Digging Deeper in a million-spectral dataset: Analysis of 3D-fractionated salivary proteome by using search algorithms for high-mass accuracy data.

摘要

Salivary proteome was analyzed using search algorithms for high mass accuracy data sets to generate a confident list of proteins and peptides. The effect of dynamic range compression ( DRC) on relative abundance was analyzed using Scaffold Q+ and proteins that are enriched after or reduced after ProteoMiner treatment were identified. The effect of DRC on relative ranking of most frequent predicted modifications was analyzed using high confidence peptides from ProteinPilot results and PDST Excel based application. The relative ranking of most predicted modifications changed significantly after ProteoMiner treatment. This orthogonal approach of using Max Quant and ProteinPilot workflow on such a large dataset provides a comprehensive analysis of dataset.