Format

Send to

Choose Destination
Nat Commun. 2017 May 19;8:15473. doi: 10.1038/ncomms15473.

Optimized fragmentation schemes and data analysis strategies for proteome-wide cross-link identification.

Author information

1
Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.
2
Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands.
3
Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95314, USA.

Abstract

We describe optimized fragmentation schemes and data analysis strategies substantially enhancing the depth and accuracy in identifying protein cross-links using non-restricted whole proteome databases. These include a novel hybrid data acquisition strategy to sequence cross-links at both MS2 and MS3 level and a new algorithmic design XlinkX v2.0 for data analysis. As proof-of-concept we investigated proteome-wide protein interactions in E. coli and HeLa cell lysates, respectively, identifying 1,158 and 3,301 unique cross-links at ∼1% false discovery rate. These protein interaction repositories provide meaningful structural information on many endogenous macromolecular assemblies, as we showcase on several protein complexes involved in translation, protein folding and carbohydrate metabolism.

PMID:
28524877
PMCID:
PMC5454533
DOI:
10.1038/ncomms15473
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Nature Publishing Group Icon for PubMed Central
Loading ...
Support Center