Chemical modificomics: a novel strategy for efficient biomarker discovery through chemical modifications on a target peptide

Abstract

This manuscript describes a proof-of-concept study to develop a novel “omics” strategy, referred to as “chemical modificomics”, for efficient biomarker discovery. Proteins and peptides are exposed to higher chemical stresses during some physiological events, such as increased oxidative stress from the degenerative diseases of aging. Therefore, the resulting chemical modifications can provide significant information about biological events. However, quantitative analyses of bioactive peptides and proteins in specific diseases have relied almost exclusively on the use of immunoassay-based procedures, without concern for possible chemical modifications and subsequent changes of activity/conformation. Therefore, we focused only on specific bioactive peptides and proteins closely related to a target disease, and exhaustively screened all chemical modifications for efficient biomarker discovery. The strategy involves two tactics: (1) backbone-specific clean-up methodology by recycling commercially available antibodies and (2) mass spectrometric screening methodology to provide an overview of unknown chemical modifications on a specific target. In this study, seven chemically modified angiotensin (Ang) IIs were employed as model compounds. The clean-up was conducted by immunoaffinity purification using commercially available anti-Ang II antibody (polyclonal). Screening was then performed by precursor ion scan using y₂ ion, which is a common C-terminal fragment without including the modifications. This strategy can be simply applied to screen various chemical modifications including posttranslational modifications on a specific peptide and protein analyzed by immunological methods.