Start using easyQC for statistical process and quality control in mass spectrometry workflows
easyQC is an external tool for statistical process and quality
control in mass spectrometry workflows that integrates nicely in the Skyline
Feature list at a glance
- Automatically sorts your data by date and time, and orders your observations with the most recent on the right. ("What? Does this mean I don't need to sort my data manually, as it is the case for some other software tools out there?", "Yes.")
- Dynamically adapts to custom report templates. (See details below.)
- Flow charts for single peptides can optionally be grouped together by their common protein accession. (See details below.)
- Plots are generated in a nice page layout, ready for printing.
- Observations are colour-coded by a beneficial four-colour-code. This makes it particularly easy to detect deviations from the norm.
- Has a built in outlier detection, which provides you with useful robust features. (See details below.)
- Plot as many flow charts for as many peptides as you like.
How to cite this software
The Harvard UoB format suggests to cite this software in the following fashion:
Möbius, T. W. D. and Malchow, S. (2014) easyQC: Statistical Process and Quality Control in Mass Spectrometry Workflows (Version 1.0) [Computer program]. Available at: http://00tau.github.io/skyline-addon-easyqc/ (Accessed 03. April, 2014)
Thank you for using (and citing) this software.
Installation using the skyline GUI
Simply follow the GUI-clicking adventure by successively clicking on
External Tools -> External Tool Store. In the appearing list select (click
easyQC. You will be promoted for the path to
Rscript, which needs to
be installed on you system.
We have realised that since the introduction of "Live Reports" in new Versions of Skyline, the import of new templates might fail. If this is the case for you, make sure two switch off "Live Reports", restart Skyline, and try the installation again.
The underlying code-base of
easyQC relies on the R-packages
ggplot2, plyr and
all these packages are hosted on CRAN, and should
automatically be installed into your R-environment, when installing
Skyline. If, for some reasons, this should not be the case for you, make sure
these three packages are installed in your R-environment.
The software comes with an exemplary report template called
recommend to just go with this template, but feel free to create your own. The
absolute necessary fields your template should contain are:
PrecursorMz. These two fields are used as
identifiers for your peptides, and, thus, all other fields should uniquely be
identifiable by these two. Optionally, the field
ProteinName can be added to
By default, the flow charts of ten peptides are grouped together into one plot
each. If your report template also contains the associated protein accession
of each peptide, namely the field
ProteinName, then all peptides which belong
to the same protein accession are grouped into one plot.
Before the calculation of the mean and standard deviations of each flow chart, the software will do some outlier detection of your data, namely Grubbs' test for outliers will be applied. Observations which are classified as outliers by this test are discarded in the estimation of the mean and standard deviations. This gives the estimated means and standard deviations some desirable robust features.
You can also use easyQC as a stand-alone command line program
On Linux, you simply need to add the directory in which you have cloned
easyQC's repository to your path. Also make sure that
% git clone https://github.com/00tau/skyline-addon-easyqc.git % cd skyline-addonn-easyqc % chmod +x easyQC.r % PATH=$(pwd):$PATH
The synopsis is as follows:
easyQC.r [OPTIONS] REPORTFILE
OPTIONS is either
verbose or noting. For example, to produce some
quality control plots from a file
some-report-file.csv that has been
generated by Skyline via some report template (e.g. the template
should come in mind here), run either one of the following two code lines from
the command line.
% easyQC.r some-report-file.csv % easyQC.r verbose some-report-file.csv
This will produce a file
some-report-file.pdf with all the plots you need.
You what to install the most recent and latest version in Skyline
If for some reasons, you are interested in installing the latest GitHub-version (or any other version of this software that is available on GitHub), the repository contains a convenient Makefile that will create the necessary files for the installation process for you. Simply type:
This will create a
easyQC.zip file which contains the needed install scripts
for Skyline. Now, just follow your Skyline-GUI.
Thomas W. D. Möbius (Maintainer, R-programming), Sebastian Malchow (Skyline wizard)