amica: an interactive and user-friendly web-platform for the analysis of proteomics data
Abstract Background Quantitative proteomics has become an increasingly prominent tool in the study of life sciences. A substantial hurdle for many biologists are, however, the intricacies involved in the associated high throughput data analysis. Results In order to facilitate this task for users wit...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-12-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-022-09058-7 |
| _version_ | 1811302080879525888 |
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| author | Sebastian Didusch Moritz Madern Markus Hartl Manuela Baccarini |
| author_facet | Sebastian Didusch Moritz Madern Markus Hartl Manuela Baccarini |
| author_sort | Sebastian Didusch |
| collection | DOAJ |
| description | Abstract Background Quantitative proteomics has become an increasingly prominent tool in the study of life sciences. A substantial hurdle for many biologists are, however, the intricacies involved in the associated high throughput data analysis. Results In order to facilitate this task for users with limited background knowledge, we have developed amica, a freely available open-source web-based software that accepts proteomic input files from different sources. amica provides quality control, differential expression, biological network and over-representation analysis on the basis of minimal user input. Scientists can use amica’s query interface interactively to compare multiple conditions and rapidly identify enriched or depleted proteins. They can visualize their results using customized output graphics, and ultimately export the results in a tab-separated format that can be shared with collaborators. The code for the application, input data and documentation can be accessed online at https://github.com/tbaccata/amica and is also incorporated in the web application. Conclusions The strong emphasis on dynamic user interactions, the integration of various databases and the option to download processed data, facilitate the analysis of complex proteomic data for both first-time users and experienced bioinformaticians. A freely available version of amica is available at https://bioapps.maxperutzlabs.ac.at/app/amica . |
| first_indexed | 2024-04-13T07:20:34Z |
| format | Article |
| id | doaj.art-c52e1ce3c43b45e59a6e49e428194612 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-13T07:20:34Z |
| publishDate | 2022-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-c52e1ce3c43b45e59a6e49e4281946122022-12-22T02:56:37ZengBMCBMC Genomics1471-21642022-12-012311910.1186/s12864-022-09058-7amica: an interactive and user-friendly web-platform for the analysis of proteomics dataSebastian Didusch0Moritz Madern1Markus Hartl2Manuela Baccarini3Max Perutz Labs, Vienna Biocenter Campus (VBC)Max Perutz Labs, Vienna Biocenter Campus (VBC)Max Perutz Labs, Vienna Biocenter Campus (VBC)Max Perutz Labs, Vienna Biocenter Campus (VBC)Abstract Background Quantitative proteomics has become an increasingly prominent tool in the study of life sciences. A substantial hurdle for many biologists are, however, the intricacies involved in the associated high throughput data analysis. Results In order to facilitate this task for users with limited background knowledge, we have developed amica, a freely available open-source web-based software that accepts proteomic input files from different sources. amica provides quality control, differential expression, biological network and over-representation analysis on the basis of minimal user input. Scientists can use amica’s query interface interactively to compare multiple conditions and rapidly identify enriched or depleted proteins. They can visualize their results using customized output graphics, and ultimately export the results in a tab-separated format that can be shared with collaborators. The code for the application, input data and documentation can be accessed online at https://github.com/tbaccata/amica and is also incorporated in the web application. Conclusions The strong emphasis on dynamic user interactions, the integration of various databases and the option to download processed data, facilitate the analysis of complex proteomic data for both first-time users and experienced bioinformaticians. A freely available version of amica is available at https://bioapps.maxperutzlabs.ac.at/app/amica .https://doi.org/10.1186/s12864-022-09058-7ProteomicsLC-MS/MSWeb applicationData analysisData visualization |
| spellingShingle | Sebastian Didusch Moritz Madern Markus Hartl Manuela Baccarini amica: an interactive and user-friendly web-platform for the analysis of proteomics data BMC Genomics Proteomics LC-MS/MS Web application Data analysis Data visualization |
| title | amica: an interactive and user-friendly web-platform for the analysis of proteomics data |
| title_full | amica: an interactive and user-friendly web-platform for the analysis of proteomics data |
| title_fullStr | amica: an interactive and user-friendly web-platform for the analysis of proteomics data |
| title_full_unstemmed | amica: an interactive and user-friendly web-platform for the analysis of proteomics data |
| title_short | amica: an interactive and user-friendly web-platform for the analysis of proteomics data |
| title_sort | amica an interactive and user friendly web platform for the analysis of proteomics data |
| topic | Proteomics LC-MS/MS Web application Data analysis Data visualization |
| url | https://doi.org/10.1186/s12864-022-09058-7 |
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