Novel algorithms for DIA based label-free quantification

[jkuharev]

Abstract

As outlined by Sander Willems in issue 1, in ion mobility based data-independent acquisition technique HDMSE (also UDMSE), ions are separated in seconds by LC, in milliseconds by Ion Mobility Separation (IMS) and in nanoseconds by MS, and the acquired data has an additional dimensionality of drift-time. So far IMS-MSE data can only be processed by Progenesis QIP and PLGS (commercial tools, Waters). There are very few solutions for postprocessing this kind of data in label-free quantification experiments. The first one available was ISOQuant. ISOQuant is written in Java, and uses a MySQL database for storing and fast accessing data imported from PLGS projects. We previously developed and evaluated algorithms for retention time alignment, feature clustering & feature intensity normalization, which have been implemented in ISOQuant. However, we feel that the implemented algorithms could be improved, especially in context of ion-mobility data.

Work plan

Basics

• Introduction into IMS-MS workflows for label-free quantification
• Introduction into mixed proteome standards and LFQBench
• Users will get acquainted with the modular structure of ISOQuant and the underlying MySQL database
• Concepts for retention time alignment, clustering and normalization

Aims

Development and implementation of novel ISOQuant modules for

• retention time alignment using MS, IMS and peptide identification information,
• multidimensional feature clustering using m/z, RT and drift time information,
• intensity normalization.

Implemented modules and their effects on LFQ precision and accuracy will be tested using LFQBench

Technical details

• Programming language
  • Java
  • SQL
  • R, Python or any scripting language
• Useful familarity
  • PLGS
  • ISOQuant
  • LFQbench & hybrid proteome concept
  • Waters data structures
    • raw
    • mass spectrum xml
    • workflow results xml
• Dataset
  • PXD001240 for testing
  • We will provide some smaller datasets for developmental purposes

Contact information

Jörg Kuharev
UNIVERSITÄTSMEDIZIN der Johannes Gutenberg-Universität Mainz
kuharev@uni-mainz.de

or

Stefan Tenzer
UNIVERSITÄTSMEDIZIN der Johannes Gutenberg-Universität Mainz
tenzer@uni-mainz.de