Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Recombinant DNA reagent | pCMV-SHP2-WT | Addgene | RRID:Addgene_8381, plasmid # 8381 | |
| Recombinant DNA reagent | migR1-IRES-GFP | Addgene | RRID:Addgene_27490, plasmid # 27490 | |
| Chemical compound, drug | SHP2 inhibitor (SHP099) | DC chemicals | Catalog # DC9737 | |
| Chemical compound, drug | Src inhibitor (AZD0530) | Dr. Nathanael Gray (Dana-Farber Cancer Institute) | ||
| Antibody | Mouse monoclonal CD3 (UCHT1) | Thermo Fisher Scientific | RRID:AB_468857; Catalog # 16-0038-85 | 10 µg/ml for TCR stimulation of Jurkat cells |
| Antibody | Rabbit monoclonal Phospho-Tyr-1000 | Cell Signaling Technology | RRID:AB_2687925; Catalog # 8954 | Western blot (1:2000); Immunoprecipitation (1:100) |
| Antibody | Rabbit polyclonal Phospho-Thr202/Tyr204-Erk1/2 | Cell Signaling Technology | RRID:AB_331646; Catalog # 9101 | Western blot (1:2000) |
| Antibody | Rabbit polyclonal Erk1/2 | Cell Signaling Technology | RRID:AB_330744; Catalog # 9102 | Western blot (1:2000) |
| Antibody | Rabbit polyclonal GAB1-pY659 | Cell Signaling Technology | RRID:AB_2798014; Catalog # 12745 | Western blot (1:1000) |
| Antibody | Rabbit polyclonal GAB1-pY627 | Cell Signaling Technology | RRID:AB_2305002; Catalog # 3231 | Western blot (1:500) |
| Antibody | Rabbit polyclonal GAB2-pY643 | Thermo Fisher Scientific | RRID:AB_2554386; Catalog # PA5-37778 | Western blot (1:1000) |
| Antibody | Rabbit polyclonal GAB1 | Cell Signaling Technology | RRID:AB_2304999; Catalog # 3232 | Western blot (1:2000) |
| Antibody | Rabbit monoclonal GAB2 | Cell Signaling Technology | RRID:AB_10698601; Catalog # 3239 | Western blot (1:2000) |
| Antibody | Rabbit polyclonal pY263-MPZL1 | Cell Signaling Technology | RRID:AB_10715080; Catalog # 5543 | Western blot (1:1000) |
| Antibody | Rabbit monoclonal pY241-MPZL1 | Cell Signaling Technology | RRID:AB_10891793; Catalog # 8131 | Western blot (1:1000) |
| Antibody | Rabbit polyclonal MPZL1 | Cell Signaling Technology | RRID:AB_1904189; Catalog # 4157 | Western blot (1:2000) |
| Antibody | Rabbit polyclonal pY1105-ARHGAP35 | Thermo Fisher Scientific | RRID:AB_2553676; Catalog # PA5-36713 | Western blot (1:1000) |
| Antibody | Rabbit polyclonal ARHGAP35 | Cell Signaling Technology | RRID:AB_2115740; Catalog # 2562 | Western blot (1:2000); Immunoprecipitation (1:100) |
| Antibody | Rabbit monoclonal SHP2 | Cell Signaling Technology | RRID:AB_2174959; Catalog # 3397 | Western blot (1:500) |
| Antibody | Rabbit polyclonal SHP2 | Bethyl | RRID:AB_1040019; Catalog # A301-544A | Western blot (1:1000) |
| Antibody | Mouse monoclonal SHP2 | Santa Cruz | RRID:AB_628252; Catalog # sc-7384 | Immunoprecipitation (2 µg antibody per500 µg cell lysate) |
| Antibody | Mouse monoclonal PLCG2 | Santa Cruz | RRID:AB_628120; Catalog # sc-5283 | Western blot (1:500); Immunoprecipitation (2 µg antibody per500 µg cell lysate) |
| Antibody | Rabbit polyclonal OCLN | Bethyl | RRID:AB_2631690; Catalog # A305-297A | Western blot (1:1000); Immunoprecipitation (5 µg antibody per1 mg cell lysate) |
| Antibody | Mouse monoclonal GRB2 | BD Transduction Laboratories | RRID:AB_397518; Catalog # 610112 | Western blot (1:2000) |
| Cell line (H. sapiens) | MDA-MB-468 | ATCC | RRID:CVCL_0419; HTB-132 | |
| Cell line (H. sapiens) | KYSE-520 | DSMZ | RRID:CVCL_1355; ACC 371 | |
