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.