Identifying Peptide and Protein Sequences Using DC-MAPP

Proteomic studies generally require the use of software to streamline analysis of tandem mass spectrometry (MS/MS) data for peptide and protein identification. In a recent study published in the Journal of the American Society for Mass Spectrometry, a research team from Vellore Institute of Technology (VIT) discusses a new standalone software that could be an improved method for this type of analysis (1).

Digital software development concept | Image Credit: © tippapatt - stock.adobe.com

The new software program, called Database Creator for Mass Analysis of Peptides and Proteins (DC-MAPP), can create custom databases that house the calculated mass-to-charge (m/z) values of fragment and precursor ions prior to conducting a database search (1). Developed using Python and equipped with a user-friendly graphical interface built with Page/Tcl, DC-MAPP represents a new way to analyze proteins (1).

The researchers describe how DC-MAPP comes with three distinct modules, designed for a specific purpose in mind: custom database creation, precise mass queries, and peptide mass fingerprinting. This division allows the user to choose the module that best fits the analysis that they are conducting.

The research team explained the three modules in-depth, talking about the benefits of each module.

• Custom Database Creation: The first module allows researchers to input peptide and protein sequences of their choice, enabling the creation of custom databases (1). This feature is particularly beneficial for those keen on understanding the intricacies of search engine processes (1).
• Precise Mass Queries: In the second module, users can query m/z values, which are then searched within the custom database to identify specific protein and peptide sequences (1). This functionality is designed to give researchers greater control over their data analysis, enhancing the accuracy and reliability of their findings (1).
• Peptide Mass Fingerprinting: The third module is designed for peptide mass fingerprinting, catering to the analysis of both electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) MS data (1). This capability opens new avenues for researchers seeking to explore post-translational modifications and protein isoforms (1).

The researchers mention that one of the main benefits of DC-MAPP is that it can present the calculated m/z values visually. This attribute is designed to help users conduct post-translational modifications and protein isoform analysis more easily (1).

The research team notes, though, that DC-MAPP is not the perfect software for proteomics applications. Although it rectifies many issues that the traditional software programs had, DC-MAPP does rely on protein and peptide sequences, which makes it less suitable for searches involving spectral libraries (1).

As proteomic research continues to advance into the future, DC-MAPP offers an alternative way for MS data analysis to be conducted, allowing researchers to work with peptide and protein identification differently.

Reference

(1) Pandeswari, P. B.; Isaac, A. E.; Sabareesh, V. Database Creator for Mass Analysis of Peptides and Proteins, DC-MAPP: A Standalone Tool for Simplifying Manual Analysis of Mass Spectral Data to Identify Peptide/Protein Sequences. J. Am. Soc. Mass. Spectrom. 2023, ASAP. DOI: 10.1021/jasms.3c00030