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Deep coverage proteome analysis of hair shaft for forensic individual identification

  • Author Footnotes
    1 These authors contributed equally to this study
    Jialei Wu
    Footnotes
    1 These authors contributed equally to this study
    Affiliations
    Graduate School, People's Public Security University of China, No.1 Muxidi Nanli, Beijing 100038, China

    National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, No.17 Muxidi Nanli, Beijing 100038, China
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  • Author Footnotes
    1 These authors contributed equally to this study
    Jianhui Liu
    Footnotes
    1 These authors contributed equally to this study
    Affiliations
    CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, National Chromatographic Research and Analysis Center, 457 Zhongshan Road, Dalian 116023, China
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  • Anquan Ji
    Affiliations
    National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, No.17 Muxidi Nanli, Beijing 100038, China
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  • Dongsheng Ding
    Affiliations
    National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, No.17 Muxidi Nanli, Beijing 100038, China
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  • Guiqiang Wang
    Affiliations
    National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, No.17 Muxidi Nanli, Beijing 100038, China
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  • Yao Liu
    Affiliations
    National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, No.17 Muxidi Nanli, Beijing 100038, China
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  • Lihua Zhang
    Correspondence
    ⁎Corresponding authors.
    Affiliations
    CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, National Chromatographic Research and Analysis Center, 457 Zhongshan Road, Dalian 116023, China
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  • Lei Feng
    Correspondence
    ⁎Corresponding authors.
    Affiliations
    National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, No.17 Muxidi Nanli, Beijing 100038, China
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  • Jian Ye
    Correspondence
    Corresponding author at: Graduate School, People's Public Security University of China, No.1 Muxidi Nanli, Beijing 100038, China.
    Affiliations
    Graduate School, People's Public Security University of China, No.1 Muxidi Nanli, Beijing 100038, China

    National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, No.17 Muxidi Nanli, Beijing 100038, China
    Search for articles by this author
  • Author Footnotes
    1 These authors contributed equally to this study

      Highlights

      • Develop a deep-coverage proteome analysis strategy to identify both variant and reference SAPs present in the hair shaft.
      • Identify more than one hundred SAPs in a single hair shaft.
      • Demonstrate the practical value of genetic information coded in hair shaft SAPs.

      Abstract

      Hair shaft is one of the most common biological evidence found at crime scenes. However, due to the biogenic degradation of nuclear DNA in hair shaft, it is difficult to achieve individual identification through routine DNA analysis. In contrast, the proteins in hair shaft are stable and contain genetic polymorphisms in the form of single amino acid polymorphisms (SAPs), translated from non-synonymous single nucleotide polymorphisms (nsSNPs) in the genome. However, the number of SAPs detected still cannot meet the requirements of practical applications. This paper developed a deep coverage proteome analysis method by combining a three-step sequential ionic liquid-based protein extraction and 2D-RPLC-MS/MS with high and low pH to identify both variant and reference SAPs from 2-cm-long hair shafts. We identified 632 ± 243 protein groups from 10 individuals, with the average number of SAPs reaching 167 ± 21/person. These were further used to calculate random match probabilities (RMPs), a widely accepted forensic statistical term for human identification. The RMPs ranged from 6.53 × 10–4 to 3.10 × 10–14 (median = 2.62 × 10–8) when calculated with frequency of matching nsSNP genotype data from exomes, and ranged from 2.62 × 10–3 to 2.07 × 10–10 (median = 4.88 × 10–6) with SAP genotype frequency. All these results indicate that the deep coverage proteomics method is beneficial for improving SAP-based forensic individual identification in hair shaft, with great potential in crime investigation.

      Graphical Abstract

      Keywords

      Abbreviations:

      SAP (Single amino acid polymorphism), GVP (Genetically variant peptide)
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