IsoForma: An R Package for Quantifying and Visualizing Positional Isomers in Top-Down LC-MS/MS Data

Area of Science:

• Proteomics
• Mass Spectrometry
• Bioinformatics

Background:

• Proteoforms, variations of proteins including post-translational modifications (PTMs), are crucial for biological processes like cell signaling.
• Top-down mass spectrometry (MS) enables direct characterization of intact proteoforms and their modifications.
• Protein positional isomers (PI) are proteoforms with identical mass and modifications but different PTM site combinations, crucial for understanding protein function.

Purpose of the Study:

• To introduce IsoForma, an open-source R package for the relative quantification of protein positional isomers (PI).
• To provide a streamlined and efficient tool for analyzing proteoform data, reducing reliance on manual annotation.

Main Methods:

• Utilized top-down tandem mass spectrometry (MS2) data for proteoform characterization.
• Developed an R package, IsoForma, for automated relative quantification of PI.
• Benchmarked IsoForma against existing workflows for performance and speed.

Main Results:

• IsoForma demonstrated comparable results to existing methods.
• IsoForma significantly improved the speed of PI quantification.
• The package offers a streamlined process, reducing analysis time and manual effort.

Conclusions:

• IsoForma provides an efficient and accessible solution for quantifying protein positional isomers.
• The R package facilitates custom proteoform analysis workflows.
• This tool advances the field of quantitative proteomics and proteoform characterization.