| Cell line (H. sapiens) | U2OS | ATCC | RRID:CVCL_0042; HTB-96 | |
| Cell line (H. sapiens) | Jurkat | ATCC | RRID:CVCL_0367; TIB-152 | |
| Cell line (H. sapiens) | NCI-H1975 | ATCC | RRID:CVCL_UE30; CRL-5908 | |
| Cell line (H. sapiens) | SHP2 knockout U2OS cell line | LaRochelle et al., 2018 | ||
| Peptide, recombinant protein | Human EGF | Gibco | PHG0311 | |
| Peptide, recombinant protein | Human PDGF-BB | Peprotech | Catalog # 10771–922 | |
| Peptide, recombinant protein | IRS1_pY1172–PEG–pY1222 peptide | This paper | SLN{pY}IDLDLVK–dPEG8–LST{pY}ASINFQK; (custom synthesized by Genscript) | |
| Peptide, recombinant protein | OCLN_pY443 peptide | This paper | TGLQE{pY}KSLQS; (custom synthesized by Genscript) | |
| Peptide, recombinant protein | PLCG2_pY818 peptide | This paper | TRIQQ{pY}FPSNY (custom synthesized by Genscript) |
|
| Peptide, recombinant protein | GRB2_pY209 peptide | This paper | MFPRN{pY}VTPVN; (custom synthesized by Genscript) |
|
| Peptide, recombinant protein | ARHGAP35_pY1105 peptide | This paper | EENI{pY}SVPHDS; (custom synthesized by Genscript) |
|
| Peptide, recombinant protein | CSF-1R_pY708 peptide | This paper | IHLEKK{pY}VRRDSGF; (custom synthesized by Genscript) | |
| Peptide, recombinant protein | TMEM134_pY57 peptide | This paper | KQSRLR{pY}QNLEND; (custom synthesized by Genscript) | |
| Peptide, recombinant protein | Lysyl Endopeptidase, Mass Spectrometry Grade (Lys-C) | FUJIFILM Wako Pure Chemical Corporation | Catalog # 125–05061 | Protein cleavage for mass spectrometry (10 µg per 1 mg total protein) |
| Peptide, recombinant protein | Sequencing Grade Modified Trypsin | Promega | Catalog # V511C | Protein cleavage for mass spectrometry (10 µg per 1 mg total protein) |
| Peptide, recombinant protein | Wild-type SHP2 purified protein | LaRochelle et al., 2016 | ||
| Commercial assay or kit | QuikChange II Site-Directed Mutagenesis kit | Agilent | Catalog # 200523 | |
| Commercial assay or kit | BCA protein assay | Pierce | Catalog # 23225 | |
| Commercial assay or kit | Malachite Green assay kit | Sigma–Aldrich | Catalog # MAK307 | |
| Commercial assay or kit | PLA kit | Sigma–Aldrich | Catalog # DUO92014 | |
| Other | NTA Magnetic Agarose beads | Qiagen | Catalog # 36113 | |
| Other | TMT 11-plex reagent | Thermo Scientific | Catalog # A37725 | |
| Software, algorithm | GraphPad Prism 9.0 | N/A | RRID:SCR_002798; https://www.graphpad.com/scientific-software/prism/ | |
| Software, algorithm | R 3.6.3 | N/A | RRID:SCR_001905; https://www.r-project.org/ | |
| Software, algorithm | CellProfiler | N/A | RRID:SCR_007358; https://cellprofiler.org/ | |
| Software, algorithm | Reactome database | N/A | RRID:SCR_003485; http://software.broadinstitute.org/gsea/msigdb/annotate.jsp | |
| Software, algorithm | Gene set enrichment analysis | Mootha et al., 2003; Subramanian et al., 2005 | RRID:SCR_003199 | |
| Software, algorithm | Hierarchical clustering | MATLAB | RRID:SCR_001622; https://www.mathworks.com/products/matlab.html | |
| Software, algorithm | Principal component analysis | Python | RRID:SCR_008394; https://www.python.org/ | |
| Software, algorithm | Dependence classification | This paper | See ‘Dependence classification of phosphorylation site time courses’ in Methods | |
| Software, algorithm | Logo analysis | Crooks, 2014 | RRID:SCR_010236 |