PLink 2: A high-speed search engine with systematic evaluation for proteome-scale identification of cross-linked peptides

ABSTRACT: Crosslinking mass spectrometry (CXMS) is a powerful technique to study protein structures and interactions. However, software tools for CXMS data analysis suffer from poor speed and credibility, especially at a proteome scale. Here, we introduce pLink 2, a search engine with higher speed and credibility for proteome-scale identification of crosslinked peptides. With a novel two-stage open search strategy facilitated by fragment indexing, pLink 2 is ~40 times faster than pLink 1 and 3~10 times faster than Kojak. Furthermore, four new analysis methods, using simulated datasets, synthetic datasets, 15N metabolically labeled datasets, and entrapment databases, were designed to evaluate the credibility of ten state-of-the-art search engines, this systematic evaluation showed that pLink 2 achieved the highest precision and sensitivity. Finally, four whole-cell lysate datasets, previously analysed by pLink 1 in months, were reanalysed by pLink 2 only in days, with up to 27.4% more crosslinks identified. The new search engine pLink 2 and the new evaluation methods are well positioned to become new benchmarks in the CXMS research field.

OTHER RELATED OMICS DATASETS IN: MODEL1109130000 MODEL1311110000 MODEL1909260003 MODEL1311110001 MODEL1909260004 MODEL1703310000 MODEL1909260005 MODEL1909260006

INSTRUMENT(S): Q Exactive

ORGANISM(S): Escherichia Coli

TISSUE(S): Whole Body

SUBMITTER: Zhenlin Chen  

LAB HEAD: Si-Min He

PROVIDER: PXD012109 | Pride | 2019-07-26

REPOSITORIES: Pride