False discovery rate estimation for cross-linked peptides identified by mass spectrometry
By T. Walzthoeni, Manfred Claassen, A. Leitner, Franz Herzog, S. Bohn, F. Förster, Martin Beck, R. Aebersold. Nature Methods, 2012
310 citations recorded by the source corpus.
The mass spectrometric identification of chemically cross-linked peptides (CXMS) specifies spatial restraints of protein complexes; these values complement data obtained from common structure-determination techniques. Generic methods for determining false discovery rates of cross-linked peptide assignments are currently lacking, thus making data sets from CXMS studies inherently incomparable. Here we describe an automated target-decoy strategy and the software tool xProphet, which solve this problem for large multicomponent protein complexes.
Subfields: Materials Chemistry, Spectroscopy
View Paper: https://www.semanticscholar.org/paper/452f510d80653be529ffcd2408f2a31df8cb85a0
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Materials Chemistry
- Andriy Kryshtafovych
- Bohdan Monastyrskyy
- Krzysztof Fidelis
- András Fiser
- Yang Zhang
- Adam Belsom
- Oliver Brock
- Michael Schneider
In Spectroscopy
- Andriy Kryshtafovych
- Bohdan Monastyrskyy
- Krzysztof Fidelis
- Adam Belsom
- Oliver Brock
- Michael Schneider
- L. Fischer
- András Fiser
Citations in the corpus
- Serum Albumin Domain Structures in Human Blood Serum by Mass Spectrometry and Computational Biology (2015, methodology): “False discovery rates (FDR) were estimated following a modified target-decoy search strategy (22, 26).”
- Assessment of chemical-crosslink-assisted protein structure modeling in CASP13 (2019, methodology): “Data analysis was performed using the in-house software xQuest, 7 and results were provided to the CASP participants with an expected error (false discovery) rate of 5%, although accurate FDR estimation is difficult if only very few crosslinks are identified.”
- Small angle X-ray scattering and cross-linking for data assisted protein structure prediction in CASP 12 with prospects for improved accuracy (2018, unknown): “15,24,29”