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Statistical Process and Quality Control in Mass Spectrometry Workflows

External tool for performing easy process and quality control tasks in Skyline

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Start using easyQC for statistical process and quality control in mass spectrometry workflows

Introduction

The program easyQC is an external tool for statistical process and quality control in mass spectrometry workflows that integrates nicely in the Skyline Targeted Proteomics Environment.

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 Tools -> External Tools -> External Tool Store. In the appearing list select (click on) 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 chron. Fortunately, all these packages are hosted on CRAN, and should automatically be installed into your R-environment, when installing easyQC in Skyline. If, for some reasons, this should not be the case for you, make sure these three packages are installed in your R-environment.

Description

The software comes with an exemplary report template called easyQC. We recommend to just go with this template, but feel free to create your own. The absolute necessary fields your template should contain are: PeptideModifiedSequence and 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 your template.

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 easyQC.r is executable.

% 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

Where 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 easyQC.skyr 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:

% make

This will create a easyQC.zip file which contains the needed install scripts for Skyline. Now, just follow your Skyline-GUI.

Authors

Thomas W. D. Möbius (Maintainer, R-programming), Sebastian Malchow (Skyline wizard)