Use of ENCODE Resources to Characterize Novel Proteoforms and Missing Proteins in the Human Proteome

We
describe the utility of integrated strategies that employ both
translation of ENCODE data and major proteomic technology pillars
to improve the identification of the “missing proteins”,
novel proteoforms, and PTMs. On one hand, databases in combination
with bioinformatic tools are efficiently utilized to establish microarray-based
transcript analysis and supply rapid protein identifications in clinical
samples. On the other hand, sequence libraries are the foundation
of targeted protein identification and quantification using mass spectrometric
and immunoaffinity techniques. The results from combining proteoENCODEdb
searches with experimental mass spectral data indicate that some alternative
splicing forms detected at the transcript level are in fact translated
to proteins. Our results provide a step toward the directives of the
C-HPP initiative and related biomedical research.