Reagent or Resource	Source	Identifier
Antibodies
PTMScan‐pY 1000 Rabbit mAB kit	Cell Signaling Technology	Catalog: 8803A
Biological Samples
Primary tumor samples	See Experimental Model and Subject Details	N/A
Chemicals and Reagents
Synthetic [C13,N15] labeled peptides	New England Peptide	N/A
HPLC‐grade water	J.T. Baker	Catalog: 4218‐03
Urea	Sigma	Catalog: U0631
Sodium chloride	Sigma	Catalog: 71376
1M Tris, pH 8.0	Invitrogen	Catalog: AM9855G
Ethylenediaminetetraacetic acid	Sigma	Catalog: E7889
Aprotinin	Sigma	Catalog: A6103
Leupeptin	Roche	Catalog: 11017101001
Phenylmethylsulfonyl fluoride	Sigma	Catalog: 78830
Sodium fluoride	Sigma	Catalog: S7920
Phosphatase inhibitor cocktail 2	Sigma	Catalog: P5726
Phosphatase inhibitor cocktail 3	Sigma	Catalog: P0044
Dithiothreitol, No‐Weigh Format	Fisher Scientific	Catalog: 20291
Iodoacetamide	Sigma	Catalog: A3221
Lysyl endopeptidase	Wako Chemicals	Catalog: 129‐02541
Sequencing‐grade modified trypsin	Promega	Catalog: V511X
Formic acid	Sigma	Catalog: F0507
Acetonitrile	Honeywell	Catalog: 34967
Trifluoroacetic acid	Sigma	Catalog: 302031
Methanol	Honeywell	Catalog: 34966
Ni‐NTA agarose beads	Qiagen	Catalog: 30410
Iron (III) chloride	Sigma	Catalog: 451649
Potassium phosphate, monobasic	Sigma	Catalog: P0662
Potassium phosphate, dibasic	Sigma	Catalog: P3786
MOPS	Sigma	Catalog: M5162
Sodium hydroxide	VWR	Catalog: BDH7225
Phosphate‐buffered saline	Fisher Scientific	Catalog: 10010023
Equipment
Reversed‐phase tC18 Sep‐Pak, 1cc 100 mg	Waters	Catalog: WAT023590
Reversed‐phase tC18 Sep‐Pak, 3cc 200 mg	Waters	Catalog: WAT054945
Solid‐phase C18 disk, for stagetips	Empore 3M	Catalog: 66883‐U
Stage‐tip needle	Cadence	Catalog: 7928
Stage‐tip puncher, PEEK tubing	IDEX Health & Science	Catalog: 1581
PicoFrit LC‐MS column	New Objective	Catalog: PF360‐75‐10‐N‐5
ReproSil‐Pur, 120 Å, C18‐AQ, 1.9‐μm resin	Dr. Maisch	Catalog: r119.aq
Nanospray column heater	Phoenix S&T	Catalog: PST‐CH‐20U
Column heater controller	Phoenix S&T	Catalog: PST‐CHC
300 μl LC‐MS autosampler vial and cap	Waters	Catalog: 186002639
96‐well microplate for BCA	Greiner	Catalog: 655101
Microplate foil cover	Corning	Catalog: PCR‐AS‐200
Vacuum centrifuge	Thermo Fisher	Catalog: SPD121P‐115
Centrifuge	Eppendorf	Catalog: 5427 R
Benchtop mini centrifuge	Corning	Catalog: 6765
Benchtop vortex	Scientific Industries	Catalog: SI‐0236
Incubating shaker	VWR	Catalog: 12620‐942
15‐ml centrifuge tube	Corning	Catalog: 352097
50‐ml centrifuge tube	Corning	Catalog: 352070
1.5‐ml microtube w/o cap	Sarstedt	Catalog: 72.607
2.0‐ml microtube w/o cap	Sarstedt	Catalog: 72.608
Instrumentation
Microplate Reader	Molecular Devices	Catalog: M2
Online LC for LC‐MS	Thermo Fisher	Catalog: LC140
Q Exactive Plus Mass Spectrometer	Thermo Fisher	Catalog: IQLAAEGA APFALGMBDK
TSQ Quantiva Triple Quadrupole Mass Spectrometer	Thermo Fisher	Catalog: IQLAAEGAAXFAOUMZZZ
Critical Commercial Assays
BCA Protein Assay Kit	Thermo Fisher	Catalog: 23225
Software and Algorithms
Software	Source (i.e., PMID or lab)	Identifier (i.e., links)
Spectrum Mill software package v7.0	Broad Institute, Cambridge, MA	https://proteomics.broadinstitute.org/
Protigy	Broad Institute, Proteomics Platform	https://github.com/broadinstitute/protigy
Skyline	University of Washington, Seattle, WA	https://skyline.ms/project/home/software/Skyline/begin.view ?
Panorama	University of Washington, Seattle, WA	https://panoramaweb.org/home/project‐begin.view ?
CausalPath	Computer Science Department, University of Massachusetts Boston, Boston, MA	www.causalpath.org