PTMphinder

PTMphinder localizes post-translational modifications within proteomic datasets and extracts surrounding motifs as an R package to generate proteome-specific motif backgrounds for statistical analysis.

Key Features:

• ParseDB: Reformats proteome databases for downstream PTM localization and motif extraction.
• PhindPTMs: Localizes PTMs to specific amino acid residues within full protein sequences.
• ExtractBackground: Extracts motifs surrounding identified PTM sites and builds proteome-specific motif backgrounds for statistical analysis.
• motif-x integration: Supports downstream motif discovery and analysis using motif-x.
• Mass-spectrometry compatibility: Processes PTM site information derived from mass-spectrometry-based proteomics datasets.

Scientific Applications:

• Developmental biology: Enables identification and localization of PTMs to study regulation during development.
• Cancer research: Supports analysis of PTM patterns relevant to oncogenesis and tumor signaling.
• Infectious diseases: Facilitates characterization of host and pathogen PTMs in infection contexts.
• Motif enrichment and statistical analysis: Provides proteome-specific backgrounds for statistical assessment of PTM-site motifs.

Methodology:

Reformats proteome databases, localizes PTMs to amino acid residues within full proteins, extracts surrounding motifs to build proteome-specific motif backgrounds, and supports downstream analysis with motif-x.