KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal ant-β-Actin | Sigma | Cat#A5441; RRID:AB_476744 |
| Rabbit monoclonal anti-Phospho MET(Tyr1234/1235) (D26)XP | Cell Signaling | Cat #3077; RRID:AB_2143884 |
| Rabbit monoclonal anti-MET (D1C2)XP | Cell Signaling | Cat #8198; RRID:AB_10858224 |
| Rabbit polyclonal anti-Phospho AKT(Ser473) | Cell Signaling | Cat #9271; RRID:AB_329825 |
| Rabbit polyclonal anti-Akt | Cell Signaling | Cat #9272; RRID:AB_329827 |
| Mouse monoclocal anti-Phospho p44/42 MAPK (Erk1/2) (Thr202/Tyr204) (E10) | Cell Signaling | Cat #9106; RRID:AB_331768 |
| Rabbit polyclonal anti-MAP kinase (ERK-1, ERK-2) | Sigma | Cat #M5670; RRID:AB_477216 |
| Rabbit monoclonal anti-Phospho Histone H3 (Ser10) (D2C8) XP | Cell Signaling | Cat #3377; RRID:AB_1549592 |
| Rabbit monoclonal Histone H3 (D1H2) XP | Cell Signaling | Cat #4499; RRID:AB_10544537 |
| Rabbit polyclonal anti-Cleaved Caspase-3 (Asp175) | Cell Signaling | Cat#9661; RRID:AB_2341188 |
| Rabbit polyclonal anti-PARP1 | Cell Signaling | Cat #9542; RRID:AB_2160739 |
| Mouse monoclonal anti-FER (5D2) | Cell Signaling | Cat#4268; RRID:AB_2278286 |
| Mouse monoclonal anti-Phospho Tyrosine (P-Tyr-100) | Cell Signaling | Cat#9411; RRID:AB_331228 |
| Mouse monoclonal anti-AIM-1 | BD Bioscience | Cat #611082; RRID:AB_2227708 |
| Rabbit monoclonal anti-Phospho FAK(Tyr397) (D20B1) | Cell Signaling | Cat #8556; RRID:AB_10891442 |
| Rabbit monoclonal anti-FAK (D2R2E) | Cell Signaling | Cat #13009 |
| Mouse IgG, HRP-linked whole Ab | GE Healthcare | Cat# NA931; RRID:AB_772210 |
| Rabbit IgG, HRP-linked whole Ab | GE Healthcare | Cat# NA934; RRID:AB_2722659 |
| Normal mouse IgG | Santa Cruz | Cat#sc-2025; RRID:AB_737182 |
| PTMScan® Phospho-Tyrosine Rabbit mAb (P-Tyr-1000) | Cell Signaling | Cat#8803 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| DMSO used in proteomics | Acros Organics | Cat#167852500; CAS: 67-68-5 |
| DMSO used in drug dilutions | Acros Organics | Cat#348445000; CAS: 67-68-5 |
| DMSO used in cell culture | Sigma | D2438; CAS: 67-68-5 |
| Foretinib | Chemietek | Cat#CT-FORE, CT-XL880; CAS: 849217-64-7 |
| XL184 (CABOZANTINIB) (FREE BASE) | Chemietek | Cat#CT-XL184; CAS: 849217-68-1 |
| GSK1120212 (TRAMETINIB) | Chemietek | Cat#CT-GSK212; CAS: 871700-17-3 |
| Motesanib (AMG-706) | Selleckchem | Cat#S5793; CAS: 453562-69-1 |
| PF-04217903 | Selleckchem | Cat#S1094; CAS: 956905-27-4 |
| AZD1152-HQPA | Selleckchem | Cat#S1147; CAS: 722544-51-6 |
| GSK1838705A | Selleckchem | Cat#S2703, CAS: 1116235-97-2 |
| PF-573228 | Selleckchem | Cat#S2013; CAS: 869288-64-2 |
| OSI-906 (LINSITINIB) | Chemietek | Cat#CT-O906; CAS: 867160-71-2 |
| Alisertib (MLN8237) | Selleckchem | Cat#S1133; CAS: 1028486-01-2 |
| i-foretinib | This Paper | N/A |
| i-cabozantinib | This Paper | N/A |
| Critical Commercial Assays | ||
| CellTiter-Glo® Luminescent Cell Viability Assay | Promega | G7573 |
| Crystal violet solution | Sigma | HT90132 |
| Caspase 3/7 reagent | Essen Bioscience | 4440 |
| Thermo Scientific™ Pierce™ Coomassie (Bradford) Protein Assay | ThermoFisher Scientific | Cat# PI23200 |
| RNeasy Mini Kit | Quiagen | Cat#74104 |
| IMAC enrichment Kit | Sigma | Cat#I1408 |
| Pierce™ Enrichment Kit ATP Probe | ThermoFisher Scientific | Cat#88310 |
| PTMScan Kit | Cell Signaling | https://media.cellsignal.com/pdf/8803.pdf |
| TMT Mass Tagging Kits and Reagent | ThermoFisher Scientific | Cat#90064 |
| Encore Complete RNA-Seq Library System | Nugen | N/A |
| KAPA library amplification kit for Illumina platform | KAPABiosystem | |
| Eurofin Kinase Profiler™ platform | Eurofins Pharma Discovery Services | https://www.eurofinsdiscoveryservices.com/cms/cms-content/services/in-vitro-assays/kinases/kinase-profiler/ |
| Reaction Biology Kinase Hotspot platform | Reaction Biology Corp | www.reactionbiology.com/webapps/site/KinaseAssay.aspx |
| Deposited Data | ||
| X-ray co-crystal structure of the MET kinase domain bound to XL880 (foretinib) | (Qian et al., 2009) | PDB ID: 3LQ8 |
| Chemical Proteomics in H1155 and A427 cells (Drug Pulldowns) | ProteomeXchange Consortium via the PRIDE partner repository (http://www.ebi.ac.uk/pride) | PXD012961 |
| Activity-based protein profiling (ABPP) | ProteomeXchange Consortium via the PRIDE partner repository (http://www.ebi.ac.uk/pride) | PXD012965 |
| Global phosphoproteomics (IMAC Phosphoproteomics) | ProteomeXchange Consortium via the PRIDE partner repository (http://www.ebi.ac.uk/pride) | PXD012963 |
| Tyrosine phosphoproteomics (Tyrosine Phosphorylation) | ProteomeXchange Consortium via the PRIDE partner repository (http://www.ebi.ac.uk/pride) | PXD012962 |
