Edmond

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Edmond – the Open Research Data Repository of the Max Planck Society

Edmond is a research data repository for Max Planck researchers. It is the place to store completed datasets of research data with open access. Edmond serves the publication of research data from all disciplines and offers scientists the ability to create citable research objects.

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21 to 30 of 205,478 Results

Fig6.dat Jul 22, 2025 - Data to support Fig.2,Fig.3 ,Fig.4 and Fig.6 Fixed Field Text Data - 74.4 KB - MD5: 20306fe6adea9bc87afa4907a9cff66b 2D array for A_diff The value is in percent and the in-plane k_x and k_y range is +/-0.3968 inverse Angstrom
Fig2_d.dat Jul 22, 2025 - Data to support Fig.2,Fig.3 ,Fig.4 and Fig.6 Fixed Field Text Data - 73.0 KB - MD5: b406eacb29ca1c5c948a841e756893ec values are in percent and the in-plane k_x and k_y range is +/-0.3968 inverse Angstrom
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.
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.

Fig6.dat

Jul 22, 2025 - Data to support Fig.2,Fig.3 ,Fig.4 and Fig.6

Fixed Field Text Data - 74.4 KB -

2D array for A_diff The value is in percent and the in-plane k_x and k_y range is +/-0.3968 inverse Angstrom

Fig2_d.dat

Jul 22, 2025 - Data to support Fig.2,Fig.3 ,Fig.4 and Fig.6

Fixed Field Text Data - 73.0 KB -

values are in percent and the in-plane k_x and k_y range is +/-0.3968 inverse Angstrom

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.

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.

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