PEAKS Studio 8.5 New Feature Highlights

SILAC Quantification

Read our application note for SILAC-based quantitative proteome analysis with PEAKS.

PEAKS SILAC quantification provides comparable results to MaxQuant.

Label Free Quantification

  • Top-three unique peptides selected for LFQ
  • Improved LFQ accuracy by enabling exclusion of 1) peptides with both modified and unmodified forms, and 2) redundant peptides
  • Peptide-level quantification provided in peptide table
  • Sample clustering and correlation views

PTM Profiling

  • Enhanced PTM profiling enabled in:
    • Identification result (LEFT): multi-sample PTM comparisons; MS2 spectra comparison of modified v.s. unmodified peptides
    • Quantification (Q) result (RIGHT): confident PTM quantitation filtered by A-score or minimum ion intensity threshold; normalized by protein expression levels; PTM site clustering; modified peptide / feature details

Global Comparative View

  • Protein/peptide spectral counts and MS1 area in each sample provided in identification result for semi-quantitative analysis

EThcD Data Analysis

  • Advantages of EThcD fragmentation enables confident peptide identification