Fig. 3: Biological validation of phosphoproteomics platforms using EGF stimulation.
From: Fast and deep phosphoproteome analysis with the Orbitrap Astral mass spectrometer
A Reproducibility of detected phosphosites across biological triplicates for three phosphoproteomics platforms—Orbitrap Astral, Orbitrap Ascend, and timsTOF Pro33. Intensity distribution of phosphosites consistently detected (3 out of 3 EGF stimulated replicates) by Orbitrap Astral with overlap indicated for (B) timsTOF Pro and (C) Orbitrap Ascend. D Intensity distribution of phosphosites consistently detected (3 out of 3 EGF stimulated replicates) by timsTOF Pro with overlap indicated for Orbitrap Astral. E Venn diagram of phosphosites detected across all three mass spectrometry platforms. F Volcano plots of phosphosites between EGF stimulation and control across platforms with phosphosites meeting the differential expression criteria (fold-change > 2, p < 0.05 via two-sided t-test without multiple testing correction) indicated in blue and EGFR phosphosites labeled. G Pathway enrichment analysis using the NCATS BioPlanet terms was performed for the three platforms with EGF/ERBB-associated terms indicated in blue. Source Data are provided as a Source Data file.
