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.