*4.5. Nano-LC-ESI-MS*/*MS Analysis*

Digested peptides were separated using a Dionex UltiMate 3000 RSLCnano system (Thermo Fisher Scientific, Waltham, MA, USA). Tryptic peptides from the bead column were reconstituted in 100 μL of 0.1% formic acid and separated on an Acclaim™ Pepmap 100 C18 column (500 mm × 75 μm i.d., 3 μm, 100 Å) equipped with a C18 Pepmap trap column (20 mm × 100 μm i.d., 5 μm, 100 Å; Thermo Fisher Scientific, Waltham, MA, USA) over 200 min (250 nL/min) using a 0–48% acetonitrile gradient in 0.1% formic acid and 5% DMSO for 150 min at 50 ◦C. The LC was coupled to a Q Exactive™ Plus Hybrid Quadrupole-Orbitrap™ mass spectrometer with a nano-ESI source. Mass spectra were acquired in a data-dependent mode with an automatic switch between a full scan and 10 data-dependent MS/MS scans. The target value for the full scan MS spectra, selected from a 350 to 1800 *m*/*z*, was 3,000,000 with a maximum injection time of 50 ms and a resolution of 70,000 at *m*/*z* 400. The selected ions were fragmented by higher-energy collisional dissociation in the following parameters: 2 Da precursor ion isolation window and 27% normalized collision energy. The ion target value for MS/MS was set to 1,000,000 with a maximum injection time of 100 ms and a resolution of 17,500 at *m*/*z* 400. Repeated peptides were dynamically excluded for 20 s. All MS data were measured once per sample and have been deposited in the PRIDE archive (www.ebi.ac.uk/pride/archive/projects/PXD016571) [57] under Project 1-20191129-77373 12.

## *4.6. Database Searching and Label-Free Quantitation*

The SwissProt human database (May 2017) was searched for acquired MS/MS spectra using SequestHT on Proteome discoverer (version 2.2, Thermo Fisher Scientific, USA) [58]. The search parameters were set as default including cysteine carbamidomethylation as a fixed modification, and N-terminal acetylation and methionine oxidation as variable modifications with two miscleavages. Peptides were identified based on a search with an initial mass deviation of the precursor ion of up to 10 ppm, with the allowed fragment mass deviation set to 20 ppm. When assigning proteins to peptides, both unique and razor peptides were used. Label-free quantitation (LFQ) was performed using peak intensity for unique peptides of each protein.