| RNA-Seq data | GEO database | GSE126850 |
| Experimental Models: Cell Lines | ||
| H1155 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| A427 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| H3122 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| H2170 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| CALU3 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| H23 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| H1437 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| HOP62 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| A549 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| H1299 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| HCC4006 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| H322 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| H292 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| H2342 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| H157 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| CALU6 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| H1395 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| H650 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| HCC2935 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| H1648 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| H661 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| H2122 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| H1944 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| H460 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| H358 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| 16HV | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| 86M1 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| H524 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| N417 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| H82 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| SW210.5 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| H69 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| DMS79 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| H209 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| DMS114 | Moffitt Lung Cancer Center of Excellence Cell Line Core | N/A |
| Oligonucleotides | ||
| ON-TARGET plus Non-target Pool | Dharmacon | D-001810-10-20 |
| SMARTPOOL: ON-TARGET plus Human MAP4K5 (11183) | Dharmacon | L-003589-00-0005 |
| SMARTPOOL: ON-TARGET plus Human AURKB (9212) | Dharmacon | L-003326-00-0005 |
| SMARTPOOL: ON-TARGET plus Human FER (2241) | Dharmacon | L-003129-00-0005 |
| Software and Algorithms | ||
| Prism 7.03 | GraphPad | https://www.graphpad.com/scientific-software/prism/ |
| R program | The R foundation | https://cran.r-project.org/mirrors.html |
| Image J - Version1.48 | NIH.gov | https://imagej.nih.gov/ij/download.html |
| M5 Spectramax plate reader - SoftMaxPro Software 6.2.1 | Molecular Devices | https://www.moleculardevices.com/products/microplate-readers/acquisition-and-analysis-software/softmax-pro-software |
| ModFitLT V3.2.1 | BD Biosciences | http://www.bdbiosciences.com/ca/c/modfit-lt-v33-for-pc/p/346033 |
| Incucyte Zoom Software 2016B | Essen Bioscience | https://www.essenbioscience.com/en/products/software/ |
| Odyssey FC Imaging System - ImageStudio Lite Software 5.2.5 | LI-COR | https://www.licor.com/bio/products/software/image_studio/is_products_fc.html#fc |
| Mascot 2.4 | Matrix Science | http://www.matrixscience.com/help/apr2012.html |
| MaxQuant 1.2.2.5 and 1.5.2.8 | Max-Planck-Institute of Biochemistry | http://coxdocs.org/doku.php?id=maxquant:start |
| Swiss-Prot | UniProt | https://www.uniprot.org/downloads#uniprotkblink |
| Scaffold 4.0 | Proteome software | http://www.proteomesoftware.com/pdf/scaffold_brochure.pdf?v=fa4ef332 |
| Skyline 4.1 | MacCoss Lab Software | https://skyline.ms/project/home/software/Skyline/begin.view |
| Htseq-count | Stanford University and EMBL Heidelberg | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4287950/ |
| DESeq2 | Biocondutor |
https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html https://www.ncbi.nlm.nih.gov/pubmed/?term=25516281 https://www.ncbi.nlm.nih.gov/pubmed/?term=20979621 |
| Gene Set Enrichment Analysis (GSEA) | Broad Institute |
http://software.broadinstitute.org/gsea/msigdb/index.jsp https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1239896/ |
| TopHat2 | Johns Hopkins University | https://www.ncbi.nlm.nih.gov/pubmed/23618408 |
| Other | ||
| LINCS (Library of Integrated Network-Based Cellular Signatures) dataset | Harvard Medical School and NIH LINCS Program | http://lincs.hms.harvard.edu/db/datasets/20176/results?items_per_page=250&sort=&search=# |