].
After protein purification with two-dimensional electrophoresis or
liquid chromatography, mass spectrometry can be used to precisely
measure the mass of peptide fragments to identify protein complex
composition. In tandem, two mass spectrometers can be used to identify
the amino acid composition of peptide fragments and thus characterize
posttranslational modifications like phosphorylations and methylations.
As an example of the utility of this technique, it was recently used to
characterize the dynamic phosphorylations of proteins associated with
T-cell activation and the inhibition of the overactive BCR-ABL kinase in
response to the cancer therapeutic STI571 (Gleevec) [61]. This study
identified 64 phosphorylation sites on 32 proteins.
Array-profiling has recently been applied to characterize intermediate
phenotypes. Protein arrays are based on the ordering of protein-binding
compounds (primarily antibodies) to indicate the presence and inten-
sity of proteins in a given sample [62]. However, since protein binding
typically requires the native conformation of a given protein to be
effective, such array approaches have been fraught with difficulty.
Nevertheless, there is emerging evidence of the utility of such approaches.
For example, 96-well microtiter plates were used to characterize ErbB
receptor tyrosine kinases in human tumor cells [63].
Together, the technologies that identify the presence of proteins
and measure their concentrations generate so-called “proteomic” data.
Additional technologies provide what has been called “metabolomic”
data, or the identification of metabolites in a cell and associated concen-
tration measurements. What questions do these technologies answer?
Under the given experimental conditions, two proteins do or do not
interact with each other. These methods provide some indication of the
mechanisms of interactions. For example, mass spectrometry can iden-
tify phosphorylation sites on a given protein. The final result of all such
techniques is the identification of which proteins are present, with which
cellular constituents they interact, and the concentrations of some of
these components. However, these data alone do not indicate how
individual signaling events or intermediate phenotypes contribute to
network properties.
FUNCTIONS OF INTERACTING COMPONENTS: BRIDGING
INTERMEDIATE PHENOTYPES TO ENDPOINT PHENOTYPES
Methods for characterizing the function of interacting components
generate data on how intermediate phenotypes contribute to global
properties and endpoint phenotypes. Perhaps one of the most common
techniques for measuring the global function of network components