A Systematic Approach to Selecting the Right Tool for Mass Spectrometry Data Analysis in Protein and Peptide Bioanalysis

Mass spectrometry (MS) has emerged as an imperative technology in protein and peptide bioanalysis, offering unparalleled sensitivity, specificity, and dynamic range. However, the complexity of MS datasets, particularly those arising from advanced acquisition methods and diverse biological samples, necessitates the use of specialized data analysis tools. Therefore, selecting the appropriate software is crucial for accurate data interpretation, reproducibility, and regulatory compliance. This review presents a systematic framework to guide researchers in selecting the most suitable MS data analysis tools, spanning key categories such as quantitative analysis, post-translational modification (PTM) identification, and data-independent acquisition (DIA) workflows, tailored to specific experimental goals in protein and peptide bioanalysis.