How to Deal With Internal Fragment Ions?

ABSTRACT: Tandem mass spectrometry of peptides and proteins generates 3mass spectra of their gas-phase fragmentation product ions, including N-terminal, C-terminal, and internal fragment ions. While N- and C-terminal ions are routinely assigned and identified using computational methods, internal fragment ions are often difficult to annotate correctly. They become particularly relevant for long peptides and full proteoforms where the peptide backbone is more likely to be fragmented multiple times. Internal fragment ions potentially offer tremendous information regarding amino acid sequences and positions of post-translational modifications of peptides and intact proteins. However, their practical application is challenged by the vast number of theoretical internal fragments that exist for long amino

SUBMITTER: Grimaud A 

PROVIDER: S-EPMC12127546 | biostudies-literature | 2025 May

REPOSITORIES: biostudies-literature