Supplemental Data

• Supplementary Figures - Supplementary Figure 1: Schematic of the new FAIMS interface. Supplementary Figure 2: Ion transmission and stability of the new FAIMS proteotype by direct infusion of Angiotensin II. Supplementary Figure 3: Resolution of the FAIMS interface using a BSA tryptic digest as benchmark. Supplementary Figure 4: Reproducibility and robustness of FAIMS-Fusion LC-MS system with 100 replicate injections of HEK293 digest at a fix CV value of -45 V. Supplementary Figure 5: Reproducibility and robustness of regular LC-MS system with 27 replicate injections of HEK293 digest. Supplementary Figure 6: Optimization of FAIMS CV stepping program. Supplementary Figure 7: Comparison between SPS and FAIMS based TMT quantifications. Supplementary Figure 8: The heat shock response affects proteins with similar functions in the same demeanor.
• Supplementary Table 1 - List of FAIMS LC-MS/MS experiments at CV -45V for 100 Replicates
• Supplementary Table 2 - List of peptide identifications of LC-MS/MS experiments with and without FAIMS for 500ng HEK293 digest/injection.
• Supplementary Table 3 - List of protein identifications of LC-MS/MS experiments with and without FAIMS for 500ng HEK293 digest/injection.
• Supplementary Table 4 - List of quantified dynamic Protein groups assigned to a cluster with a membership > 0.9. These proteins have at least 2 unique peptides and TMT reporters present in at least 7 TMT channels.