Reagent/Resource	Reference or Source	Identifier or Catalog Number
Chemicals, enzymes, and other reagents
Guanidine hydrochloride	Sigma‐Aldrich	G3272
Ammonium carbonate	Merck	1.59504.0250
Ammonium hydroxide	Acros Organics	255210010
Optima™ LC/MS grade water	Fisher Scientific	W6‐4
Optima™ LC/MS grade acetonitrile	Fisher Scientific	A955‐4
SeQuant ZIC‐pHILIC analytical column (150 × 2.1 mm, 5 μm)	Merck	1.50460.0001
SeQuant ZIC‐pHILIC guard (20 × 2.1 mm, 5 μm)	Merck	1.50438.0001
Complete mini EDTA‐free protease inhibitor cocktail	Roche	04693124001
1.4 mm zirconium oxide beads	Bertin Technologies	KT03961‐1‐103.BK
2.8 mm zirconium oxide beads	Bertin Technologies	KT03961‐1‐102.BK
Tris(2‐carboxyethyl)phosphine	Sigma‐Aldrich	C4706
Chloroacetamide	Sigma‐Aldrich	22790
Lys‐C	Wako Chemicals	129‐02541
Trizma base	Sigma‐Aldrich	T1503
Trypsin	Sigma‐Aldrich	T6567
C18 Sep‐Pak Cartridges	Waters	WAT054955
TMT10plex isobaric label reagent set	Thermo Fischer Scientific	90406
TMT11‐131C Label Reagent	Thermo Fischer Scientific	A34807
5 μm Titansphere	GL Sciences	GS 502075000
2,5‐dihydroxybenzoic acid	Sigma‐Aldrich	85707
Empore C8 SPE Disks, 47mm	Empore	66882‐U
Ammonia solution 25%	Merck	1054321011
Ammonium bicarbonate	Sigma‐Aldrich	09830
Acetonitrile	Merck	1.00030.2500
Formic Acid	Merck	1.00264.1000
Trifluoro acetic acid	Sigma‐Aldrich	8.08260.0501
1.9 μm Reprosil‐Pur 120 C18 beads	Dr. Maisch	R119.aq.0003
75 μm ID capillary material	CM Scientific	TSP075375
Guanidine hydrochloride	Sigma‐Aldrich	G3272
Complete mini EDTA‐free protease inhibitor cocktail	Roche	04693124001
1.4 mm zirconium oxide beads	Bertin Technologies	KT03961‐1‐103.BK
2.8 mm zirconium oxide beads	Bertin Technologies	KT03961‐1‐102.BK
Tris(2‐carboxyethyl)phosphine	Sigma‐Aldrich	C4706
Chloroacetamide	Sigma‐Aldrich	22790
Lys‐C	Wako Chemicals	129‐02541
Trizma base	Sigma‐Aldrich	T1503
Trypsin	Sigma‐Aldrich	T6567
C18 Sep‐Pak Cartridges	Waters	WAT054955
TMT10plex isobaric label reagent set	Thermo Fischer Scientific	90406
TMT11‐131C Label Reagent	Thermo Fischer Scientific	A34807
5 μm Titansphere	GL Sciences	GS 502075000
2,5‐dihydroxybenzoic acid	Sigma‐Aldrich	85707
Empore C8 SPE Disks, 47mm	Empore	66882‐U
Ammonia solution 25%	Merck	1054321011
Ammonium bicarbonate	Sigma‐Aldrich	09830
Acetonitrile	Merck	1.00030.2500
Formic Acid	Merck	1.00264.1000
Trifluoro acetic acid	Sigma‐Aldrich	8.08260.0501
1.9 μm Reprosil‐Pur 120 C18 beads	Dr. Maisch	R119.aq.0003
75 μm ID capillary material	CM Scientific	TSP075375
RNAeasyMini Kit	Qiagen	74106
KAPA RNA Hyperprep Kit	Roche	KR1351
Software
MaxQuant 1.6.0.17	https://maxquant.net/
Xcalibur QuanBrowser and QualBrowser (version 3.1)	Thermo Fisher Scientific
R (version 4.0.2)	R Core Team (2020)
CPLEX Optimizer (version 12.7.1.0)	IBM corp
Other
Denator Stabilizor T1	Denator
Precellys 24 lysis & homogenization	Bertin Technologies
Sonics Vibra‐Cell Sonicator	Sonics & Materials
SpeedVac Concentrator Plus	Eppendorf
Nanodrop 2000 Spectrophotometer	Thermo Fischer Scientific
Reversed‐phase Acquity CSH C18 1.7 μm 1 × 150 mm column	Waters
UltiMate 3000 high‐pressure liquid chromatography (HPLC) system	Dionex
Q Exactive HF‐X	Thermo Fischer Scientific
EASY‐nLC 1200 UHPLC system	Thermo Fischer Scientific
Denator Stabilizor T1	Denator
NovaSeq	Illumina
Precellys 24 lysis & homogenization	Bertin Technologies
Sonics Vibra‐Cell Sonicator	Sonics & Materials
SpeedVac Concentrator Plus	Eppendorf
Nanodrop 2000 Spectrophotometer	Thermo Fischer Scientific
Reversed‐phase Acquity CSH C18 1.7 μm 1 × 150 mm column	Waters
UltiMate 3000 high‐pressure liquid chromatography (HPLC) system	Dionex
Q Exactive HF‐X	Thermo Fischer Scientific
EASY‐nLC 1200 UHPLC system	Thermo Fischer Scientific