Biology Reference
In-Depth Information
software and database development. Most proteomics journals have actu-
ally defined guidelines for publishing proteomics data that comply with
standards. Publicly accessible standardized proteomic data resources will
grow and spread. Automated procedures for the design and update of
such databases will therefore be essential to keep up with the production
and with the increasing need to retrieve and mine the data. Section 4 of
this chapter emphasizes these aspects.
Thirdly, protein expression is yet to be adequately measured and
quantified for the extraction of reliable differential quantitative data from
MS experiments. In this context, comparative tools will remain essential
for data interpretation. 2-DE gels now share the proteomics scene with
other high-resolution separation techniques (e.g. LC), which when com-
bined with MS, produces large, highly correlated datasets. Exploiting the
correlations that exist within these datasets allows for the extraction of
information that cannot be visible when exclusively analyzing individual
spectra. The 2-D visual representation of LC-MS data helps in tracking
biomarkers and comparing peptide profiles. Adding tools for the quanti-
tative analysis of MS data from isotope-labeled or label-free complex mix-
tures is the next requisite. Incidentally, a current bottleneck is the huge
size of data files that would warrant a universal format for compressed
raw spectrum storage. We are also committed to solving this critical
point, as mentioned throughout the text.
2. Proteome Imaging
Protein separation techniques exploit the diversity of proteins, including
their size, shape, electrical charge, molecular weight, hydrophobicity, and
predisposition to interact with other proteins. A number of technologies
performing large-, medium-, or small-scale separation of complex protein
mixtures have been investigated, such as capillary and gel electrophore-
sis, microchannel, protein chips, LC, and high-performance liquid chro-
matography (HPLC). Among these separation technologies, gel
electrophoresis and LC coupled to mass spectrometers are well suited to
display proteomes in a form that is amenable to human vision and com-
puter analysis; this can subsequently facilitate the comparison of two or
more samples and assist protein identification.
