Large scale proteomic strategies rely on database interrogation.
Thus, only referenced proteins can be identified. Recently, Alternative
Proteins (AltProts) translated from nonannotated Alternative Open
reading frame (AltORFs) were discovered using customized databases.
Because of their small size which confers them peptide-like physicochemical
properties, they are more difficult to detect using standard proteomics
strategies. In this study, we tested different preparation workflows
for improving the identification of AltProts in NCH82 human glioma
cell line. The highest number of identified AltProts was achieved
with RIPA buffer or boiling water extraction followed by acetic acid
precipitation.
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