🔍 Supported Search Engines & Input Format

QuickSearchProt currently supports the following search engines:

• 🧪 Sage
• 🧬 X!Tandem

These engines are integrated to ensure flexible and efficient proteomics data analysis.

📄 Supported MS Data Format

• ✅ MGF (Mascot Generic Format)

Only .mgf files are supported as input for MS data at this stage. Make sure your spectra are properly formatted before initiating the search.

More search engines and formats will be added in future releases.

📦 Download

For testing the system, download the latest release:

➡️ QSProt.zip

This archive contains everything needed to run QuickSearchProt locally, including:

• 🧩 The QuickSearchProt.jar executable
• 🧪 Sample .mgf file for MS data input
• 🧬 Sample .fasta file containing protein sequences
• ⚙️ Example .par file compatible with SearchGUI

⚠️ Notes

• 📁 The searchengines/ folder includes essential binaries and configurations for Sage and X!Tandem.
  Do not modify or delete this folder, as it is required for proper execution.
• 📂 The test_data/ folder provides example input files to help you quickly test and validate the system.
• 🧾 The .par file can be reused directly in SearchGUI for reproducible and customizable searches.

This structure ensures a plug-and-play experience for testing and deploying QuickSearchProt in proteomics workflows.

📦 Be sure to extract all contents before launching the application.

Using QSProt

Unzip the downloaded file:

Locate the downloaded demo.zip file on your computer.

Right-click on the file and select "Extract All" or use a tool like WinRAR or 7-Zip to unzip the file.

Extract the contents to a folder of your choice.

Execute QSProt

QSProt requires Java 19 and Visual C++ Redistributable for Visual Studio 2012 Update 4.

Ensure that JVM 19 is installed on your computer. You can download it from the official Oracle website.

Open a command prompt or terminal window.

Navigate to the directory where the extracted JAR file is located using the cd command.

🚀 Running QuickSearchProt with Custom Memory Settings

To launch QuickSearchProt.jar with a minimum of 1 GB and a maximum of 30 GB of memory, use the following command:

java -Xms1g -Xmx30g -jar QuickSearchProt.jar

To configure the order of search parameters, you can modify the configurations.json file.

🧬 QuickSearchProt Usage Guide

• 📂 Enter the path to your MS data file (currently supports only .mgf format).
• 🧫 Provide the path to your FASTA file containing protein sequences.
• ⚙️ Specify the search parameter file (.par), which can be exported from SearchGUI.
• 🔧 Configure additional search specifications as needed.

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📁 Output Structure

Once the search is complete, the output folder will contain:

• ✅ Result files generated by the selected search engines.
• 📂 A dedicated folder for each search engine, containing:
  • The corresponding .par file with search parameters.
  • These .par files can be directly reused in SearchGUI for further analysis or reproducibility.

This structure ensures clarity, modularity, and compatibility with downstream proteomics workflows.

If you need further assistance with the specific syntax or examples, feel free to ask!