The generation of high-quality peptide spectrum annotations is critical for ensuring data quality and the assignment of novel modifications. While many existing tools provide basic spectrum annotation capacities, they often lack the flexibility and specificity required for complex spectral annotation, particularly those involving multiple labile modifications. This limitation makes large-scale analyses of extensively modified peptides prohibitively labor-intensive and inefficient, hindering detailed investigations of such datasets. Here, we present a highly customizable interactive “MassSpectrum Analyzer”, that integrates peptide fragmentation associated ion types (a/b/c’/x/y/z.) with user-defined custom ion series associated with labile modifications and diagnostic ions. This tool supports bulk analysis of peptide spectra and allows high-throughput export of publication-ready mass spectrum visualizations from peptide-spectrum matches generated by popular software tools such as MSFragger and MaxQuant. A distinctive feature of MassSpectrum Analyzer is its capability to rescore spectra by incorporating labile fragment ions, which dramatically improves the scoring of extensively modified peptides and more accurately reflects assignable features. Additionally, the software allows extraction and comparison of fragment ion counts and intensities between differentially modified peptides to assess distinct fragmentation patterns. Using MassSpectrum Analyzer, complex labile losses associated with peptides multiply derivatized with the fixed-charge molecule (2-Aminoethyl)trimethylammonium chloride hydrochloride (AETMA) on carboxyl groups were easily identified using the spectral annotation module (1). Furthermore, improvements in ETD fragmentation of protein C-terminal peptides modified with AETMA were quantified by comparing fragment ion counts, allowing straightforward assessment of fragmentation efficiency (1). Combined, MassSpectrum Analyzer streamlines the annotation of complex peptide fragmentation patterns and enabling rapid, high-throughput extraction of publication-ready spectra through an intuitive and user-friendly interface.