A reference database enabling in-depth proteome and PTM analysis of mouse immune cells
Abstract Spectral libraries fulfill multiple functions in biological and analytical applications. For biologists, these libraries provide a valuable resource to verify the presence and abundance of proteins or pathways within a selected cell type thus determine the feasibility of further experiments...
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| Format: | Article |
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Nature Portfolio
2025-04-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-025-04829-9 |
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| author | Devon Siemes Hannah Voss Federica Benvenuti Francesca Simoncello Dominik Kopczynski Bente Siebels Hartmut Schlüter Laxmikanth Kollipara Albert Sickmann Daniel Robert Engel Olga Shevchuk |
| author_facet | Devon Siemes Hannah Voss Federica Benvenuti Francesca Simoncello Dominik Kopczynski Bente Siebels Hartmut Schlüter Laxmikanth Kollipara Albert Sickmann Daniel Robert Engel Olga Shevchuk |
| author_sort | Devon Siemes |
| collection | DOAJ |
| description | Abstract Spectral libraries fulfill multiple functions in biological and analytical applications. For biologists, these libraries provide a valuable resource to verify the presence and abundance of proteins or pathways within a selected cell type thus determine the feasibility of further experiments. Despite advances, existing libraries are incomplete and provide researchers only a limited amount of information. To address this, we introduce the reference database - Spectral Library of Immune Cells (SpLICe), a resource covering B-cells, CD4 and CD8 T-cells, macrophages and dendritic cells containing nearly 9,000 protein groups and 110,346 proteotypic peptides. Additionally, the database provides data on > 20,000 post-translationally modified proteotypic peptides (oxidation, phosphorylation, methylation, acetylation, deamidation and N-glycosylation) across the selected immune cell populations. SpLICe supports the quantification of more than half of total murine proteins annotated by UniProtKB/Swiss-Prot, enabling monitoring of selected proteins or pathways from Reactome pathways and Gene Ontology databases. The platform provides relative protein abundances and supports the generation of targeted mass spectrometry assays by identifying and scoring proteotypic peptides. |
| format | Article |
| id | doaj-art-5c03690bccd84b719708bcdb34fc3888 |
| institution | OA Journals |
| issn | 2052-4463 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj-art-5c03690bccd84b719708bcdb34fc38882025-08-20T02:11:51ZengNature PortfolioScientific Data2052-44632025-04-011211810.1038/s41597-025-04829-9A reference database enabling in-depth proteome and PTM analysis of mouse immune cellsDevon Siemes0Hannah Voss1Federica Benvenuti2Francesca Simoncello3Dominik Kopczynski4Bente Siebels5Hartmut Schlüter6Laxmikanth Kollipara7Albert Sickmann8Daniel Robert Engel9Olga Shevchuk10Department of Immunodynamics, Institute for Experimental Immunology and Imaging, University Duisburg-EssenDepartment of Immunodynamics, Institute for Experimental Immunology and Imaging, University Duisburg-EssenCellular Immunology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB)Cellular Immunology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB)Institute for Analytical Chemistry, University of ViennaSection Mass Spectrometry and Proteomics, Center for Diagnostics, University Medical Center Hamburg-EppendorfSection Mass Spectrometry and Proteomics, Center for Diagnostics, University Medical Center Hamburg-EppendorfLeibniz-Institut für Analytische Wissenschaften-ISAS-e.V.Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V.Department of Immunodynamics, Institute for Experimental Immunology and Imaging, University Duisburg-EssenDepartment of Immunodynamics, Institute for Experimental Immunology and Imaging, University Duisburg-EssenAbstract Spectral libraries fulfill multiple functions in biological and analytical applications. For biologists, these libraries provide a valuable resource to verify the presence and abundance of proteins or pathways within a selected cell type thus determine the feasibility of further experiments. Despite advances, existing libraries are incomplete and provide researchers only a limited amount of information. To address this, we introduce the reference database - Spectral Library of Immune Cells (SpLICe), a resource covering B-cells, CD4 and CD8 T-cells, macrophages and dendritic cells containing nearly 9,000 protein groups and 110,346 proteotypic peptides. Additionally, the database provides data on > 20,000 post-translationally modified proteotypic peptides (oxidation, phosphorylation, methylation, acetylation, deamidation and N-glycosylation) across the selected immune cell populations. SpLICe supports the quantification of more than half of total murine proteins annotated by UniProtKB/Swiss-Prot, enabling monitoring of selected proteins or pathways from Reactome pathways and Gene Ontology databases. The platform provides relative protein abundances and supports the generation of targeted mass spectrometry assays by identifying and scoring proteotypic peptides.https://doi.org/10.1038/s41597-025-04829-9 |
| spellingShingle | Devon Siemes Hannah Voss Federica Benvenuti Francesca Simoncello Dominik Kopczynski Bente Siebels Hartmut Schlüter Laxmikanth Kollipara Albert Sickmann Daniel Robert Engel Olga Shevchuk A reference database enabling in-depth proteome and PTM analysis of mouse immune cells Scientific Data |
| title | A reference database enabling in-depth proteome and PTM analysis of mouse immune cells |
| title_full | A reference database enabling in-depth proteome and PTM analysis of mouse immune cells |
| title_fullStr | A reference database enabling in-depth proteome and PTM analysis of mouse immune cells |
| title_full_unstemmed | A reference database enabling in-depth proteome and PTM analysis of mouse immune cells |
| title_short | A reference database enabling in-depth proteome and PTM analysis of mouse immune cells |
| title_sort | reference database enabling in depth proteome and ptm analysis of mouse immune cells |
| url | https://doi.org/10.1038/s41597-025-04829-9 |
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