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Proteome Analytics

The spatio-temporal remodeling of the proteome, the cellular complement of all proteoforms, is a primary phenotype determinant. As such we are interested in quantifying protein expression dynamics, i.e. the changing abundance, subcellular localization, post translational modification and interaction of proteins in various biological scenarios. It is our goal to gain an understanding of the intricate mechanisms of plant proteome biology.

Fig.1 and 2. Cutting edge mass spectrometry is used to measure peptides and proteins.
Fig.1 and 2. Cutting edge mass spectrometry is used to measure peptides and proteins.

Recently our research group has streamlined and optimized the discovery proteomics approach and adapted it to plants. This technology now allows us to routinely quantify from 6,000 to 9,000 proteins (protein groups) per tissue sample with at least one unique peptide and a peptide and protein FDR threshold of 1%.

A primary research interest of the group is the effects of phytohormones in biotic and abiotic stress adaption. We are applying the deep proteomics strategy in combination with metabolomics and targeted proteomics measurements to shed more light on the interplay of the canonical defense phytohormones salicylic acid, jasmonate and ethylene but also on the role of auxin in the hormone signal signature in reshaping the proteome to resist pathogen attack.

Deep proteomics measurements of various tissues throughout plant development led to date to the accumulation of mass spectrometric evidence of nearly 16,000 protein coding genes which is about 60% of Arabidopsis thaliana open reading frames. This extensive coverage of the Arabidopsis genome is being used to investigate proteome wide correlation of protein abundance in different tissues as well as correlated local protein expression of genes in smaller and larger neighborhoods.

Fig. 3. Deep coverage of the Arabidopsis thaliana proteome
Fig. 3. Deep coverage of the Arabidopsis thaliana proteome

Targeted proteomics approaches are also well established in the group as a complement to discovery proteomics. These were particularly advanced by accurate measurement of fragment ion masses with the QExactive Plus mass spectrometer. This allows interpretation of MS/MS spectra and assignment of PTMs to peptide primary structure with low error probability. Reversible, multi-site PTM has as much an impact on protein function as translation of the nascent polypeptide itself. Numerous directed and undirected proteomics studies that quantify site-specific protein PTM are being performed with a growing interest in histone modification and epigenetics.

Equipment and Instrumentation


Mass Spectrometry

  • Orbitrap Velos Pro (Thermo Scientific)
  • QExactive Plus (Thermo Scientific)



  • EASY-nLC II (Thermo Scientific)
  • EASY-nLC 1000 (Thermo Scientific)
  • Ultimate 3000 (Thermo Scientific)



  • Mascot v.2.5
  • Mascot Distiller
  • Proteome Discoverer v.1.4
  • Progenesis QIP
  • Scaffold 4 / Scaffold PTM 2 Image Quant TL
  • Skyline
  • MaxQuant
  • Perseus
  • MapMan

The Team

Dr. Wolfgang Hoehenwarter

Staff Member
Abukhalaf, Mohammad PhD Student
Herr, Tobias Research Assistant
Proksch, Carsten Technician
Thieme, Domenika Technician

Publications by Tag: Proteomics

Displaying results 1 to 1 of 1.

Books and chapters

Beckers G.J.; Hoehenwarter, W.; Röhrig, H.; Conrath, U.; Weckwerth, W. Tandem metal-oxide affinity chromatography for enhanced depth of phosphoproteomeanalysis  (Jorrin-Novo, J. V.; Komatsu, S.; Weckwerth, W.; Wienkoop, S.). Methods Mol Biol. 1072, 621-32, (2014) ISBN: 978-1-62703-630-6 DOI: 10.1007/978-1-62703-631-3_42

In eukaryotic cells many diverse cellular functions are regulated by reversible protein phosphorylation. In recent years, phosphoproteomics has become a powerful tool to study protein phosphorylation because it allows unbiased localization, and site-specific quantification, of in vivo phosphorylation of hundreds of proteins in a single experiment. A common strategy to identify phosphoproteins and their phosphorylation sites from complex biological samples is the enrichment of phosphopeptides from digested cellular lysates followed by mass spectrometry. However, despite the high sensitivity of modern mass spectrometers the large dynamic range of protein abundance and the transient nature of protein phosphorylation remained major pitfalls in MS-based phosphoproteomics. Tandem metal-oxide affinity chromatography (MOAC) represents a robust and highly selective approach for the identification and site-specific quantification of low abundant phosphoproteins that is based on the successive enrichment of phosphoproteins and -peptides. This strategy combines protein extraction under denaturing conditions, phosphoprotein enrichment using Al(OH)3-based MOAC, tryptic digestion of enriched phosphoproteins followed by TiO2-based MOAC of phosphopeptides. Thus, tandem MOAC effectively targets the phosphate moiety of phosphoproteins and phosphopeptides and, thus, allows probing of the phosphoproteome to unprecedented depth.

This page was last modified on 14.11.2018.

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