KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal anti-CD8 (C8/144B) | Cellmarque | Catalog #108M |
| Rabbit monoclonal anti-CD4 (SP35) | Roche | Catalog #790-4423 |
| Liquid Concentrated Monoclonal Antibody anti-CD163 | Leica Biosystems | Catalog #NCL-L-163 |
| PTMScan Acetyl-lysine Kit | Cell Signaling Technology | Catalog: 13416 |
| Biological Samples | ||
| Primary tumor samples | See Experimental Model and Subject Details | N/A |
| Chemicals and Reagents | ||
| 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 |
| Dithiothretiol, 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 |
| Tandem Mass Tag reagent kit – 11plex | ThermoFisher | Catalog: A34808 |
| 0.5M HEPES, pH 8.5 | Alfa Aesar | Catalog: J63218 |
| Hydroxylamine solution, 50% (vol/vol) in H2O | Aldrich | Catalog: 467804 |
| Methanol | Honeywell | Catalog: 34966 |
| Ammonium hydroxide solution, 28% (wt/vol) in H2O | Sigma | Catalog: 338818 |
| Ni-NTA agarose beads | Qiagen | Catalog: 30410 |
| Iron (III) chloride | Sigma | Catalog: 451649 |
| Acetic acid, glacial | Sigma | Catalog: AX0073 |
| Potassium phosphate, monobasic | Sigma | Catalog: P0662 |
| Potassium phosphate, dibasic | Sigma | Catalog: P3786 |
| MOPS | Sigma | Catalog: M5162 |
| Sodium hydroxide | VWR | Catalog: BDH7225 |
| Sodium phosphate, dibasic | Sigma | Catalog: S9763 |
| Phosphate-buffered saline | Fisher Scientific | Catalog: 10010023 |
| iVIEW DAB Detection Kit | Roche | Catalog: 760-091 |
| Equipment | ||
| Reversed-phase tC18 SepPak, 3cc 200mg | Waters | Catalog: WAT054925 |
| Solid-phase C18 disk, for Stage-tips | Empore | 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 |
| Offline HPLC column, 3.5-μm particle size, 4.6 um × 250 mm | Agilent | Catalog: Custom order |
| Offline 96-well fractionation plate | Whatman | Catalog: 77015200 |
| 700 μL bRP fractionation autosampler vial | ThermoFisher | Catalog: C4010-14 |
| 700 μL bRP fractionation autosampler cap | ThermoFisher | Catalog: C4010-55A |
| 96-well microplate for BCA | Greiner | Catalog: 655101 |
| Microplate foil cover | Corning | Catalog: PCR-AS-200 |
| Vacuum centrifuge | ThermoFisher | 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 |
| Microtube caps | Sarstedt | Catalog: 72.692 |
| 1.5 mL snapcap tube | ThermoFisher | Catalog: AM12450 |
| 2.0 mL snapcap tube | ThermoFisher | Catalog: AM12475 |
| Instrumentation | ||
| Microplate Reader | Molecular Devices | Catalog: M2 |
| Offline HPLC System for bRP fractionation | Agilent 1260 | Catalog: G1380-90000 |
| Online LC for LC-MS | ThermoFisher | Catalog: LC140 |
| Q Exactive Plus Mass Spectrometer | ThermoFisher | Catalog: IQLAAEGA APFALGMBDK |
| Q Exactive HF-X Mass Spectrometer | ThermoFisher | Catalog: 0726042 |
| Orbitrap Fusion Lumos Tribrid Mass Spectrometer | ThermoFisher | Catalog: IQLAAEGA APFADBMBHQ |
| Critical Commercial Assays | ||
| TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold | Illumina | Catalog: RS-122-2301 |
| Infinium MethylationEPIC Kit | Illumina | Catalog: WG-317-1003 |
| Nextera DNA Exosome Kit | Illumina | Catalog: 20020617 |
| KAPA Hyper Prep Kit, PCR-free | Roche | Catalog: 07962371001 |
| BCA Protein Assay Kit | ThermoFisher | Catalog: 23225 |
| Deposited Data | ||
| PhosphoSitePlus | (Hornbeck et al., 2012) | https://www.phosphosite.org |
| Connectivity Map (CMAP) | (Lamb et al., 2006; Subramanian et al., 2017) | https://www.broadinstitute.org/connectivity-map-cmap |
| Human Protein Atlas (HPA) | (Uhlén et al., 2005) | https://www.proteinatlas.org |
| CT Antigen database | (Almeida et al., 2009) | http://www.cta.lncc.br |
| Software and Algorithms | ||
| methylationArrayAnalysis (version 3.9) | (Maksimovic et al., 2016) | https://master.bioconductor.org/packages/release/workflows/html/methylationArrayAnalysis.html |
