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Anal Chem. 2020 Jan 7;92(1):1122-1129. doi: 10.1021/acs.analchem.9b04188. Epub 2019 Dec 24.

Optimized Sample Preparation Workflow for Improved Identification of Ghost Proteins.

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Inserm, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM) , Université de Lille , F-59000 Lille , France.
Department of Biochemistry , Université de Sherbrooke , Quebec , Sherbrooke , Canada.
Institut Universitaire de France (IUF) , Paris , France.


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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