viQC - Visual&Intuitive quality control for bottom-up proteomics experiments

Requirements

• Python 3.x
• matplotlib
• pyteomics
• pandas
• seaborn
• statsmodels
• scipy
• sklearn

Installation via pip

sudo apt-get install python-setuptools python-dev build-essential

sudo easy_install pip

sudo pip install -U lxml numpy matplotlib pyteomics pandas seaborn statsmodels

Before use

Convert your raw files to mzML format. MSconvert can be used for this purpose. For the angle score calculation a list with PSMs is required (by default viQC works with MPscore/Scavager results, but it can be changed by optional parameters).

For the additional information about viQC program and user cases check the article; Russian speakers can enjoy the mother-tongue version.

For the additional information about angle score see the article

How to use

To install viQC, clone the repository and install with pip or distutils:

$ git clone https://github.com/lisavetasol/viQC
$ cd viQC
$ pip install .

To run viQC:

viQC input_mzML(s)

In case of multiple files, the program builds summarizing graphs as well as separate pictures for each analysis. For easier interpreting results start/stop parameters should be specified, otherwise, they will be calculated for each file separately and corresponding graphs (precursor intensity and MS/MS injection time) may not be comparable between files.

For help on parameters:

viQC --help

Optional parameters

-o - path to save result, by default save in the same folder as an input file

-start - delay time before sample elution; using for precursor intensity and injection time (MS/MS) calculation; 0 by default

-stop - time of wash starting; using for precursor intensity and injection time (MS/MS) calculation. By default maximum analysis time

-charge - max charge of precursor ions; by default, all charges are considered

-pic - the output figure format (png or svg for vector graphic)

ANGLE SCORE

-refFile - mzML or mgf file for angle score calculation

-refPSM - csv file with psm identifications for angle score calculation (should be based on mzML or mgf file specified in refFile parameter)

-d - delimiter in csv file with psm identifications for angle score calculation; tab by default

-cn- column name with spectra names in csv file with psm identifications for angle score calculation; "spectrum" by default

Output

The output file has the name "InputFileName_viQC.png" and contains 8 quality metrics based on MS and MS/MS spectra characteristics. The program doesn't require identifications, allowing fast and unbiased control of instrument performance.

Citing viQC

Solovyeva E.M. et al. viQC: Visual and Intuitive Quality Control for Mass Spectrometry-Based Proteome Analysis. J Anal Chem 74, 1363–1370 (2019). https://doi.org/10.1134/S1061934819140119

Solovyeva E.M. et al. Semi-supervised quality control method for proteome analyses based on tandem mass spectrometry. International Journal Of Mass Spectrometry 427, 59-64 (2018). https://doi.org/10.1016/j.ijms.2017.09.008

Questions

• Create an issue.
• Email us at pyteomics@googlegroups.com.