Reagent/Resource	Source	Identifier
Chemicals, Enzymes, and other reagents
Bovine Serum Albumin (BSA)	New England BioLabs Inc.	P8108S
HeLa tryptic digest	Pierce	1862824
Yeast (S. cerevisiae) tryptic digest	Promega	V746A
E. coli tryptic digest	Waters	186003196
Triethylammonium bicarbonate (TEAB)	Sigma Aldrich	T7408
Ammonium bicarbonate (ABC)	Merck	1.01131
Urea	Sigma Aldrich	U1250
Dithiothreitol (DTT)	Sigma Aldrich	D0632
Chloroacetamide (CAA)	Sigma Aldrich	C0267
Formaldehyde: ‘light’ (CH2O)	Sigma Aldrich	F8775
Formaldehyde‐d2‐solution: ‘intermediate’ (CD2O)	Sigma Aldrich	492620
Formaldehyde‐13C, d2‐solution: ‘heavy’ (13CD2O)	Sigma Aldrich	596388
Sodium cyanoborohydride: ‘light’ (NaBH3CN)	Sigma Aldrich	156159
Sodium cyanoborodeuteride: ‘heavy’ (NaBD3CN)	Sigma Aldrich	190020
Lichropur® ammonia solution, 25%	Merck	5.33003
LC–MS‐grade water	Fisher Chemical	W6‐4
Trifluoroacetic acid (TFA)	Sigma Aldrich	8.08260
Formic acid (FA)	Sigma Aldrich/Merck	#64‐18‐6
Acetonitrile	Sigma Aldrich/Merck	#75‐05‐8
CDS Empore C18 Extraction Disks	Empore	13‐110‐018
Trypsin	Sigma‐Aldrich	T6567
Lys‐C	FUJIFILM Wako	125‐05061
Lys‐N	ImmunoPrecise Antibodies (Europe) BV	L101
Software
MaxQuant (2.0.1)	https://maxquant.org/	N/A
DIA‐NN (1.8.1)	https://github.com/vdemichev/DiaNN	N/A
RStudio (2022.07.2) and R (4.2.2)	https://posit.co/download/rstudio‐desktop/	N/A
Jupyter Notebook	https://jupyter.org/	N/A
RefQuant	https://github.com/MannLabs/refquant	N/A
Other
384‐well plates	Eppendorf	#0030129547
Adhesive PCR Sealing Foil Sheets	Thermo Scientific	#AB‐0626
Bravo robot	Agilent
ThermoMixer	Eppendorf	#460‐0223
Mastercycler X50h	Eppendorf	#63160000
NanoDrop One/OneC Microvolume UV–Vis Spectrophotometer	Thermo Fisher	@ND‐ONEC‐W
EvoSep One	EvoSep	#EV‐1000
Evotip Pure	EvoSep	#EV‐2011
timsTOF HT	Bruker Daltonik GmbH	N/A
timsTOF SCP	Bruker Daltonik GmbH	N/A
timsTOF Ultra	Bruker Daltonik GmbH	N/A
Orbitrap Exploris 480	Thermo Scientific	N/A
Column oven	Sonation lab solutions	#PRSO‐V2
Aurora Elite CSI	IonOpticks	AUR3‐15075C18‐CSI