| Deposited data |
|
| Human immunopeptidomic datasets |
PRIDE
MassIVE |
https://www.ebi.ac.uk/pride/https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp |
| Uniprot database |
UniProt |
https://www.uniprot.org/ |
| SysteMHC Atlas peptide identifications |
(Shao et al., 2018) |
https://systemhcatlas.org |
| GTEx RNASeq data |
GTEx Portal |
https://gtexportal.org/home/ |
| TCGA RNASeq data |
Genomic Data Commons Data Portal |
https://portal.gdc.cancer.gov/ |
| CT Database |
(Almeida et al., 2009) |
http://www.cta.lncc.br/ |
| 512 Testicular proteins list |
(Pineau et al., 2019) |
https://pubs.acs.org/doi/10.1021/acs.jproteome.9b00351 |
| TCGA pan-cancer copy number alteration data |
(Schaub et al., 2018) |
https://gdc.cancer.gov/about-data/publications/pancanatlas |
| TCGA pan-cancer methylation data |
(Saghafinia et al., 2018) |
https://gdc.cancer.gov/about-data/publications/pancanatlas |
| GRCh37 dbSNP database |
(Sherry et al., 2001) |
https://www.ncbi.nlm.nih.gov/snp/ |
| Ensembl database |
(Hubbard et al., 2002) |
https://useast.ensembl.org/ |
| Top 100,000 ICGC mutations |
(Zhang et al., 2019) |
https://dcc.icgc.org/ |
|
| Software and algorithms |
|
| MSconvert v3.0.19014 |
(Adusumilli and Mallick, 2017) |
https://proteowizard.sourceforge.io/ |
| MSDataConverter v1.3 |
Sciex |
https://sciex.com/ |
| Comet v201801 |
(Eng et al., 2013) |
http://comet-ms.sourceforge.net/ |
| MaxQuant v1.6.5 |
(Cox and Mann, 2008) |
https://www.maxquant.org/ |
| MS-GF+ v2019.02.28 |
(Kim and Pevzner, 2014) |
https://omics.pnl.gov/software/ms-gf |
| Open-pFind v3.1.5 |
(Chi et al., 2018) |
http://pfind.ict.ac.cn/ |
| X!Tandem v2017.2 |
(Craig and Beavis, 2004) |
https://www.thegpm.org/tandem/ |
| PGA v1.9.1 |
(Wen et al., 2016) |
https://github.com/wenbostar/PGA |
| PTMiner v1.0 |
(An et al., 2019) |
http://fugroup.amss.ac.cn/software/PTMiner/PTMiner.html |
| PDV v1.6 |
(Li et al., 2019) |
https://github.com/wenbostar/PDV |
| NetMHCpan v4.0 |
(Hoof et al., 2009) |
http://www.cbs.dtu.dk/services/NetMHCpan-4.0/ |
| PepQuery v1.2 |
(Wen et al., 2019) |
http://www.pepquery.org/ |
| Customprodbj v1.0 |
(Wen et al., 2020) |
https://github.com/bzhanglab/customprodbj |
| RNA-SeQC v2.3.5 |
(DeLuca et al., 2012) |
https://software.broadinstitute.org/cancer/cga/rna-seqc |
