sample processing, biomarker discovery, and validation for DM was recently
presented by Shao et al.^173 The authors present complete strategy for biomarker
discovery based on antibody-based methods and mass-spectrometry-based proteo-
mics (including 1 and 2-D electrophoresis-MS/MS and LC-MS/MS), as well as
other high-resolution MS methods, followed by methods for validation of new
biomarker candidates. The mostly used sample for these studies is human plasma.
However, the above-discussed high dynamic range of protein expression in this
body fluid complicates the high-throughput analysis and alternative specimens of
other body fluids such as tears and saliva, and finally, the use of fresh frozen tissue
samples was also discussed. Unfortunately, no alternative validated and registered
new biomarkers for early detection of this disease are yet discovered (see also Chen
et al.^174 ).
5.6 Allergy
Allergy can be considered as IgE antibody-mediated response of an organism
toward an allergen (type I hypersensitivity). Elevated levels of IgE in plasma
evoke immunological disorder upon exposure to molecules (allergens) that in a
highly specific manner binds to these IgE. Allergens can be classified according to
their ways of interacting with the host: airborne allergens invade the respiratory
system, food allergens are taken up by the gastrointestinal tract (GIT), and contact
allergens act through the skin.
A wide (and most important) group of allergens are proteins. Thus, proteomics is
of high importance for the identification and structure analysis of proteinaceous
allergens and characterization of immunologically important PTMs of proteins.
Basic and widely applied proteomic approaches for identification of new allergens
are based on 1D and 2D electrophoretic separations of potentially allergenic
extracts and IgE immunoblot detection. Next level involves partial protein structure
determination using mass spectrometry (MS), as well as demonstrated by Chuang
et al.^175 A gel-based proteomic approach was used in combination with MS for
partial primary structure determination of cockroach allergens with one step for-
ward using bioinformatic analysis of allergen databases (e.g., the Food Allergy
Research and Resource Program Allergen Database) in order to identify potentially
homologous or cross-reactive allergens. However, partial sequence determination
is not enough to offer reliable conclusions about potential interactions of allergens
with IgE, but according to the authors, this was a step toward personalized immu-
notherapies. Detail analysis of all four levels of protein (allergen) structure is a first
(^173) Shao et al. ( 2015 ).
(^174) Chen et al. ( 2012 ), pp. 1293–1307.
(^175) Chuang et al. ( 2010 ), pp. 3854–3867.
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