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

doi:10.1038/nbt.4236

. 2018 Oct 8.

doi: 10.1038/nbt.4236. Online ahead of print.

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

Hao Chi^{1

2}, Chao Liu^{1

2}, Hao Yang^{1

2}, Wen-Feng Zeng^{1

2}, Long Wu^{1

2}, Wen-Jing Zhou^{1

2}, Rui-Min Wang^{1

2}, Xiu-Nan Niu^{1

2}, Yue-He Ding³, Yao Zhang^{4

5}, Zhao-Wei Wang^{1

2}, Zhen-Lin Chen^{1

2}, Rui-Xiang Sun^{1

2}, Tao Liu¹, Guang-Ming Tan¹, Meng-Qiu Dong³, Ping Xu⁴, Pei-Heng Zhang¹, Si-Min He^{1

2}

Affiliations

¹ Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China.
² University of Chinese Academy of Sciences, Beijing, China.
³ National Institute of Biological Sciences, Beijing, Beijing, China.
⁴ State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.
⁵ State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, China.

PMID: 30295672
DOI: 10.1038/nbt.4236

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

Hao Chi et al. Nat Biotechnol. 2018.

. 2018 Oct 8.

doi: 10.1038/nbt.4236. Online ahead of print.

Authors

Affiliations

¹ Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China.
² University of Chinese Academy of Sciences, Beijing, China.
³ National Institute of Biological Sciences, Beijing, Beijing, China.
⁴ State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.
⁵ State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, China.

PMID: 30295672
DOI: 10.1038/nbt.4236

Abstract

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.

PubMed Disclaimer

Cited by

Acquisition and Analysis of DIA-Based Proteomic Data: A Comprehensive Survey in 2023.
Lou R, Shui W. Lou R, et al. Mol Cell Proteomics. 2024 Feb;23(2):100712. doi: 10.1016/j.mcpro.2024.100712. Epub 2024 Jan 3. Mol Cell Proteomics. 2024. PMID: 38182042 Free PMC article. Review.
msqrob2PTM: Differential Abundance and Differential Usage Analysis of MS-Based Proteomics Data at the Posttranslational Modification and Peptidoform Level.
Demeulemeester N, Gébelin M, Caldi Gomes L, Lingor P, Carapito C, Martens L, Clement L. Demeulemeester N, et al. Mol Cell Proteomics. 2024 Feb;23(2):100708. doi: 10.1016/j.mcpro.2023.100708. Epub 2023 Dec 26. Mol Cell Proteomics. 2024. PMID: 38154689 Free PMC article.
Ubiquitination-mediated Golgi-to-endosome sorting determines the toxin-antidote duality of fission yeast wtf meiotic drivers.
Zheng JX, Du TY, Shao GC, Ma ZH, Jiang ZD, Hu W, Suo F, He W, Dong MQ, Du LL. Zheng JX, et al. Nat Commun. 2023 Dec 14;14(1):8334. doi: 10.1038/s41467-023-44151-9. Nat Commun. 2023. PMID: 38097609 Free PMC article.
Structural mechanism of HP1α-dependent transcriptional repression and chromatin compaction.
Sokolova V, Miratsky J, Svetlov V, Brenowitz M, Vant J, Lewis T, Dryden K, Lee G, Sarkar S, Nudler E, Singharoy A, Tan D. Sokolova V, et al. bioRxiv [Preprint]. 2023 Nov 30:2023.11.30.569387. doi: 10.1101/2023.11.30.569387. bioRxiv. 2023. PMID: 38076844 Free PMC article. Preprint.
Fast alignment of mass spectra in large proteomics datasets, capturing dissimilarities arising from multiple complex modifications of peptides.
Prunier G, Cherkaoui M, Lysiak A, Langella O, Blein-Nicolas M, Lollier V, Benoist E, Jean G, Fertin G, Rogniaux H, Tessier D. Prunier G, et al. BMC Bioinformatics. 2023 Nov 8;24(1):421. doi: 10.1186/s12859-023-05555-y. BMC Bioinformatics. 2023. PMID: 37940845 Free PMC article.

See all "Cited by" articles

References

1. J Proteome Res. 2011 Apr 1;10(4):1785-93 - PubMed
1. Anal Chem. 2017 Jan 17;89(2):1244-1253 - PubMed
1. Anal Chem. 1994 Dec 15;66(24):4390-9 - PubMed
1. Anal Chem. 2003 Dec 1;75(23):6415-21 - PubMed
1. Expert Rev Proteomics. 2015;12(6):579-93 - PubMed

LinkOut - more resources

Full Text Sources
- Nature Publishing Group
Other Literature Sources
- The Lens - Patent Citations

[1] J Proteome Res. 2011 Apr 1;10(4):1785-93 - PubMed

[2] J Proteome Res. 2011 Apr 1;10(4):1785-93 - PubMed

[3] Anal Chem. 2017 Jan 17;89(2):1244-1253 - PubMed

[4] Anal Chem. 2017 Jan 17;89(2):1244-1253 - PubMed

[5] Anal Chem. 1994 Dec 15;66(24):4390-9 - PubMed

[6] Anal Chem. 1994 Dec 15;66(24):4390-9 - PubMed

[7] Anal Chem. 2003 Dec 1;75(23):6415-21 - PubMed

[8] Anal Chem. 2003 Dec 1;75(23):6415-21 - PubMed

[9] Expert Rev Proteomics. 2015;12(6):579-93 - PubMed

[10] Expert Rev Proteomics. 2015;12(6):579-93 - PubMed

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

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

Affiliations

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

Authors

Affiliations

Abstract

Similar articles

Cited by

References

LinkOut - more resources

Full Text Sources

Other Literature Sources