Proteomics

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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.

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

Dataset's files

Source:
Action DRS
Disuf_150mM_rej12.raw Raw
Disuf_150mM_rej12_90min.raw Raw
Disuf_250mM_rej12.raw Raw
Disuf_250mM_rej12_90min.raw Raw
Disuf_350mM_rej12.raw Raw
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Publications

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

Chen Zhen-Lin ZL   Meng Jia-Ming JM   Cao Yong Y   Yin Ji-Li JL   Fang Run-Qian RQ   Fan Sheng-Bo SB   Liu Chao C   Zeng Wen-Feng WF   Ding Yue-He YH   Tan Dan D   Wu Long L   Zhou Wen-Jing WJ   Chi Hao H   Sun Rui-Xiang RX   Dong Meng-Qiu MQ   He Si-Min SM  

Nature communications 20190730 1


We describe pLink 2, a search engine with higher speed and reliability for proteome-scale identification of cross-linked peptides. With a 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, using simulated datasets, synthetic datasets, <sup>15</sup>N metabolically labeled datasets, and entrapment databases, four analysis methods were designed to evaluate the credibility of ten state-of-the-art se  ...[more]

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