Database Creator for Protein/Peptide Mass Analysis, DC-PPMA: A novel
standalone computational tool for simplifying the analysis of MS/MS data
to identify protein/polypeptide sequences by different proteomic
approaches
Abstract
Rationale: Proteomic studies typically involve use of different types of
softwares for annotating experimental tandem mass spectrometric data
(MS/MS) and thereby simplify the process of peptide and protein
identification. For such annotations, these softwares calculate the m/z
values of the peptide/protein precursor and fragment ions, for which a
database of protein sequences must be provided as input file. The
calculated m/z values are stored as another database, which the user
usually cannot view. ‘Database Creator for Protein/Peptide Mass
Analysis’ (DC-PPMA) is a novel standalone software that can create
custom databases and the user can view the custom database containing
the calculated m/z values of precursor and fragment ions. Methods:
Python language was used for implementation and the graphical user
interface was built with Page/Tcl, making this tool more user-friendly
and easier to analyze. DC-PPMA is freely available at
https://vit.ac.in/PPMA/. Results: DC-PPMA contains three modules.
Protein/peptide sequences as per user’s choice can be entered as input
to the first module for creating custom database. In the second module,
m/z values must be queried-in, which are searched within the custom
database to identify protein/peptide sequences. The third module is
suited for peptide mass fingerprinting, for which data arising from both
ESI and MALDI MS can be utilized. Conclusions: Mass spectral data
acquired from any proteomic approach: bottom-up, middle-down and
top-down can be interrogated with DC-PPMA. A major facet of DC-PPMA is
that the user can ‘view’ the custom database containing the m/z values
of the precursor ions (e.g., proteolytic peptides) and the respective
fragment ions (e.g., b & y ions), prior to the database search. The
feature of ‘viewing’ the custom database cannot only be helpful for
better understanding the search engine processes; but also, for
‘designing multiple reaction monitoring (MRM) methods’.
Post-translational modifications and protein isoforms too can be
analyzed.