Blind testing cross-linking/mass spectrometry under the auspices of the 11th critical assessment of methods of protein structure prediction (CASP11)

ABSTRACT: We report the first blind test on the readiness of combining high-density cross-linking/mass spectrometry data in conjunction with ab initio structure prediction, through the help of Critical Assessment of protein Structure Prediction (CASP). This blind test was coordinated by the CASP organizers and utilized the experimental protocol developed in our lab for providing high-density cross-linking/mass spectrometry data in a matter of days. The CASP organizing committee identified and acquired suitable targets and published resulting data on the CASP web page for the community of structure predictors. We provided high-density cross-linking/mass spectrometry data for four targets in CASP11, revealing to us some of the current limitations of cross-linking. These are areas where the method must now develop. With CASP taking place biannually into the future, blind testing low-resolution structure analysis tools is a worthwhile and feasible undertaking.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human) Bacteroides Caccae Staphylococcus Aureus Ruminococcus Gnavus

SUBMITTER: Adam Belsom  

LAB HEAD: Juri Rappsilber

PROVIDER: PXD003643 | Pride | 2016-12-02

REPOSITORIES: Pride