JUMPptm

JUMPptm performs integrative identification and analysis of post-translational modifications (PTMs) from unenriched, ultra-deep whole-proteome mass spectrometry datasets to enable pan-PTM discovery and quantitative comparison across conditions.

Key Features:

• Integration of multiple search engines: Integrates JUMP, MSFragger, and Comet to enhance sensitivity and specificity of PTM detection.
• Iterative multi-stage strategy: Employs an iterative multi-stage strategy using de novo sequencing tags, customized database searches, peptide filtering techniques, and analysis of unassigned spectra.
• Pan-PTM identification: Identifies a wide array of PTMs including phosphorylation, methylation, acetylation, and ubiquitination from unenriched datasets.
• TMT-based quantification: Incorporates TMT-based quantification to evaluate abundance changes of PTM peptides across conditions or disease stages.

Scientific Applications:

• Alzheimer's disease proteome analysis: Applied to deep brain proteome data from Alzheimer's disease samples, identifying 34,954 unique peptides carrying various PTMs.
• Disease progression and mitochondrial acetylation: Identified 482 PTM peptides dysregulated across AD progression and a notable decrease in acetylation of multiple mitochondrial proteins.
• Tau protein PTM mapping: Mapped 60 PTM sites on the Tau protein to characterize its modification landscape.

Methodology:

Integration of JUMP, MSFragger, and Comet; iterative multi-stage analysis using de novo sequencing tags, customized database searches, peptide filtering, and analysis of unassigned spectra; and TMT-based quantitative analysis.