Medizinische Universität Graz Austria/Österreich - Forschungsportal - Medical University of Graz
Gewählte Publikation:
SHR Neuro Krebs Kardio Lipid Stoffw Microb
Schittmayer, M; Fritz, K; Liesinger, L; Griss, J; Birner-Gruenberger, R.
Cleaning out the Litterbox of Proteomic Scientists' Favorite Pet: Optimized Data Analysis Avoiding Trypsin Artifacts.
J Proteome Res. 2016; 15(4):1222-1229
Doi: 10.1021/acs.jproteome.5b01105
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- Führende Autor*innen der Med Uni Graz
- Birner-Grünberger Ruth
- Schittmayer-Schantl Matthias
- Co-Autor*innen der Med Uni Graz
- Fritz Katarina
- Liesinger Laura
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- Abstract:
- Chemically modified trypsin is a standard reagent in proteomics experiments but is usually not considered in database searches. Modification of trypsin is supposed to protect the protease against autolysis and the resulting loss of activity. Here, we show that modified trypsin is still subject to self-digestion, and, as a result, modified trypsin-derived peptides are present in standard digests. We depict that these peptides commonly lead to false-positive assignments even if native trypsin is considered in the database. Moreover, we present an easily implementable method to include modified trypsin in the database search with a minimal increase in search time and search space while efficiently avoiding these false-positive hits.
- Find related publications in this database (using NLM MeSH Indexing)
- Amino Acid Sequence -
- Animals -
- Artifacts -
- Brain Chemistry -
- Breast Neoplasms - chemistry
- Cell Line -
- Chromatography, Liquid -
- Data Interpretation, Statistical -
- Databases, Protein -
- Humans -
- Membrane Proteins - analysis
- Membrane Proteins - chemistry
- Mice -
- Neoplasm Proteins - analysis
- Neoplasm Proteins - chemistry
- Nerve Tissue Proteins - analysis
- Nerve Tissue Proteins - chemistry
- Peptide Fragments - analysis
- Protein Structure, Secondary -
- Proteolysis -
- Proteomics - methods
- Saccharomyces cerevisiae - chemistry
- Saccharomyces cerevisiae Proteins - analysis
- Saccharomyces cerevisiae Proteins - chemistry
- Tandem Mass Spectrometry -
- Trypsin - chemistry
- Find related publications in this database (Keywords)
- proteomics
- autolysis protected trypsin
- database search
- search space restriction
- misassigned spectra
- false positives