quality control of thousands of experiments with qcml

quality control of thousands of experiments with qcML

pieter kelchtermans

pieter.kelchtermans@vib-ugent.becomputational omics and systems biology groupVIB / Ghent University, Ghent, Belgium

How do you want to do quality control

What we tried to look at and how we did it

What we're looking forward to

We automated OpenMS

Process 5098 raw files to output qcML

Using Mathias Walzer’s workflow

Completely automated, on 11 linux computers

Preliminary analysis shows

You choose how to control the quality

qcML is a universal format

Captures metrics and metadata about all kinds of experiments

Separate from the actual analysis, only a container

Metrics are added with controlled vocabulary

qcML offers fast and easy access

QCExporter/QCExtractor gets data in tabular format

Java library under development by Wout Bittremieux

R integration with library by Laurent Gatto

Metrics can be generated by OpenMS

QuaMeter

Simpatiqco

You

Large-scale is not intractable

Automated deployment of virtual machines

OpenMS updates/installationConfigurationBatch data processing

Shared folder between all computers?

Be the master of your puppets

http://www.puppetlabs.com/ since 2005

Open source, cross platform agent

package { “openms”: ensure => "installed"}file { “/etc/openms.ini”: source => “puppet:///modules/openms/openms.ini“}

Each kind of experiment has different quality thresholds

Experiments vary a lot

Classification between experiments

Boundaries need to be determined by large-scale analysis

qcML allows for thresholds: flag bad experiments

Ratio of +1/+2 charged features

Ratio of +3/+2 charged features

Mean precursor m/z

900

600

Total Ion Current jumps

4000

1000

2000

3000

We’re shipping by the end of this year

Format definition: http://code.google.com/p/qcml/

Advanced analyses on differences between runs

Get in touch!

www.compomics.com@compomics

Wout BittremieuxMathias WalzerJonathan Vandenbussche, Kris Gevaert lab