Protein post-translational modifications (PTMs) play crucial roles in regulation of protein function and cell signaling, and abnormalities in protein PTMs are both causes and consequences of disease. Mass spectrometry (MS) is widely used to analyze protein PTMs. In this study, we developed an original database, ModProt (Post-Translational Modification Map of Proteome), to integrate our laboratory data and literature information regarding PTM sites. To develop the ModProt database, we constructed a web-based laboratory information management system (LIMS). This system allows us to administer the ModProt database and to view PTM site maps and corresponding protein information including amino acid sequences, official gene symbols, UniProt accessions/IDs, chromosome number/positions, and additional description. The ultimate goal of the ModProt database is to achieve PTM-based diagnosis and personalized medicine through detection of abnormal PTMs by comparing PTM site maps in healthy and disease states using the database.

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S-nitrosylation, a post-translational modification of the thiol group of cysteine residues by nitric oxide (NO), has emerged as a new mode of signal transduction and regulation of protein function. It has recently been shown that S-nitrosylation may result in various protein dysfunctions. However, an improved S-nitrosylation analysis method is needed to achieve high sensitivity and quantitative accuracy. We hypothesized that an analysis method using fluorescence dye could detect S-nitrosylated proteins at a higher sensitivity than that of the conventional method. In this study, we developed a procedure for analyzing S-nitrosylated proteins using CyDye (the CyDye switch method). This CyDye switch method for detecting S-nitrosylated proteins was developed based on the biotin-switch method for analyzing S-nitrosylated proteins. We analyzed NO donor-induced S-nitrosylated proteins in a model protein and at the cellular level. We demonstrated that this CyDye switch method could detect specific S-nitrosylated proteins using SDS-PAGE and mass spectrometry. Our results indicate that the optimized CyDye switch method is suitable for the detection of the post-translational S-nitrosylation of proteins.

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