LRP2: A proteogenomics pipeline for long-read informed protein isoform analysis and discovery.

LRP2 is an end-to-end long-read proteogenomics pipeline that integrates transcript discovery and mass spectrometry to detect novel peptides and improve protein isoform inference.

• Why it matters: Although long-read RNA sequencing plus mass spectrometry can empirically support which RNA isoforms are translated, comprehensive workflows spanning isoform discovery, ORF prediction, peptide identification, and protein inference are limited.
• What they did: LRP2, implemented in Nextflow, scales transcript discovery to hundreds of samples using PacBio Isocall, applies SQANTI QC, predicts proteomes with CPAT and SQANTI Protein, performs differential expression/usage with edgeR, DRIMSeq, and a long-read LeafCutter adaptation, and integrates DDA/DIA evidence via FragPipe.
• The result: When used as an integrated pipeline, LRP2 enables detection of novel peptides and improves protein isoform inference to confirm protein isoform translation.