Reagent/Resource	Reference or source	Identifier or catalog number
Experimental models
BY4741 derived MATa, his3∆1 leu2∆0 met15∆0 ura3∆0, arg4Δ, Lys9Δ	This study
MG1655 derived F‐, Lambda‐, rph‐1 ΔlysA ΔargA	Starosta et al (2014)
Chemicals, enzymes and other reagents
Silica beads	Fluka	S5631‐500g
Guanidine thiocyanate	Thermo Fisher Scientific	BP221‐1
RNaseA+T1 mix	Ambion	AM2286
4–20% Mini‐PROTEAN TGX gel	Biorad	4561095
Imperial protein stain	Thermo Fisher Scientific	24615
DNase I	New England Biolabs	M0303
Cyanase	Serva	18542.01
Nuclease P1	Sigma	N8630
Urea	Acros organics	327380050
Vivaspin polyethersulfone concentrator	GE Healthcare	28‐9323‐61
MagTrypsin	Takara	635646
TiO2 Mag Sepharose	GE healthcare	28‐9440‐10
Lambda phosphatase	New England Biolabs	P0753S
[13C6]‐lysine	Cambridge Isotope Laboratories	CLM‐2247
[13C6]‐arginine	Cambridge Isotope Laboratories	CLM‐2265
Software
Xi v 1.6.731	https://github.com/Rappsilber-Laboratory/XiSearch
MaxQuant 1.6.1	Cox and Mann (2008)
Perseus 1.6.0.7	Tyanova et al (2016)
imputeLCMD package version 2.0 for R	https://rdrr.io/cran/imputeLCMD/ and Lazar et al (2016)
Other
QExactive mass spectrometer	Thermo Fisher Scientific
Fusion Lumos mass spectrometer	Thermo Fisher Scientific