DIA-MS2pep: a library-free framework for comprehensive peptide identification from data-independent acquisition data

Junjie Hou; Jifeng Wang; Fuquan Yang; Tao Xu

doi:10.52601/bpr.2022.220011

Volume 8 Issue 5-6

Dec. 2022

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Article Navigation > Biophysics Reports > 2022 > 8(5-6): 253-268

Junjie Hou, Jifeng Wang, Fuquan Yang, Tao Xu. DIA-MS2pep: a library-free framework for comprehensive peptide identification from data-independent acquisition data[J]. Biophysics Reports, 2022, 8(5-6): 253-268. doi: 10.52601/bpr.2022.220011

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Junjie Hou, Jifeng Wang, Fuquan Yang, Tao Xu. DIA-MS2pep: a library-free framework for comprehensive peptide identification from data-independent acquisition data[J]. Biophysics Reports, 2022, 8(5-6): 253-268. doi: 10.52601/bpr.2022.220011

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DIA-MS2pep: a library-free framework for comprehensive peptide identification from data-independent acquisition data

doi: 10.52601/bpr.2022.220011

Junjie Hou^{1
,
,},
Jifeng Wang²,
Fuquan Yang^{3, 4},
Tao Xu^{1, 4
,
,}

1.
National Laboratory of Biomacramolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
2.
Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
3.
Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
4.
College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China

More Information

Corresponding author: houjunjie@ibp.ac.cn (J. Hou); xutao@ibp.ac.cn (T. Xu)
Received Date: 28 May 2022
Accepted Date: 06 June 2022

Available Online: 25 July 2022

Publish Date: 31 December 2022

Abstract

Abstract

Identifying peptides directly from data-independent acquisition (DIA) data remains challenging due to the highly multiplexed MS/MS spectra. Spectral library-based peptide detection is sensitive, but it is limited to the depth of the library and mutes the discovery potential of DIA data. We present here, DIA-MS2pep, a library-free framework for comprehensive peptide identification from DIA data. DIA-MS2pep uses a data-driven algorithm for MS/MS spectrum demultiplexing using the fragments data without the need of a precursor. With a large precursor mass tolerance database search, DIA-MS2pep can identify the peptides and their modified forms. We demonstrate the performance of DIA-MS2pep by comparing it to conventional library-free tools in accuracy and sensitivity of peptide identifications using publicly available DIA datasets of varying samples, including HeLa cell lysates, phosphopeptides, plasma, etc. Compared with data-dependent acquisition-based spectral libraries, spectral libraries built directly from DIA data with DIA-MS2pep improve the accuracy and reproducibility of the quantitative proteome.
- DIA-MS,
- Spectral library-free,
- Spectrum demultiplexing,
- Large precursor mass tolerance,
- Mass spectrometry

Junjie Hou, Jifeng Wang, Fuquan Yang and Tao Xu declare that they have no conflict of interest.
This article does not contain any studies with human or animal subjects performed by any of the authors.

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References(42)

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