Proteomics service offered by the core facility

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

Research focus

Relevant background information.

The current focus of the group is the proteome analysis of body fluids (serum/plasma and tears) and to develop methods to better characterize therapeutic proteins such as monoclonal antibodies (mAbs).

Aims:

  • To increase the number of identifiable proteins in serum/plasma.
  • To find protein biomarkers in eye diseases.
  • To localize posttranslational modifications (PTMs) and single amino acid variants (SAVs) in mAbs.
  • To improve the analysis of host cell proteins (HCPs) which are generated during mAbs production.

Current work:

Current projects in the Thiede Group

Research achievements

  • Mass spectrometry-based proteome and phosphoproteome analyses were performed using different drugs (e.g., cisplatin, sorafenib, S-trityl-L-cysteine, taxol, and 5-fluorouracil) employed 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.
  • Isobaric peptide termini labeling (IPTL) including the software IsobariQ was developed, a strategy for isobaric quantification by peptide fragment ions.
  • Top-down quantitative proteomics of apoptotic cells with high resolution was performed by combining SILAC, 2D gel electrophoresis (2-DE) and LC-MS.
  • Automatic glycopeptide analysis was implemented using the search engine Mascot.

Techniques

More detailed information available

Quantification techniques

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

Instrumentation

  • UHPLC-TimsTOF Pro mass spectrometer

Software used

  • Frag-Pipe (including MSFragger)
  • IsobariQ
  • Mascot
  • PEAKS
  • Scaffold

Selected publications

PUBMED - Bernd Thiede

  1. Sargautis, D., Thiede, B. (2026) LC-MS peptide mapping of monoclonal antibodies using the mirror proteases trypsin and Tryp-N, J. Pharm. Biomed. Anal., 272, 117361.
  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.