Cancer Proteomics and Proteomics Facility - Thiede

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, the discovery of diagnostic, predictive and prognostic markers and the characterization of therapeutic proteins.

The scientific focus is on:

- Anti-cancer drug action

- Protein biomarker discovery

- Therapeutic protein characterization


Proteomics service offered by the core facility can be found here.

The proteomics facility at IBV is part of the National network of Advanced Proteomics Infrastructure (NAPI).

Research focus

Relevant background information.

A focus of our research of anti-cancer drugs (e.g., Cisplatin, sorafenib, taxol) has been on apoptosis, but we also investigated other processes such as mitotic arrest, ER stress and DNA damage. For this purpose, total cell lysates, subcellular compartments, and posttranslational modifications have been studied.

For relative quantitation of proteomes, we apply different approaches (e.g., SILAC, dimethylation, and label-free quantification) and developed isobaric peptide termini labelling (IPTL) including the data analysis software IsobariQ.

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 discover and validate biomarkers for the diagnosis of prostate cancer. 

Another aim is to develop tools for qualitative and quantitative analysis of therapeutic proteins.


  • 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 fully characterize proteins
  • 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.



More detailed information available



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


  • UHPLC-TimsTOF Pro mass spectrometer
  • UHPLC-Q Exactive mass spectrometer
  • MALDI-TOF/TOF mass spectrometer



Selected publications

PUBMED - Bernd Thiede

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

2. Tran, 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.

3. Bollineni, R.C., Koehler, C.J., Gislefoss, R.E., Anonsen, J.H., Thiede, B. (2018) Large-scale intact glycopeptide identification by Mascot database search. Sci. Rep. 8, 2117.

4. Tran, T.T., Bollineni, R.C., Koehler, C.J., Thiede, B. (2018) Absolute two-point quantification of proteins using dimethylated proteotypic peptides. Analyst, 143, 4359-4365.

5. Koehler, C.J., Thiede, B. (2020) Predominant cleavage of proteins N-terminal to serines and threonines using scandium(III) triflate. J. Biol. Inorg. Chem., 25, 61-66.


Published Feb. 19, 2018 7:32 PM - Last modified Feb. 2, 2021 2:57 PM