A graphical user interface for RAId, a knowledge integrated proteomics analysis suite with accurate statistics
Abstract Objective RAId is a software package that has been actively developed for the past 10 years for computationally and visually analyzing MS/MS data. Founded on rigorous statistical methods, RAId’s core program computes accurate E-values for peptides and proteins identified during database sea...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2018-03-01
|
| Series: | BMC Research Notes |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13104-018-3289-6 |
| _version_ | 1811289437382901760 |
|---|---|
| author | Brendan Joyce Danny Lee Alex Rubio Aleksey Ogurtsov Gelio Alves Yi-Kuo Yu |
| author_facet | Brendan Joyce Danny Lee Alex Rubio Aleksey Ogurtsov Gelio Alves Yi-Kuo Yu |
| author_sort | Brendan Joyce |
| collection | DOAJ |
| description | Abstract Objective RAId is a software package that has been actively developed for the past 10 years for computationally and visually analyzing MS/MS data. Founded on rigorous statistical methods, RAId’s core program computes accurate E-values for peptides and proteins identified during database searches. Making this robust tool readily accessible for the proteomics community by developing a graphical user interface (GUI) is our main goal here. Results We have constructed a graphical user interface to facilitate the use of RAId on users’ local machines. Written in Java, RAId_GUI not only makes easy executions of RAId but also provides tools for data/spectra visualization, MS-product analysis, molecular isotopic distribution analysis, and graphing the retrieval versus the proportion of false discoveries. The results viewer displays and allows the users to download the analyses results. Both the knowledge-integrated organismal databases and the code package (containing source code, the graphical user interface, and a user manual) are available for download at https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads/raid.html. |
| first_indexed | 2024-04-13T03:54:48Z |
| format | Article |
| id | doaj.art-a6bb175c924040f8a5c19792e8fc6a80 |
| institution | Directory Open Access Journal |
| issn | 1756-0500 |
| language | English |
| last_indexed | 2024-04-13T03:54:48Z |
| publishDate | 2018-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Research Notes |
| spelling | doaj.art-a6bb175c924040f8a5c19792e8fc6a802022-12-22T03:03:40ZengBMCBMC Research Notes1756-05002018-03-011111710.1186/s13104-018-3289-6A graphical user interface for RAId, a knowledge integrated proteomics analysis suite with accurate statisticsBrendan Joyce0Danny Lee1Alex Rubio2Aleksey Ogurtsov3Gelio Alves4Yi-Kuo Yu5National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthNational Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthNational Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthNational Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthNational Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthNational Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthAbstract Objective RAId is a software package that has been actively developed for the past 10 years for computationally and visually analyzing MS/MS data. Founded on rigorous statistical methods, RAId’s core program computes accurate E-values for peptides and proteins identified during database searches. Making this robust tool readily accessible for the proteomics community by developing a graphical user interface (GUI) is our main goal here. Results We have constructed a graphical user interface to facilitate the use of RAId on users’ local machines. Written in Java, RAId_GUI not only makes easy executions of RAId but also provides tools for data/spectra visualization, MS-product analysis, molecular isotopic distribution analysis, and graphing the retrieval versus the proportion of false discoveries. The results viewer displays and allows the users to download the analyses results. Both the knowledge-integrated organismal databases and the code package (containing source code, the graphical user interface, and a user manual) are available for download at https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads/raid.html.http://link.springer.com/article/10.1186/s13104-018-3289-6Peptide identificationProtein identificationProteomicsTandem mass spectrometry |
| spellingShingle | Brendan Joyce Danny Lee Alex Rubio Aleksey Ogurtsov Gelio Alves Yi-Kuo Yu A graphical user interface for RAId, a knowledge integrated proteomics analysis suite with accurate statistics BMC Research Notes Peptide identification Protein identification Proteomics Tandem mass spectrometry |
| title | A graphical user interface for RAId, a knowledge integrated proteomics analysis suite with accurate statistics |
| title_full | A graphical user interface for RAId, a knowledge integrated proteomics analysis suite with accurate statistics |
| title_fullStr | A graphical user interface for RAId, a knowledge integrated proteomics analysis suite with accurate statistics |
| title_full_unstemmed | A graphical user interface for RAId, a knowledge integrated proteomics analysis suite with accurate statistics |
| title_short | A graphical user interface for RAId, a knowledge integrated proteomics analysis suite with accurate statistics |
| title_sort | graphical user interface for raid a knowledge integrated proteomics analysis suite with accurate statistics |
| topic | Peptide identification Protein identification Proteomics Tandem mass spectrometry |
| url | http://link.springer.com/article/10.1186/s13104-018-3289-6 |
| work_keys_str_mv | AT brendanjoyce agraphicaluserinterfaceforraidaknowledgeintegratedproteomicsanalysissuitewithaccuratestatistics AT dannylee agraphicaluserinterfaceforraidaknowledgeintegratedproteomicsanalysissuitewithaccuratestatistics AT alexrubio agraphicaluserinterfaceforraidaknowledgeintegratedproteomicsanalysissuitewithaccuratestatistics AT alekseyogurtsov agraphicaluserinterfaceforraidaknowledgeintegratedproteomicsanalysissuitewithaccuratestatistics AT gelioalves agraphicaluserinterfaceforraidaknowledgeintegratedproteomicsanalysissuitewithaccuratestatistics AT yikuoyu agraphicaluserinterfaceforraidaknowledgeintegratedproteomicsanalysissuitewithaccuratestatistics AT brendanjoyce graphicaluserinterfaceforraidaknowledgeintegratedproteomicsanalysissuitewithaccuratestatistics AT dannylee graphicaluserinterfaceforraidaknowledgeintegratedproteomicsanalysissuitewithaccuratestatistics AT alexrubio graphicaluserinterfaceforraidaknowledgeintegratedproteomicsanalysissuitewithaccuratestatistics AT alekseyogurtsov graphicaluserinterfaceforraidaknowledgeintegratedproteomicsanalysissuitewithaccuratestatistics AT gelioalves graphicaluserinterfaceforraidaknowledgeintegratedproteomicsanalysissuitewithaccuratestatistics AT yikuoyu graphicaluserinterfaceforraidaknowledgeintegratedproteomicsanalysissuitewithaccuratestatistics |