ProSAP (Protein Stability Analysis Pod) is standalone and user-friendly software with graphical user interface (GUI). ProSAP provides an integrated analysis workflow for thermal shift assay, which includes five modules: data preprocessing, data visualization, TPP analysis, NPARC analysis and iTSA analysis. With the assistance of the user-friendly interface, researchers can easily compare several statistical strategies, analyze the results and draw the conclusion from the proteomics quantitative table obtained by Proteome Discoverer or MaxQuant. Users would also benefit from a comprehensive overview of the performance of different algorithms, and apply appropriate algorithms to their dataset easily.

Installation

Stable version:

Windows: ProSAP-0.99.5b-Windows.zip
Linux: ProSAP-0.99.5b-Linux.tar.xz
MacOS: ProSAP-0.99.5b-Mac.zip

For Windows:

The installer version should be preferred but might require administrator permissions. Please follow the video of the installation at video folder.

Note:

1. Since we do not pay Microsoft for certification, you might have to confirm that you want to trust "software from an unknown source".
2. When installing, please do not change the default path, because sometimes we find it does not run correctly with customized path.
3. We observed unknown errors happened if you have installed multiple versions of R. Uninstall all version of R and reinstall the latest version will fix the error.
4. When running for the first time, it may need a long time to install the R package. There will be some requirements showing in the command prompt window, you should just follow the instructions.

For Linux:

Please follow the following installation steps and refer the video of the installation at video folder:

1. Install R

    sudo apt-get install r-base
   

2. Install extra dependency of QT:

    sudo apt-get install libxcb-xinerama0
   

3. Download the tgz file and unzip to any folder and execute ProSAP.

4. Execute the binary file:

    ./ProSAP
   

5. When running for the first time, it may need a long time to install the R package. There will be some requirements showing in the command prompt window, you should just follow the instructions.

For MacOS:

Please follow the following installation steps and refer the video of the installation at video folder:

1. Allow software from unknown developers:

    sudo spctl --master-disable
   

2. Install R

3. Download the zip file and unzip to any folder and execute ProSAP.

4. Execute the binary file:

    ./ProSAP
   

5. When running for the first time, it may need a long time to install the R package. There will be some requirements showing in the command prompt window, you should just follow the instructions.

For MacOS with M1 chip:

1. If you are using MacBook Pro with M1 chip, you should install Rosetta.

    softwareupdate --install-rosetta --agree-to-license
   

2. Install R of High Sierra version (Inter 64 based). This is because rpy2 has not support ARM64 based R yet. We will update if rpy2 support it in the future.

3. Follow the same step 1 ~ step 5 of MacOS.

Note: ProSAP has been test on Windows 7, Windows 10, Windows 11, Ubuntu 20.04 and MacOS 11.6.1. However, it does not work on Windows XP.

Development version

For Windows or MacOS::

1. Install Anaconda or Miniconda

2. Install R

3. Install Git

4. Open commond line, create environment and enter with the following commands:

    conda create -n ProSAP python=3.8
    conda activate ProSAP
   

Note: MacBook Pro with M1 chip may need python=3.9 and make sure R version is suitable.
5. Clone the repository and enter:

    git clone https://github.com/hcji/ProSAP.git
    cd ProSAP

6. Install dependency with the following commands:

    pip install -r requirements.txt
   

7. Run ProSAP.py:

    python ProSAP.py
   

8. Or, you may want to compile binary and run exe:

    pyinstaller ProSAP.py -i ./img/ProSAP.ico --hidden-import=“sklearn.utils._weight_vector” 
    cd dist/ProSAP
    ProSAP.exe
   

For Linux:

1. Most Linux distributions have included git and conda, but you may need install extra dependency of QT:

    sudo apt-get install libxcb-xinerama0
   

2. Install R

    sudo apt-get install r-base
   

3. Refer the step 3 ~ step 7 of Windows or MacOS.

Document

The detailed usage is included in the ProSAP website.
The videos for using the software are available at the video folder.

Citation

@article{10.1093/bib/bbac057,
    author = {Ji, Hongchao and Lu, Xue and Zheng, Zhenxiang and Sun, Siyuan and Tan, Chris Soon Heng},
    title = "{ProSAP: a GUI software tool for statistical analysis and assessment of thermal stability data}",
    journal = {Briefings in Bioinformatics},
    year = {2022},
    month = {03}
    issn = {1477-4054},
    doi = {10.1093/bib/bbac057},
    url = {https://doi.org/10.1093/bib/bbac057},
    eprint = {https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbac057/42704881/bbac057.pdf}}

Contact

Ji Hongchao
E-mail: ji.hongchao@foxmail.com

https://orcid.org/0000-0002-7364-0741

WeChat public account: Chemocoder