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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31 to 40 of 205,478 Results

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...
Source Data Table 19.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 - 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...
Source Data Table 2.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 - 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.
Source Data Table 20.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 - 314.4 KB - MD5: a5614357a2aa2f915298e1b113aecd8a Peptide sequences identified with the group specific FDR estimation. This file contains .csv files of peptide sequences filtered for 1% FDR identified with the group specific FDR estimation combined strategy using either MW filtered, MW-RT filtered or MW-RT-HLA-I binding filtered reference databases, respectively. Furthermore, peptide sequences ide...
Source Data Table 3.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 - 54.9 KB - MD5: 07ac6d02e874305e8dfb21f439a72ff1 Ratios of nonspecific/tryptic peptides in K562 cell line. An .xlsx table, reporting the numbers of unique peptides in GENCODE-informed and RNA-seq informed strata, across filtering steps. Includes the ratios of nonspecific/tryptic peptide counts.
Source Data Table 4.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 - 206.1 KB - MD5: 6c277adf5086dcd71eca9728509e657a Gene fusion detection in K562 cell line. An .xlsx table, derived from the Arriba gene fusion detection tool, reporting the identified gene fusions and corresponding biological replicates of K562 cells.
Source Data Table 5.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 - 77.8 KB - MD5: 976c9c2f80056769fb6277ef289fa6ad 703 PTMs investigated in Fig. 2d and Supplementary Fig. 3e. PTMs from Unimod database in tabular format.
Source Data Table 6.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 - 403.7 KB - MD5: fd37a2246d94884debcbb9c3765b7a72 PTM-peptide forms per protein. Number of unmodified peptides and PTM combinations in unfiltered search spaces and upon molecular weight filter.
Source Data Table 7.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 - 168.7 KB - MD5: 99ff04cc6e8fd97f876f940815b0fbd9 Strata search space sizes across SPIsnake filtering steps in K562. 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 K562-A02:01 and K562-B07:02 cell lines.

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...

Source Data Table 19.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 - 329.3 KB -

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...

Source Data Table 2.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 - 1.4 GB -

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.

Source Data Table 20.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 - 314.4 KB -

Peptide sequences identified with the group specific FDR estimation. This file contains .csv files of peptide sequences filtered for 1% FDR identified with the group specific FDR estimation combined strategy using either MW filtered, MW-RT filtered or MW-RT-HLA-I binding filtered reference databases, respectively. Furthermore, peptide sequences ide...

Source Data Table 3.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 - 54.9 KB -

Ratios of nonspecific/tryptic peptides in K562 cell line. An .xlsx table, reporting the numbers of unique peptides in GENCODE-informed and RNA-seq informed strata, across filtering steps. Includes the ratios of nonspecific/tryptic peptide counts.

Source Data Table 4.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 - 206.1 KB -

Gene fusion detection in K562 cell line. An .xlsx table, derived from the Arriba gene fusion detection tool, reporting the identified gene fusions and corresponding biological replicates of K562 cells.

Source Data Table 5.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 - 77.8 KB -

703 PTMs investigated in Fig. 2d and Supplementary Fig. 3e. PTMs from Unimod database in tabular format.

Source Data Table 6.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 - 403.7 KB -

PTM-peptide forms per protein. Number of unmodified peptides and PTM combinations in unfiltered search spaces and upon molecular weight filter.

Source Data Table 7.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 - 168.7 KB -

Strata search space sizes across SPIsnake filtering steps in K562. 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 K562-A*02:01 and K562-B*07:02 cell lines.

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