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

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

doi: 10.52601/bpr.2022.220011
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  • 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
  • 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.

  • 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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