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31 to 40 of 141,660 Results

FigS5.zip Jul 23, 2025 - Realization of a Rydberg-dressed extended Bose-Hubbard model ZIP Archive - 20.6 KB - MD5: 3cb9202ac7abc4cb17a3a742364e05f6
FigS6.zip Jul 23, 2025 - Realization of a Rydberg-dressed extended Bose-Hubbard model ZIP Archive - 52.0 KB - MD5: 822c0739a8ebcb1c68b95242cec27f3d
FigS7.zip Jul 23, 2025 - Realization of a Rydberg-dressed extended Bose-Hubbard model ZIP Archive - 2.3 KB - MD5: 31e88540c8e04b3efbb502a7aebd8026
FigS8.zip Jul 23, 2025 - Realization of a Rydberg-dressed extended Bose-Hubbard model ZIP Archive - 4.9 KB - MD5: 0e2625f312a5316500320730fbf03880
FigS9.zip Jul 23, 2025 - Realization of a Rydberg-dressed extended Bose-Hubbard model ZIP Archive - 14.6 KB - MD5: 867d1737640ab96d5c4e16dfc6f70f75
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 10.xlsx 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." MS Excel Spreadsheet - 3.7 MB - MD5: 336716d13899598876da4869ed42544d Peptide multi-mapping within strata. This file contains the numbers of peptides per number of multimapping origins within proteogenomic strata. For exhaustive transcriptomic and genomic ORFs the peptide mapping was checked on ORF level, for reference proteome, CDS off-frame and cis25-spliced peptides the mapping was checked also on gene level. Both...
Source Data Table 11.xlsx 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." 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.
Source Data Table 12.xlsx 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." 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...
Source Data Table 13.xlsx 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." 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.

FigS5.zip

Jul 23, 2025 - Realization of a Rydberg-dressed extended Bose-Hubbard model

ZIP Archive - 20.6 KB -

FigS6.zip

Jul 23, 2025 - Realization of a Rydberg-dressed extended Bose-Hubbard model

ZIP Archive - 52.0 KB -

FigS7.zip

Jul 23, 2025 - Realization of a Rydberg-dressed extended Bose-Hubbard model

ZIP Archive - 2.3 KB -

FigS8.zip

Jul 23, 2025 - Realization of a Rydberg-dressed extended Bose-Hubbard model

ZIP Archive - 4.9 KB -

FigS9.zip

Jul 23, 2025 - Realization of a Rydberg-dressed extended Bose-Hubbard model

ZIP Archive - 14.6 KB -

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 10.xlsx

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."

MS Excel Spreadsheet - 3.7 MB -

Peptide multi-mapping within strata. This file contains the numbers of peptides per number of multimapping origins within proteogenomic strata. For exhaustive transcriptomic and genomic ORFs the peptide mapping was checked on ORF level, for reference proteome, CDS off-frame and cis25-spliced peptides the mapping was checked also on gene level. Both...

Source Data Table 11.xlsx

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."

MS Excel Spreadsheet - 13.4 KB -

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.

Source Data Table 12.xlsx

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."

MS Excel Spreadsheet - 1.5 MB -

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...

Source Data Table 13.xlsx

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."

MS Excel Spreadsheet - 30.9 KB -

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.

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