PepQuery2 democratizes public MS proteomics data for rapid peptide searching
Abstract We present PepQuery2, which leverages a new tandem mass spectrometry (MS/MS) data indexing approach to enable ultrafast, targeted identification of novel and known peptides in any local or publicly available MS proteomics datasets. The stand-alone version of PepQuery2 allows directly search...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-04-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-023-37462-4 |
| _version_ | 1797840935803944960 |
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| author | Bo Wen Bing Zhang |
| author_facet | Bo Wen Bing Zhang |
| author_sort | Bo Wen |
| collection | DOAJ |
| description | Abstract We present PepQuery2, which leverages a new tandem mass spectrometry (MS/MS) data indexing approach to enable ultrafast, targeted identification of novel and known peptides in any local or publicly available MS proteomics datasets. The stand-alone version of PepQuery2 allows directly searching more than one billion indexed MS/MS spectra in the PepQueryDB or any public datasets from PRIDE, MassIVE, iProX, or jPOSTrepo, whereas the web version enables users to search datasets in PepQueryDB with a user-friendly interface. We demonstrate the utilities of PepQuery2 in a wide range of applications including detecting proteomic evidence for genomically predicted novel peptides, validating novel and known peptides identified using spectrum-centric database searching, prioritizing tumor-specific antigens, identifying missing proteins, and selecting proteotypic peptides for targeted proteomics experiments. By putting public MS proteomics data directly into the hands of scientists, PepQuery2 opens many new ways to transform these data into useful information for the broad research community. |
| first_indexed | 2024-04-09T16:22:52Z |
| format | Article |
| id | doaj.art-6aa48a4a42e7483ca686d58f80e5a959 |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-04-09T16:22:52Z |
| publishDate | 2023-04-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-6aa48a4a42e7483ca686d58f80e5a9592023-04-23T11:21:39ZengNature PortfolioNature Communications2041-17232023-04-0114111310.1038/s41467-023-37462-4PepQuery2 democratizes public MS proteomics data for rapid peptide searchingBo Wen0Bing Zhang1Lester and Sue Smith Breast Center, Baylor College of MedicineLester and Sue Smith Breast Center, Baylor College of MedicineAbstract We present PepQuery2, which leverages a new tandem mass spectrometry (MS/MS) data indexing approach to enable ultrafast, targeted identification of novel and known peptides in any local or publicly available MS proteomics datasets. The stand-alone version of PepQuery2 allows directly searching more than one billion indexed MS/MS spectra in the PepQueryDB or any public datasets from PRIDE, MassIVE, iProX, or jPOSTrepo, whereas the web version enables users to search datasets in PepQueryDB with a user-friendly interface. We demonstrate the utilities of PepQuery2 in a wide range of applications including detecting proteomic evidence for genomically predicted novel peptides, validating novel and known peptides identified using spectrum-centric database searching, prioritizing tumor-specific antigens, identifying missing proteins, and selecting proteotypic peptides for targeted proteomics experiments. By putting public MS proteomics data directly into the hands of scientists, PepQuery2 opens many new ways to transform these data into useful information for the broad research community.https://doi.org/10.1038/s41467-023-37462-4 |
| spellingShingle | Bo Wen Bing Zhang PepQuery2 democratizes public MS proteomics data for rapid peptide searching Nature Communications |
| title | PepQuery2 democratizes public MS proteomics data for rapid peptide searching |
| title_full | PepQuery2 democratizes public MS proteomics data for rapid peptide searching |
| title_fullStr | PepQuery2 democratizes public MS proteomics data for rapid peptide searching |
| title_full_unstemmed | PepQuery2 democratizes public MS proteomics data for rapid peptide searching |
| title_short | PepQuery2 democratizes public MS proteomics data for rapid peptide searching |
| title_sort | pepquery2 democratizes public ms proteomics data for rapid peptide searching |
| url | https://doi.org/10.1038/s41467-023-37462-4 |
| work_keys_str_mv | AT bowen pepquery2democratizespublicmsproteomicsdataforrapidpeptidesearching AT bingzhang pepquery2democratizespublicmsproteomicsdataforrapidpeptidesearching |