41 to 50 of 142,139 Results
MS Excel Spreadsheet - 13.4 KB -
MD5: b67a7ed20bcc54bc467f4e736bb91f30
Comparison between theoretical and computationally explored strata sizes. Number of unique unspecific peptide sequences and number of theoretical peptide sequences for RNA-seq informed and GENCODE driven strata is shown per peptide length. This table refers to Supplementary Fig. 7e. The data refers to K562 cell line. |
MS Excel Spreadsheet - 1.5 MB -
MD5: d0a2e1291f7666686916c6dbe1dc694d
Peptide multi-mapping across strata pairs. This file contains the pairwise comparisons of distinct peptide sets between proteogenomic strata. For every pair of databases, peptide length and catalytic rule, provided are the numbers of peptides distinct for each stratum as well as the intersection size and ratios of intersection to each set. Unfilter... |
MS Excel Spreadsheet - 30.9 KB -
MD5: dea2726c20e431f766a2ffcb969202c8
Strata search space sizes across SPIsnake filtering steps in B721.221. Number of unique peptides derived by tryptic or proteasomal digestion from RNA-seq informed and uninformed search spaces for all peptide lengths. Strata reduction during data-driven filtering is reported for B721.221 cell line expressing HLA-A02:01 or HLA-B07:02. |
ZIP Archive - 20.0 GB -
MD5: b74511615010607270b9a8f42025ebe8
FASTA Files of MW-filtered canonical and expanded reference databases. The zip file contains two FASTA files of target and decoy peptide sequences for canonical and expanded databases. Decoy sequences are indicated by the label “rev_” in the FASTA header. |
ZIP Archive - 7.3 GB -
MD5: 45447fd1fec537a575ee6ba49189da98
FASTA Files of MW-RT-filtered canonical and expanded reference databases. The zip file contains two FASTA files of target and decoy peptide sequences for canonical and expanded databases. Decoy sequences are indicated by the label “rev_” in the FASTA header. |
ZIP Archive - 260.0 MB -
MD5: ab5ae2c2969311bc6123d094dfdd5de1
FASTA Files of MW-RT-affinity-filtered canonical and expanded reference databases. The zip file contains two FASTA files of target and decoy peptide sequences for canonical and expanded databases. Decoy sequences are indicated by the label “rev_” in the FASTA header. |
ZIP Archive - 292.9 MB -
MD5: 441e90e56b3dd8c54590ea305a756c25
MSFragger original search engine outputs. The zip file contains subfolders each containing ‘pepXML’ output files from MSFragger for the MS raw files which were searched. Folder titles indicate the model system, whether the search results come from the canonical or expanded reference database search and which SPIsnake filters were applied. |
ZIP Archive - 400.6 KB -
MD5: 102b0e8fe7483141efd70b33139578c1
Peptide sequences identified with the naïve strategy. This file contains .csv files of peptide sequences filtered for 1% FDR identified with the naïve strategy canonical and expanded reference databases using MW-filters, MW-RT-filters or MW-RT-HLA-I binding filters. Furthermore, peptide sequences identified with MSFragger at 1% FDR and subsequently... |
ZIP Archive - 329.3 KB -
MD5: 970f392d5f0984ec9b1e17a9fc124f7e
Peptide sequences identified with the combined strategy. This file contains .csv files of peptide sequences filtered for 1% FDR identified with the combined strategy using either MW filtered, MW-RT filtered or MW-RT-HLA-I binding filtered reference databases, respectively. Furthermore, peptide sequences identified with MSFragger at 1%FDR and subseq... |
ZIP Archive - 1.4 GB -
MD5: 9f0fc5f535d92409036abcf20d4e426d
SPIsnake user parameter settings. This file contains a list of folders with pre-set SPIsnake job inputs, with all corresponding settings and hyperparameters used in this study. |
