REAGENT or RESOURCE	SOURCE	IDENTIFIER
Chemicals, peptides, and recombinant proteins
Water, Optima, LC-MS Grade, Optima, Fisher Chemical	Fisher Scientific	Cat#10509404; CAS: 7732-18-5
Acetonitrile, Optima, LC-MS Grade, Fisher Chemical	Fisher Scientific	Cat#10489553; CAS: 75-05-8
Thermo Scientific Pierce Formic Acid, LC-MS Grade	Fisher Scientific	Cat#13454279; CAS: 64-18-6
Methanol, Optima LC/MS Grade, Thermo Scientific	Fisher Scientific	Cat#10767665; CAS: 67-56-1
Yeast nitrogen base without amino acids	Sigma-Aldrich	Cat#Y0262
D-(+)-Glucose	Sigma-Aldrich	Cat#G7021; CAS: 50-99-7
DL-Dithiothreitol (BioUltra, for molecular biology, >=99.5%)	Sigma Aldrich	Cat#43815; CAS: 3483-12-3
Iodoacetamide (BioUltra)	Sigma Aldrich	Cat#I1149; CAS: 144-48-9
solid-glass beads (borosilicate, diam 4 mm)	Sigma Aldrich	Cat#Z143936
ammonium bicarbonate (eluent additive for LC-MS)	Sigma Aldrich	Cat#40867; CAS: 1066-33-7
Urea (puriss. P.a., ACS reagent, reag. Ph. Eur., >=99.5%)	Honeywell Research Chemicals	Cat#33247H; CAS: 57-13-6
Acetic acid (Eluent additive for LC-MS)	Honeywell Research Chemicals	Cat#49199; CAS: 64-19-7
Trypsin (Sequence grade)	Promega	Cat#V5117
iRT peptides	Biognosys	Cat#Ki-3002-b
Deposited data
Raw proteome data	This study	ProteomeXchange: PXD036062
Processed proteome data	This study	Mendeley Data:http://doi.org/10.17632/w8jtmnszd9.1
Growth rates	This study	Mendeley Data:http://doi.org/10.17632/w8jtmnszd9.1
Yeast reference proteome databases	Uniprot	https://www.uniprot.org
Ribosomal profiling data	McManus et al.56	http://doi.org/10.1101/gr.164996.113
Protein turnover rates	Martin-Perez and Vill57	https://doi.org/10.1016/j.cels.2017.08.008
Gene networks	Kim et al.34	https://www.inetbio.org/yeastnet/
Complex data	Medal et al.87–89	https://www.ebi.ac.uk/complexportal/
Glycine concentrations	Mulleder et al.15	http://doi.org/10.1016/j.cell.2016.09.007
Full GO term annotation	Gene Ontology Consortium	http://current.geneontology.org/products/ pages/downloads.html
GO slim terms	Cherry et al.37	https://www.yeastgenome.org/
Colony size	Cherry et al.37	https://www.yeastgenome.org/
Reactome	Gillespie et al.90	https://reactome.org/
KEGG	Kanehisa and Goto69; Kanehisa70	https://www.genome.jp/kegg/
BioGRID	Stark et al.91	https://thebiogrid.org
Yeast phenotype data (e.g. gene essentiality)	Cherry92	http://sgd-archive.yeastgenome.org/curation/ literature/phenotype_data.tab
Protein abundances for all yeast proteins (meta-analysis)	Ho et al.93	https://doi.org/10.1016/j.cels.2017.12.004
List of uncharacterised yeast genes	YeastMine	https://yeastmine.yeastgenome.org/yeastmine/bagDetails.do?scope=all&bagName=Uncharacterized_ORFs
Citations mapped to yeast genes	Saccharomyces Genome Database	http://sgd-archive.yeastgenome.org/curation/ literature/gene_literature.tab
S. cerevisiae Ohnologs	Yeast gene order browser35	http://ygob.ucd.ie/
Classification of duplicates	Kuepfer et al.36	http://doi.org/10.1101/gr.3992505
COMPLEAT	Vinayagam et al.74	http://www.flyrnai.org/compleat
Genetic interactions	Costanzo et al.78	https://thecellmap.org/costanzo2016/
STRING	Szklarczyk et al.73	https://string-db.org
Experimental models: Organisms/strains
Prototrophic Saccharomyces cerevisiae deletion collection (MATa, restored prototrophy)	Winzler et al.5; Mülleder et al.94	http://www.euroscarf.de/
Software and algorithms
Proteomics data analysis via Deep Neural Networks, DIA-NN	Demichev et al.28	https://github.com/vdemichev/DiaNN
DIA-NN R package	Demichev et al.28	https://github.com/vdemichev/diann-rpackage
R Statistical Computing Software	The R Foundation	https://www.r-project.org/
tidyverse	Wickham et al.95	https://cran.r-project.org/web/packages/tidyverse/
treeClust R package	Buttrey and Whitaker96	https://CRAN.R-project.org/package=treeClust
caret R package for regression modeling	Kuhn et al.97	https://CRAN.R-project.org/package=caret
Impute R package	Hastie et al.98	https://bioconductor.org/packages/impute/
randomForest R package	Liaw and Wiener99	https://CRAN.R-project.org/package=randomForest
WGCNA R package	Zhang and Horvath100; Langfelder and Horvath101	https://CRAN.R-project.org/package=WGCNA
PRROC R package	Grau et al.102	https://CRAN.R-project.org/package=PRROC
ComplexHeatmap R package	Guet al.103	https://bioconductor.org/packages/ComplexHeatmap/
Circlize R package	Guet al.104	https://CRAN.R-project.org/package=circlize
Piano R package	Väremo et al.105	https://github.com/varemo/piano
clusterProfiler	Väremo et al.105	https://bioconductor.org/packages/clusterProfiler/
topGO R package	Alexa and Rahnenfuhrer106	https://bioconductor.org/packages/topGO/
limma R package	Ritchie et al.107	https://bioconductor.org/packages/limma/
Other
96-Well MACROSpin C18, 50–450 μL	The Nest Group	Cat#SNS SS18VL
HSS T3 column (150 mm x 300 mm, 1.8 μm particles)	Waters	Cat#186009249
Breathe-Easy sealing membrane for multiwell plates	Sigma Aldrich	Cat#Z763624
Adhesive PCR plate foil	Thermo Scientific	Cat#AB0626
ABgene storage plates	Thermo Scientific	Cat#AB-0661
Glass beads, acid-washed (425-600 μm)	Sigma Aldrich	Cat#G8772
Cap mats	Spex	Cat#2201
Corning multiwell plates, plate lids and sealing mats	Sigma Aldrich	Cat#CLS3098
96-well Sample Collection plate (700 μl round well)	Waters	Cat#186005837
Pierce Quantitative Peptide Assays & Standards	Thermo Scientific	Cat#23290