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A python command line tool for the quantification of peptidoform/proteoforms

Project description


Proteoformquant is a Python tool for quantitative analysis of proteoforms from mass spectrometry data.


Via PyPi repository (Recommended)

1. Install Proteoformquant package

The simplest way to use Proteformquant is to downloading it as a package from the PyPi repository using pip.

pip install proteoformquant

You should then be able to run Proteoformquant by running the following line in a terminal

2. Run Proteoformquant


Access help by running

proteoformquant -h

More information on how to use proteoformquant is avaible in the 'usage' section of this document.

Via github (Alternative) (not available currently)

You also have the possibility to clone the repository from github and manually install the dependencies. You will need to create a Conda environment.

1. Install Conda (and Mamba)

If not already done, install Conda (

If you wish to use Mamba to create the Conda environment (faster) you can install mamba by running the following command in a terminal:

conda install mamba -n base -c conda-forge

2. Clone proteoformquant repository

git clone

3. Create and activate the environment

Next, create the environment using either Conda or Mamba by running the following command in the folder where 'environment.yml' is located

# With Conda
conda env create --file environment.yml
#With Manba
mamba env create --file environment.yml

you should now be able to activate the environment with:

mamba activate pfq-env

4. Run Proteoformquant

Run Proteoformquant by running the '' script in 'src/proteoformquant'

python3 src/proteoformquant/


(n.b the command line listed here are given for the installation of Proteoformquant as a package. you will need to adapt the commands if you use the second installation method)

Proteoform requires 3 input files: -spectra file (.mgf or .mzml) -indentification file (.mzid) -a parameter file (.json)

A parameter file can be generated by running.

proteoformquant -cp

If you do not change the name or location of the parameter file you can run proteoformquant as follow

proteoformquant -i path/to/identification/file.mzid -s path/to/spectra/file.mgf

by default this will create an output file 'output/' in the local directory. If you wish to change that use the -d parameter

proteoformquant -i path/to/identification/file.mzid -s path/to/spectra/file.mgf -d path/to/my_output_folder

similarly you can change the outfile name with the -o parameter

proteoformquant -i path/to/identification/file.mzid -s path/to/spectra/file.mgf -d path/to/my_output_folder -o output_file_1


To update


To update

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