Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine

Peptide identification in proteomics data is improved using an efficient open search engine. We present a sequence-tag-based search engine, Open-pFind, to identify peptides in an ultra-large search space that includes coeluting peptides, unexpected modifications and digestions. Our method detects pe...

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Bibliographic Details
Published in:Nature biotechnology 2018-12, Vol.36 (11), p.1059-1061
Main Authors: Chi, Hao, Liu, Chao, Yang, Hao, Zeng, Wen-Feng, Wu, Long, Zhou, Wen-Jing, Wang, Rui-Min, Niu, Xiu-Nan, Ding, Yue-He, Zhang, Yao, Wang, Zhao-Wei, Chen, Zhen-Lin, Sun, Rui-Xiang, Liu, Tao, Tan, Guang-Ming, Dong, Meng-Qiu, Xu, Ping, Zhang, Pei-Heng, He, Si-Min
Format: Article
Language:English
Subjects:
631/114/2784
631/114/794
631/1647/2067
631/61/475
82/58
Agriculture
Bioinformatics
Biomedical Engineering/Biotechnology
Biomedicine
Biotechnology
brief-communication
Life Sciences
Mass spectra
Mass spectrometry
Mass spectroscopy
Online information services
Peptides
Proteins
Proteomes
Proteomics
Search engines
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Summary:Peptide identification in proteomics data is improved using an efficient open search engine. We present a sequence-tag-based search engine, Open-pFind, to identify peptides in an ultra-large search space that includes coeluting peptides, unexpected modifications and digestions. Our method detects peptides with higher precision and speed than seven other search engines. Open-pFind identified 70–85% of the tandem mass spectra in four large-scale datasets and 14,064 proteins, each supported by at least two protein-unique peptides, in a human proteome dataset.
ISSN:1087-0156
1546-1696
DOI:10.1038/nbt.4236