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Updated news with latest updates on Proteomics Sandbox
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jacobfh1 committed Nov 20, 2023
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The Proteomics Sandbox App is an excellent resource for biomedical students and non-computational researchers to learn and apply clinical proteomics. It provides a stable platform for proteomics software tools and offers a user-friendly interface. It is easy to use and does not require extensive coding knowledge. Furthermore, the app's lightweight clone feature optimizes storage requirements when working with datasets.

### Software
The software available in the Proteomics Sandbox includes [FragPipe](https://fragpipe.nesvilab.org/), [MaxQuant](https://www.maxquant.org/), [PDV](https://github.com/wenbostar/PDV), [SearchGUI](https://compomics.github.io/projects/searchgui.html), [ThermoRawFileParser](https://github.com/compomics/ThermoRawFileParser), and [PeptideShaker](https://compomics.github.io/projects/peptide-shaker.html). These software tools provide automated peptide and protein identification and quantification, comprehensive proteomics data analysis, visualization tools for spectral matches, a user-friendly interface for performing peptide searches, and a tool for visualizing and analyzing peptide search results. An overview table with a short description of each software tool is listed below for reference.
The software available in the Proteomics Sandbox includes [FragPipe](https://fragpipe.nesvilab.org/), [MaxQuant](https://www.maxquant.org/), [PDV](https://github.com/wenbostar/PDV), [SearchGUI](https://compomics.github.io/projects/searchgui.html), [ThermoRawFileParser](https://github.com/compomics/ThermoRawFileParser), [PeptideShaker](https://compomics.github.io/projects/peptide-shaker.html), [MZmine 3](https://mzmine.github.io/), and [DIA-NN](https://github.com/vdemichev/DiaNN). These software tools provide automated peptide and protein identification and quantification, comprehensive proteomics data analysis, visualization tools for spectral matches, a user-friendly interface for performing peptide searches, and a tool for visualizing and analyzing peptide search results. An overview table with a short description of each software tool is listed below for reference.

| Software | Description |
| ------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------- |
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| [SearchGUI](https://compomics.github.io/projects/searchgui.html) | User-friendly interface for performing peptide searches using multiple search engines (e.g., MSFragger, X!Tandem, OMSSA). Supports a wide range of search options and post-processing features. |
| [ThermoRawFileParser](https://github.com/compomics/ThermoRawFileParser) | A tool for converting Thermo Scientific RAW files to an open format mzML file that can be read by other proteomics software. Includes options for filtering, peak picking, and data conversion. |
| [PeptideShaker](https://compomics.github.io/projects/peptide-shaker.html) | Tool for visualizing and analyzing the results of peptide searches performed with SearchGUI. Includes features for filtering, annotation, and visualization of results. Supports integration with other proteomics databases and software. |
| [MZmine 3](https://mzmine.github.io/) | Open-source software for LC-MS data processing, MZmine 3 is a complete redesign of the original MZmine toolbox. It offers a flexible, user-friendly platform with modules for the full LC-MS data analysis workflow. |
| [DIA-NN](https://github.com/vdemichev/DiaNN) | DIA-NN is a universal tool for DIA proteomics data. It features robust algorithms for reliable, large-scale experiments, emphasizing ease of use, reproducibility, and high throughput, processing up to 1000 runs per hour. |


### Efficient and User-Friendly Proteomics Software Access
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