Conclusions
Due to continuous advancements in computational methods, the software and databases used for proteomics are also rapidly evolving. The significance of optimal database for protein identification by MS/MS has been lucidly delineated by Kumar et al. 2017 [18]. Even to devise optimal scoring algorithm for better peptide/protein identification from the data of MS/MS, firstly it is imperative to construct a good database. Consequently, the need to build custom database has become inevitable. The custom databases can be built: (i) according to the individual researcher’s specific project and objectives; (ii) for in-house requirements and (iii) to expedite the data analysis and interpretations. These are only a few reasons/purposes (among many), as to, why custom databases are essential for proteomics. Therefore, our objective was to make a standalone computational tool that can ease the process of creating custom database, which can simplify the analysis of MS/MS data of proteome/protein/peptidome. The custom database built with DC-PPMA enables the user to know, what are the ‘m/z values’ that are involved in the MS and MS/MS database search process, for a given ‘protein/peptide sequence database’.
Though some or all of the aforementioned features of DC-PPMA are available in several proprietary software tools that comes along with mass spectrometer, such proprietary tools are either not accessible to everyone or would have limited access. Further, there are online tools which also have the same or very similar functionalities as that of DC-PPMA. However, to the best of our knowledge, we believe that DC-PPMA is unique in that it is a standalone tool, which is freely downloadable. So, DC-PPMA is accessible to everyone. Furthermore, using a particular custom database created by DC-PPMA, both MALDI MS/MS and ESI MS/MS data can be analysed, irrespective of the manufacturer. Another important aspect is that DC-PPMA can be successfully applied for any of the three proteomic approaches, viz., bottom-up, middle-down and top-down. Thus, it can be helpful for both academicians and industrial researchers, particularly for biotechnology industries involved in protein/proteomic/peptidomic investigations. Academicians can consider DC-PPMA as a tool to teach novices and students.