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ionFinder

Search MS2 spectra for diagnostic neutral loss ions.

Configuring and building ionFinder

System requirements

ionFinder in written in c++ 11 and be compiled on Linux or macOS. Windows is not supported. Additional helper scripts are written in Python 3.

  • GCC or other compiler compatible with c++ 11
  • Cmake (>= 3.9)
  • Python (> 3.6) with pandas package installed.

Configuring

The following example assumes that the program is being built in ~/code/ionFinder

mkdir -p ~/code/ionFinder
cd ~/code/ionFinder
git clone --recurse-submodules https://github.com/weerapana-lab/ionFinder
mkdir -p ~/code/ionFinder/build
cd ~/code/ionFinder/build
cmake ~/code/ionFinder/ionFinder

You can set CMake configuration variables adding -DVARIABLE=VALUE options when calling CMake. The most important CMake variables are:

Variable Description
CMAKE_CXX_COMPILER Defines the C++ compiler to use.
PYTHON_EXE Define python interpreter to use.

Building

To build ionFinder run:

make

If everything worked, the executable files should be in the bin directory

$ ls bin
ionFinder
parse_maxquant
parse_scaffold

Usage

ionFinder works with 2 input modes.

  1. dtafilter which reads PSMs from DTASelect-filter.txt files
  2. tsv which reads PSMs from .tsv files
ionFinder -i dtafilter --citStats <directory> [...] # dtafilter mode
ionFinder -i tsv --citStats <tsv_file>              # tsv mode

Run:

ionFinder --help

to get a comprehensive list of optional arguments and settings.

See the examples folder in the ionFinder parent directory for examples of each type of input file.

Citation

Please cite:

Maurais, A. J.; Salinger, A. J.; Tobin, M.; Shaffer, S. A.; Weerapana, E.; Thompson, P. R., A Streamlined Data Analysis Pipeline for the Identification of Sites of Citrullination. Biochemistry 2021.