Proteome Discoverer—A Community Enhanced Data Processing Suite for Protein Informatics
Proteomics researchers today face an interesting challenge: how to choose among the dozens of data processing and analysis pipelines available for converting tandem mass spectrometry files to protein identifications. Due to the dominance of Orbitrap technology in proteomics in recent history, many r...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-03-01
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| Series: | Proteomes |
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| Online Access: | https://www.mdpi.com/2227-7382/9/1/15 |
| _version_ | 1797540392756838400 |
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| author | Benjamin C. Orsburn |
| author_facet | Benjamin C. Orsburn |
| author_sort | Benjamin C. Orsburn |
| collection | DOAJ |
| description | Proteomics researchers today face an interesting challenge: how to choose among the dozens of data processing and analysis pipelines available for converting tandem mass spectrometry files to protein identifications. Due to the dominance of Orbitrap technology in proteomics in recent history, many researchers have defaulted to the vendor software Proteome Discoverer. Over the fourteen years since the initial release of the software, it has evolved in parallel with the increasingly complex demands faced by proteomics researchers. Today, Proteome Discoverer exists in two distinct forms with both powerful commercial versions and fully functional free versions in use in many labs today. Throughout the 11 main versions released to date, a central theme of the software has always been the ability to easily view and verify the spectra from which identifications are made. This ability is, even today, a key differentiator from other data analysis solutions. In this review I will attempt to summarize the history and evolution of Proteome Discoverer from its first launch to the versions in use today. |
| first_indexed | 2024-03-10T12:59:26Z |
| format | Article |
| id | doaj.art-e46c90e857fb41bcb21d925009d318e3 |
| institution | Directory Open Access Journal |
| issn | 2227-7382 |
| language | English |
| last_indexed | 2024-03-10T12:59:26Z |
| publishDate | 2021-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Proteomes |
| spelling | doaj.art-e46c90e857fb41bcb21d925009d318e32023-11-21T11:39:21ZengMDPI AGProteomes2227-73822021-03-01911510.3390/proteomes9010015Proteome Discoverer—A Community Enhanced Data Processing Suite for Protein InformaticsBenjamin C. Orsburn0Department of Pharmacology and Molecular Sciences, Johns Hopkins University, Baltimore, MD 21205, USAProteomics researchers today face an interesting challenge: how to choose among the dozens of data processing and analysis pipelines available for converting tandem mass spectrometry files to protein identifications. Due to the dominance of Orbitrap technology in proteomics in recent history, many researchers have defaulted to the vendor software Proteome Discoverer. Over the fourteen years since the initial release of the software, it has evolved in parallel with the increasingly complex demands faced by proteomics researchers. Today, Proteome Discoverer exists in two distinct forms with both powerful commercial versions and fully functional free versions in use in many labs today. Throughout the 11 main versions released to date, a central theme of the software has always been the ability to easily view and verify the spectra from which identifications are made. This ability is, even today, a key differentiator from other data analysis solutions. In this review I will attempt to summarize the history and evolution of Proteome Discoverer from its first launch to the versions in use today.https://www.mdpi.com/2227-7382/9/1/15proteomicsprotein informaticsglycoproteomicsmass spectrometry |
| spellingShingle | Benjamin C. Orsburn Proteome Discoverer—A Community Enhanced Data Processing Suite for Protein Informatics Proteomes proteomics protein informatics glycoproteomics mass spectrometry |
| title | Proteome Discoverer—A Community Enhanced Data Processing Suite for Protein Informatics |
| title_full | Proteome Discoverer—A Community Enhanced Data Processing Suite for Protein Informatics |
| title_fullStr | Proteome Discoverer—A Community Enhanced Data Processing Suite for Protein Informatics |
| title_full_unstemmed | Proteome Discoverer—A Community Enhanced Data Processing Suite for Protein Informatics |
| title_short | Proteome Discoverer—A Community Enhanced Data Processing Suite for Protein Informatics |
| title_sort | proteome discoverer a community enhanced data processing suite for protein informatics |
| topic | proteomics protein informatics glycoproteomics mass spectrometry |
| url | https://www.mdpi.com/2227-7382/9/1/15 |
| work_keys_str_mv | AT benjamincorsburn proteomediscovereracommunityenhanceddataprocessingsuiteforproteininformatics |