Thiede group

The proteomics group provides service and performs independent research on method development to study cancer.

Cancer proteome studies encompass tumor tissues, cells and biological fluids to decipher signaling pathways, identifying signatures related to tumor initiation, invasion and metastasis, and the discovery of diagnostic, predictive and prognostic markers.

On signaling pathways, we have focused our research on the proteome analysis of anti-cancer drug-induced apoptosis of total cell lysates, subcellular compartments, and posttranslational modifications. For relative quantitation of proteomes, we apply different approaches (e.g., SILAC and label-free quantification) and developed isobaric peptide termini labelling (IPTL) including the data analysis software IsobariQ.

Proteomics service can be found here.
 

Research focus

Relevant background information.

To consolidate cancer proteomics data, we have created the ApoptoProteomics, Cell Death Proteomics and Cancer Proteomics databases.

Currently, a particular focus of the group is on the proteome, phosphoproteome and glycoproteome analysis of body fluids to find and validate biomarkers for the diagnosis of prostate cancer. 

Aims:

  • To study proteins and to find protein biomarkers involved in cancer.
  • To investigate proteins involved in processes leading up to apoptosis, including mitotic arrest, DNA damage, and ER stress triggered by different chemotherapeutic drugs.
  • To establish methods for quantitative analysis of posttranslational modifications.
  • To provide proteomics service for customers.

Current work:

Current projects in the Thiede Group

 

Research achievements

  • We have established and performed proteome analyses using different drugs (e.g., cisplatin, sorafenib, S-trityl-L-cysteine, taxol, and 5-fluorouracil) used or in development for chemotherapy of total cell lysates and subcellular protein assemblies (e.g., proteasome, and lipid rafts).
  • The ApoptoProteomics, Cell Death Proteomics and Cancer Proteomics databases were created for consolidating proteomics data which allows browsing, and analysis of large scale proteome analyses.
  • We have established isobaric peptide termini labeling (IPTL), a novel strategy for isobaric quantification based on the derivatization of peptide termini with complementary isotopically labelled reagents.
  • The software IsobariQ was developed to extract the quantitative information of IPTL data.
  • We have performed quantitative phosphoproteome studies of apoptotic cells.
  • High resolution quantitative proteomics of apoptotic cells was performed by combining SILAC/2-DE/LC-MS.
  • Automatic glycopeptide analysis was implemented using the search engine Mascot.

 

Techniques

More detailed information available

 

Techniques

  • SILAC - Stable isotope labeling with amino acids in cell culture
  • IPTL - Isobaric peptide termini labeling
  • LFQ - Label-free quantification


Instrumentation

  • UHPLC-Q Exactive mass spectrometer
  • UHPLC-LTQ Orbitrap-XL-ETD mass spectrometer
  • UHPLC-LTQ Orbitrap-XL mass spectrometer
  • MALDI-TOF/TOF mass spectrometer

 

Software

  • Mascot
  • Proteome Discoverer
  • Scaffold
  • MaxQuant
  • IsobariQ 


Selected publications

PUBMED - Bernd Thiede

1. Koehler, C.J., Arntzen, M.Ø., de Souza, G.A., Thiede, B. (2013) An approach for triplex-isobaric peptide termini labeling (Triplex-IPTL). Anal. Chem., 85, 2478-2485.

2. Thiede, B., Koehler, C.J., Strozynski, M., Treumann, A., Stein, R., Zimny-Arndt, U., Schmid, M., Jungblut, P.R. (2013) High resolution quantitative proteomics of HeLa cells protein species using stable isotope labeling with amino acids in cell culture (SILAC), two-dimensional gel electrophoresis (2DE) and nano-liquid chromatography coupled to an LTQ-Orbitrap mass spectrometer. Mol. Cell. Proteomics, 12, 529-538.

3. Arntzen, M.A., Boddie, P., Frick, R., Koehler, C.J., Thiede, B. (2015) Consolidation of proteomics data in the Cancer proteomics database. Proteomics, 15, 3765-3771.

4. Trung, T.T., Strozynski, M.A., Thiede, B. (2017) Quantitative phosphoproteome analysis of cisplatin-induced apoptosis in Jurkat T cells, Proteomics, 17, 1600470.

5. Trung, T.T., Bollineni, R.C., Strozynski, M.A., Koehler, C.J., Thiede, B. (2017) Identification of alternative splice variants using unique tryptic peptide sequences for database searches, J. Proteome Res., 16, 2571-2578.

 

Published Oct. 27, 2015 4:02 PM - Last modified Aug. 30, 2017 11:02 AM