KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
|
| ||
| Software and algorithms | ||
|
| ||
| CysDB | This paper | https://backuslab.shinyapps.io/cysdb/,https://github.com/lmboat/cysdb_app |
| Human proteome | UniProtKB | UP000005640 |
| UniProtKB/Swiss-Prot Fasta | 2201-release | https://www.uniprot.org/ |
| UniProtKB/Swiss-Prot | 2209-release | https://www.uniprot.org/ |
| COSMIC | 2209-release | https://cancer.sanger.ac.uk/census |
| ClinVar | 2209-release | https://cancer.sanger.ac.uk/census |
| Human Protein Atlas (HPA) | Version 21.1 | https://www.proteinatlas.org |
| Enrichr Panther | 2016 | http://www.pantherdb.org/pathway/ |
| Enrichr Pfam Domains | 2019 | https://pfam.xfam.org/ |
| Enrichr OMIM Disease | https://www.omim.org/downloads | |
| R version 4.2.1 | R project | https://www.r-project.org |
| RStudio Version 2022.07.1 | https://rstudio.com | |
| ImageJ | NIH | https://imagej.nih.gov/ij/ |
| Enrichr | Accessed Sept. 2022 | https://maayanlab.cloud/Enrichr/ |
|
| ||
| Other | ||
|
| ||
| Quantitative reactivity profiling predicts functional cysteines in proteomes | 41586_2010_BFnature09472_ MOESM204_ESM.xlsx |
PMID: 21085121 |
| Proteome-wide covalent ligand discovery in native biological systems | 41586_2016_BFnature18002_ MOESM54_ESM.xlsx |
PMID: 27309814 |
| An activity-guided map of electrophile-cysteine interactions in primary human T cells | NIHMS1616434-supplement-mmc4.xlsx | PMID: 32730809 |
| Reimagining high-throughput profiling of reactive cysteines for cell-based screening of large electrophile libraries | 41587_2020_778_S4_ESM.xlsx, 41587_2020_778_S6_ESM.xlsx, 41587_2020_778_S7_ESM.xlsx, 41587_2020_778_S8_ESM.xlsx |
PMID: 33398154 |
| SP3-FAIMS Chemoproteomics for High-Coverage Profiling of the Human Cysteinome |
cbic202000870-sup-0001-table_s4.xlsx, cbic202000870-sup-0001-table_s6.xlsx | PMID: 33442901 |
| Multiplexed CuAAC Suzuki–Miyaura Labeling for Tandem Activity-Based Chemoproteomic Profiling |
ac0c04726_si_002.xlsx, ac0c04726_si_003.xlsx | PMID: 33470097 |
| From chemoproteomic-detected amino acids to genomic coordinates: insights into precise multi-omic data integration | msb20209840-sup-0020-datasetev18.xlsx | PMID: 33599394 |
| Quantitative Chemoproteomic Profiling with Data-Independent Acquisition-Based Mass Spectrometry |
ja1c11053_si_002.xlsx, ja1c11053_si_003.xlsx | PMID: 34986311 |
| Benchmarking Cleavable Biotin Tags for Peptide-Centric Chemoproteomics |
pr2c00174_si_002.xlsx, pr2c00174_si_003.xlsx, pr2c00174_si_004.xlsx, pr2c00174_si_005.xlsx, pr2c00174_si_006.xlsx | PMID: 35467356 |