simsi-transfer 0.1.0

Software-assisted reduction of missing values in phosphoproteomics and proteomics isobaric labeling data using MS2 spectrum clustering

SIMSI-Transfer

Tool for increasing PSM gain from MaxQuant output file. Requires "Experiment" set in MaxQuant!

Example usage:

python -m simsi_transfer --mq_txt_folder </path/to/txt/folder> --raw_folder </path/to/raw/folder> --output_folder </path/to/output/folder>

Stuff left to do:

• Implement masking analysis for FDR estimation (?)

Installation

pip install simsi-transfer

Building the GUI on Windows

Create a conda environment

Try importing conda_environment.yml in the Anaconda environment tab.

If that does not work, try the following:

1. Set up a new environment, either through the Anaconda UI, or by running the following on the command line:

conda create -n simsi_transfer_gui python=3.6
activate simsi_transfer_gui

2. There are some caveats with installing the dependencies. We want to avoid dependence on the MKL (Math Kernel Library) package by numpy/scipy, as this blows up the size of the .exe file over 200MB (see here).

conda install -c conda-forge nomkl numpy pandas pyqt pyinstaller

Building a self-contained executable

Use the build_gui.bat script to create a self-contained executable.

Reducing size of the executable

Download UPX (https://upx.github.io/) to reduce the DLL file sizes, change the path in build_gui.bat to point to the UPX folder.