Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit monoclonal anti-mTOR | Cell Signaling Technology | 2983S |
| Rabbit monoclonal anti-FLAG | Cell Signaling Technology | 14793S |
| Rabbit monoclonal anti-GFP | Cell Signaling Technology | 2956S |
| Goat anti-Rabbit secondary antibody, HRP conjugate | Cell Signaling Technology | 7074S |
| Chemicals, peptides, and recombinant proteins | ||
| MLN4924 | Active Biochem | A-1139 |
| Polybrene | Santa Cruz | sc-134220 |
| Critical commercial assays | ||
| QIAEX II Gel Extraction Kit | QIAGEN | 20051 |
| PCR purification kit | QIAGEN | 28106 |
| Gentra Puregene Cell Kit | QIAGEN | 158767 |
| Deposited data | ||
| GPS peptidome processed screen data and raw images | This paper | http://dx.doi.org/10.17632/32h94v2yv2.2 (Mendeley Data) |
| GPS peptidome raw and processed screen data | This paper |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?&acc=GSE240610 (Gene Expression Omnibus) |
| Experimental models: Cell lines | ||
| HEK293T | ATCC | ATCC CRL-3216 |
| Oligonucleotides | ||
| sg-FEM1B: GTGACATAGCCAAGCAGATAG | Integrated DNA Technologies | N/A |
| sg-KLHL15: GATTTCGGCGTAAACATCGA | Integrated DNA Technologies | N/A |
| sg-ASB7: GCCAACATCGACATTCAGAA | Integrated DNA Technologies | N/A |
| Recombinant DNA | ||
| pHAGE-GPS6.0-DEST | This paper | N/A |
| pHAGE-GPS6.0-peptide libraries | This paper | N/A |
| lentiCRISPR v2 | Addgene | 52961 |
| Ultimate ORF Collection | Thermo Fisher Scientific | https://www.thermofisher.com/us/en/home/life-science/cloning/clone-collections/ultimate-orf-clone-collection.html |
| Software and algorithms | ||
| Bowtie 2 | Langmead and Salzberg, 2012; Langmead et al., 200950,51 | http://bowtie-bio.sourceforge.net/index.shtml |
| Cutadapt | Martin, 201149 | http://cutadapt.readthedocs.io/en/stable/index.html |
| MAGeCK | Li et al., 201452 | https://sourceforge.net/projects/mageck/ |
| Flowjo | Flowjo | https://www.flowjo.com |
| ColabFold | Mirdita et al., 202237 | https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb |
| ChimeraX | Pettersen et al., 202155 | https://www.rbvi.ucsf.edu/chimerax/ |
| Proteus2 | Montgomerie et al., 200832 | http://www.proteus2.ca/proteus2/ |
| JPred4 | Drozdetskiy et al., 201519 | https://www.compbio.dundee.ac.uk/jpred/ |
| DegronID | This paper |
https://doi.org/10.5281/zenodo.8103915 (Zenodo) |
| R 4.1.2 | R Core Team | https://www.r-project.org/ |
| Caret | Kuhn, 200854 | https://doi.org/10.18637/jss.v028.i05 |
| Tidyverse | Wickham et al., 201957 | http://dx.doi.org/10.21105/joss.01686 |
| Biostrings | Bioconductor | https://doi.org/10.18129/B9.bioc.Biostrings |
| aplot | CRAN | https://cran.r-project.org/web/packages/aplot |
| ggdendro | CRAN | https://cran.r-project.org/web/packages/ggdendro |