Proteomics Sandbox¶
Operating System:
Terminal:
Shell:
Editor:
Package Manager:
Programming Language:
Utility:
Operating System:
Terminal:
Shell:
Editor:
Package Manager:
Programming Language:
Utility:
Operating System:
Terminal:
Shell:
Editor:
Package Manager:
Programming Language:
Utility:
Operating System:
Terminal:
Shell:
Editor:
Package Manager:
Programming Language:
Utility:
Operating System:
Terminal:
Shell:
Editor:
Package Manager:
Programming Language:
Utility:
Operating System:
Terminal:
Shell:
Editor:
Package Manager:
Programming Language:
Utility:
Operating System:
Terminal:
Shell:
Editor:
Package Manager:
Programming Language:
Utility:
Operating System:
Terminal:
Shell:
Editor:
Package Manager:
Programming Language:
Utility:
Operating System:
Terminal:
Shell:
Editor:
Package Manager:
Programming Language:
Utility:
The Proteomics Sandbox 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.
Initialization¶
For information on how to use the Initialization parameter, please refer to the Initialization: Bash Script section of the documentation.
Configure SSH Access¶
The app provides optional support for SSH access from an external client. An SSH public key must be uploaded using the corresponding panel in Resources section of the UCloud side menu.
By checking on Enable SSH server a random port is opened for connection. The connection command is shown in the job progress view page.
Software Tools¶
The software tools available in the Proteomics Sandbox feature 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, as well as other data management and analysis tasks.
A complete list of the available software and its functionalities is repoted below:
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Universal software for DIA proteomics data processing, revolutionizing proteomics in 2018 with innovative algorithms.
Focuses on reliability, robustness, and reproducibility with stringent statistical control, flexible data modeling, and meticulous recording of all analysis steps.
User-friendly with a high degree of automation, no bioinformatics expertise required, and showcases scalability by processing up to 1000 mass spec runs per hour.
The newly developed GUI for Linux further enhances the user-friendliness for Proteomics Sandbox App users, making DIA-NN even more accessible.
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Automated peptide and protein identification and quantification using the MSFragger search engine.
Supports the identification of arbitrary PTMs.
Includes additional tools for post-processing and visualization of search results.
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Comprehensive software suite for proteomics data analysis.
Includes protein and peptide identification, quantification, and visualization of spectral matches.
Features an advanced search engine; only the command-line tool is available on Linux as the GUI is incompatible.
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Open-source software for LC-MS data processing.
Offers a user-friendly, adaptable, and expandable platform.
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Open-source framework for LC-MS data amangement and analysis.
Includes a C++ library with Python bindings and a collection of command-line tools.
PDV:
Visualization tool for spectral matches, particularly those obtained from MSFragger searches.
Allows users to inspect and evaluate the quality of the matches.
Supports annotation and customization of plots.
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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.
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A GUI application allowing you to submit your proteomics dataset directly from UCloud to the PRIDE archive.
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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.
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Converts 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.
VMD:
High-performance molecular visualization program for displaying, animating, and analyzing large biomolecular systems.
Supports various molecular dynamics simulations and bioinformatics analyses.
Analyzing Datasets¶
When working with the Proteomics Sandbox application, it is crucial to ensure that all your work is saved in the designated /work directory.
Failure to do so may result in permanent loss of your work when the session ends or expires.
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