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File Type: Archive

1 to 10 of 10,892 Results

cns_bench.zip Jul 22, 2025 - CNS-Bench ZIP Archive - 2.5 GB - MD5: 1709014fe58470e5b6d87967b01453f4 CNS-Bench images.
filtering_dataset_images.zip Jul 22, 2025 - CNS-Bench ZIP Archive - 249.6 MB - MD5: 97b88d4150571f1d622825074778a6a0 Out-of-class filtering dataset.
lora_adapters.zip Jul 22, 2025 - CNS-Bench ZIP Archive - 13.7 GB - MD5: 0f1a289d27c50a0d70a45493695c21d2 LoRA adapters for shifting.
results.zip Jul 22, 2025 - CNS-Bench ZIP Archive - 72.8 MB - MD5: 7f88096bcd433c36b91d6b3baeeb752c CNS-Bench model evaluations.
Source Data Table 1.zip Jul 22, 2025 - Source Data from "An automated workflow to address proteome complexity and the large-search-space problem in proteomics and HLA-I immunopeptidomics." ZIP Archive - 6.4 GB - MD5: 78db2330172cd21cd3fc15663b4907cf Sequoia constructed reference databases. This file contains GENCODE driven and RNA-seq informed reference databases in FASTA format and ORF annotations in tabular format (37.8 GB on disk). RNA-seq data were derived from K562 cell line and used for reference-guided transcriptome assembly, quantification and ORF prediction. Provided are the GENCODE v...
Source Data Table 14.zip Jul 22, 2025 - Source Data from "An automated workflow to address proteome complexity and the large-search-space problem in proteomics and HLA-I immunopeptidomics." 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.
Source Data Table 15.zip Jul 22, 2025 - Source Data from "An automated workflow to address proteome complexity and the large-search-space problem in proteomics and HLA-I immunopeptidomics." 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.
Source Data Table 16.zip Jul 22, 2025 - Source Data from "An automated workflow to address proteome complexity and the large-search-space problem in proteomics and HLA-I immunopeptidomics." 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.
Source Data Table 17.zip Jul 22, 2025 - Source Data from "An automated workflow to address proteome complexity and the large-search-space problem in proteomics and HLA-I immunopeptidomics." 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.
Source Data Table 18.zip Jul 22, 2025 - Source Data from "An automated workflow to address proteome complexity and the large-search-space problem in proteomics and HLA-I immunopeptidomics." 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...

cns_bench.zip

Jul 22, 2025 - CNS-Bench

ZIP Archive - 2.5 GB -

CNS-Bench images.

filtering_dataset_images.zip

Jul 22, 2025 - CNS-Bench

ZIP Archive - 249.6 MB -

Out-of-class filtering dataset.

lora_adapters.zip

Jul 22, 2025 - CNS-Bench

ZIP Archive - 13.7 GB -

LoRA adapters for shifting.

results.zip

Jul 22, 2025 - CNS-Bench

ZIP Archive - 72.8 MB -

CNS-Bench model evaluations.

Source Data Table 1.zip

Jul 22, 2025 - Source Data from "An automated workflow to address proteome complexity and the large-search-space problem in proteomics and HLA-I immunopeptidomics."

ZIP Archive - 6.4 GB -

Sequoia constructed reference databases. This file contains GENCODE driven and RNA-seq informed reference databases in FASTA format and ORF annotations in tabular format (37.8 GB on disk). RNA-seq data were derived from K562 cell line and used for reference-guided transcriptome assembly, quantification and ORF prediction. Provided are the GENCODE v...

Source Data Table 14.zip

Jul 22, 2025 - Source Data from "An automated workflow to address proteome complexity and the large-search-space problem in proteomics and HLA-I immunopeptidomics."

ZIP Archive - 20.0 GB -

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.

Source Data Table 15.zip

Jul 22, 2025 - Source Data from "An automated workflow to address proteome complexity and the large-search-space problem in proteomics and HLA-I immunopeptidomics."

ZIP Archive - 7.3 GB -

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.

Source Data Table 16.zip

Jul 22, 2025 - Source Data from "An automated workflow to address proteome complexity and the large-search-space problem in proteomics and HLA-I immunopeptidomics."

ZIP Archive - 260.0 MB -

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.

Source Data Table 17.zip

Jul 22, 2025 - Source Data from "An automated workflow to address proteome complexity and the large-search-space problem in proteomics and HLA-I immunopeptidomics."

ZIP Archive - 292.9 MB -

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.

Source Data Table 18.zip

Jul 22, 2025 - Source Data from "An automated workflow to address proteome complexity and the large-search-space problem in proteomics and HLA-I immunopeptidomics."

ZIP Archive - 400.6 KB -

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...

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