Getting Started

Published

December 2, 2024

Getting Started

!!! note “Section Overview”

🕰 **Time Estimation:** 10 minutes

💬 **Learning Objectives:**    
    1. Launch the Proteomics Sandbox App and become proficient in using it for proteomics data analysis.  
    2. Familiarize oneself with the software tools available within the app, such as FragPipe, MaxQuant, PDV, SearchGUI, and PeptideShaker.  
    3. Develop skills in utilizing the Proteomics Sandbox App's lightweight clone feature, in order to reduce storage requirements while analyzing large datasets.

Introduction

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, MaxQuant, PDV, SearchGUI, ThermoRawFileParser, PeptideShaker, MZmine 3, DIA-NN, and VMD. 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
FragPipe 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.
MaxQuant 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.
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.
SearchGUI 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 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 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 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 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.
VMD Visual Molecular Dynamics (VMD) is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3D graphics and built-in scripting. Supports various molecular dynamics simulations and bioinformatics analyses.

Efficient and User-Friendly Proteomics Software Access

!!! tip “Advantages of using the Proteomics Sandbox App” 1. Access to stable proteomics software tools. 2. User-friendly interface that does not require extensive coding knowledge. 3. Lightweight clone feature that optimizes storage requirements when working with datasets.

The Clinical Proteomics Sandbox is an excellent resource for biomedical students and non-computational researchers seeking to expand their knowledge and skills in clinical proteomics.

Future Plans

The Clinical Proteomics Sandbox is constantly evolving to provide an accessible platform for learning and practicing clinical proteomics data analysis. In the future, the sandbox will expand its content to include new modules such as:

  • Protein quantification and analysis of post-translational modifications, which will provide an even more comprehensive resource for those interested in clinical proteomics.
  • Introducing mass-spectrometry imaging (MSi) for clinical specimen. Data for MS imaging is available and public clinical datasets could also be included.
  • Generate course material based on clinical proteomics data using FragPipe.
  • Investigate protein complexes.

In addition, the sandbox aims to:

  • Make clinical proteomics data available for education and training purposes, offering students and researchers the opportunity to work with real-world clinical data and gain practical experience in analyzing and interpreting such data.
  • Move into statistical and functional analysis of quantitative proteomics data and meta-analysis of clinical proteomics data.

As the sandbox continues to evolve, it will offer an invaluable resource for those seeking to enhance their knowledge and skills in clinical proteomics data analysis.

In Brief

The Clinical Proteomics Sandbox App provides a stable platform for proteomics software tools and a user-friendly interface for non-computational researchers and biomedical students to learn and apply clinical proteomics. The app’s lightweight clone feature optimizes storage requirements when working with datasets. Software tools available include FragPipe, MaxQuant, PDV, SearchGUI, ThermoRawFileParser, and PeptideShaker. The Sandbox will expand its content in the future, including modules for protein quantification and analysis of post-translational modifications, and will make clinical proteomics data available for education and training purposes.