Deep Coverage and Extended Sequence Reads Obtained with a Single Archaeal Protease Expedite <i>de novo</i> Protein Sequencing by Mass Spectrometry.

ABSTRACT: The ability to sequence proteins without reliance on a genomic template defines a critical frontier in modern proteomics. This approach, known as de novo protein sequencing, is essential for applications such as antibody sequencing, microbiome proteomics, and antigen discovery, which require accurate reconstruction of peptide and protein sequences. While trypsin remains the gold-standard protease in proteomics, its restricted cleavage specificity limits peptide diversity. This constraint is especially problematic in antibody sequencing, where the functionally critical regions often lack canonical tryptic sites. As a result, exclusively trypsin-based approaches yield sparse reads, leading to sequence gaps. Multi-protease and hybrid-fragmentation strategies can improve the sequence co

SUBMITTER: Shamorkina TM 

PROVIDER: S-EPMC12154832 | biostudies-literature | 2025 May

REPOSITORIES: biostudies-literature