| Illumina EPIC methylation array (3.9) | Hansen KD, 2019 | https://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylationEPICanno.ilm10b2.hg19.html |
| Methylation array analysis pipeline for CPTAC | Li Ding Lab | https://github.com/ding-lab/cptac_methylation |
| miRNA-Seq analysis pipeline for CPTAC | Li Ding Lab | https://github.com/ding-lab/CPTAC_miRNA |
| Somatic variant calling pipeline for CPTAC | Li Ding Lab | https://github.com/ding-lab/somaticwrapper |
| VarDict | (Lai et al., 2016) | https://github.com/AstraZeneca-NGS/VarDict |
| Strelka2 | (Kim et al., 2018b) | https://github.com/Illumina/strelka |
| MUTECT1.1.7 | (Cibulskis et al., 2013) | https://software.broadinstitute.org/gatk/download/archive |
| VarScan2.3.8 | (Koboldt et al., 2012) | http://varscan.sourceforge.net |
| Pindel0.2.5 | (Ye et al., 2009) | http://gmt.genome.wustl.edu/packages/pindel/ |
| SignatureAnalyzer | (Kim et al., 2016) | https://software.broadinstitute.org/cancer/cga/msp |
| Fusion calling pipeline for CPTAC | Li Ding Lab | https://github.com/cuidaniel/Fusion_hg38 |
| CNVEX | Marcin Cieslik Lab | https://github.com/mctp/cnvex |
| CRISP | Marcin Cieslik Lab | https://github.com/mcieslik-mctp/crisp-build |
| Spectrum Mill | Karl R. Clauser, Steven Carr Lab | https://proteomics.broadinstitute.org/ |
| ComBat (v3.20.0) | (Johnson et al., 2007) | https://bioconductor.org/packages/release/bioc/html/sva.html |
| DreamAI | Pei Wang Lab | https://github.com/WangLab-MSSM/DreamAI |
| GISTIC2.0 | (Mermel et al., 2011) | ftp://ftp.broadinstitute.org/pub/GISTIC2.0/GISTIC_2_0_23.tar.gz |
| iProFun | (Song et al., 2019) | https://github.com/WangLab-MSSM/iProFun |
| ESTIMATE | (Yoshihara et al., 2013) | https://bioinformatics.mdanderson.org/public-software/estimate/ |
| WebGestaltR | (Wang et al., 2017) | http://www.webgestalt.org/ |
| Joint Random Forest | (Petralia et al., 2016) | https://github.com/WangLab-MSSM/ptmJRF |
| GSVA | (Hänzelmann et al., 2013) | https://bioconductor.org/packages/release/bioc/html/GSVA.html |
| TCGAbiolinks | (Colaprico et al., 2016) | http://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html |
| TSNet | (Petralia et al., 2018) | https://github.com/WangLab-MSSM/TSNet |
| xCell | (Aran et al., 2017) | http://xcell.ucsf.edu/ |
| CPTAC LUAD Data Viewer | Steven Carr lab | http://prot-shiny-vm.broadinstitute.org:3838/CPTAC-LUAD2020/ |
| MODMatcher | (Yoo et al., 2014) | https://github.com/integrativenetworkbiology/Modmatcher |
| ConsensusClusterPlus | (Wilkerson and Hayes, 2010) | http://bioconductor.org/packages/release/bioc/html/CancerSubtypes.html |
| pyQUILTS (v1.0) | (Ruggles et al., 2016) | http://openslice.fenyolab.org/cgi-bin/pyquilts_cgi.pl |
| MS-GF+ | (Kim and Pevzner, 2014) | https://github.com/MSGFPlus/msgfplus |
| NeoFlow | Bing Zhang lab | https://github.com/bzhanglab/neoflow |
| netMHCpan | (Jurtz et al., 2017) | http://www.cbs.dtu.dk/services/NetMHCpan/ |
| Optitype | (Szolek et al., 2014) | https://github.com/FRED-2/OptiType |
| Customprodbj | (Wang and Zhang, 2013) | https://github.com/bzhanglab/customprodbj |
| PDV | (Li et al., 2019) | https://github.com/wenbostar/PDV |
| PepQuery | (Wen et al., 2019) | http://pepquery.org |
| PTM-SEA | (Krug et al., 2018) | https://github.com/broadinstitute/ssGSEA2.0 |
| Terra | Broad Institute data science platform. | https://terra.bio/ |
| CMap | (Lamb et al., 2006; Subramanian et al., 2017) | https://due.io/cmap |
| PTM-SEA | (Krug et al., 2018) | https://github.com/broadinstitute/ssGSEA2.0 |
| LIMMA v3.36 (R Package) | (Ritchie et al., 2015) | https://bioconductor.org/packages/release/bioc/html/limma.html |
| FactoMineR v1.41NMF (R - package) | (Gaujoux and Seoighe, 2010; Lê et al., 2008) | https://cran.r-project.org/web/packages/FactoMineR/index.html |
| MClust v5.4 (R package) | (Scrucca, Fop, Murphy and Raftery, 2017) | https://cran.r-project.org/web/packages/mclust/index.html |